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Wyly S, Jinon N, Francis T, Evans H, Kao TL, Lambert S, Montgomery S, Newlove M, Mariscal H, Nguyen H, Cole H, Aispuro I, Robledo D, Tenaglia O, Weinberger N, Nguyen B, Waits H, Jorian D, Koch-Kreher L, Myrdal H, Antoniou V, Warrier M, Wunsch L, Arce I, Kirchner K, Campos E, Nguyen A, Rodriguez K, Cao L, Halmekangas A, Wilson RC. The psychophysiology of Mastermind: Characterizing response times and blinking in a high-stakes television game show. Psychophysiology 2024; 61:e14485. [PMID: 37966011 DOI: 10.1111/psyp.14485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/16/2023]
Abstract
Television game shows have proven to be a valuable resource for studying human behavior under conditions of high stress and high stakes. However, previous work has focused mostly on choices-ignoring much of the rich visual information that is available on screen. Here, we take a first step to extracting more of this information by investigating the response times and blinking of contestants in the BBC show Mastermind. In Mastermind, contestants answer rapid-fire quiz questions while a camera slowly zooms in on their faces. By labeling contestants' behavior and blinks from 25 episodes, we asked how accuracy, response times, and blinking varied over the course of the game. For accuracy and response times, we tested whether contestants responded more accurately and more slowly after an error-exhibiting the "post-error increase in accuracy" and "post-error slowing" which has been repeatedly observed in the lab. For blinking, we tested whether blink rates varied according to the cognitive demands of the game-decreasing during periods of cognitive load, such as when pondering a response, and increasing at event boundaries in the task, such as the start of a question. In contrast to the lab, evidence for post-error changes in accuracy and response time was weak, with only marginal effects observed. In line with the lab, blinking varied over the course of the game much as we predicted. Overall, our findings demonstrate the potential of extracting dynamic signals from game shows to study the psychophysiology of behavior in the real world.
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Affiliation(s)
- Skyler Wyly
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Neryanne Jinon
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Timothy Francis
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Hailey Evans
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Tsai Lieh Kao
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Shelby Lambert
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Shayne Montgomery
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Marvelene Newlove
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Haley Mariscal
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Henry Nguyen
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Harrison Cole
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Israel Aispuro
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Daniela Robledo
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Olivia Tenaglia
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Nina Weinberger
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Bill Nguyen
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Hailey Waits
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Daisy Jorian
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Lucas Koch-Kreher
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Hunter Myrdal
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Victoria Antoniou
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Meghana Warrier
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Leah Wunsch
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Iram Arce
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Kayla Kirchner
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Elena Campos
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - An Nguyen
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | | | - Lanqin Cao
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Avery Halmekangas
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
- McKnight Brain Research Foundation, University of Arizona, Tucson, Arizona, USA
- Cognitive Science Program, University of Arizona, Tucson, Arizona, USA
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Horta M, Shoenfelt A, Lighthall NR, Perez E, Frazier I, Heemskerk A, Lin T, Wilson RC, Ebner NC. Author Correction: Age-group differences in trust-related decision-making and learning. Sci Rep 2024; 14:5132. [PMID: 38429420 PMCID: PMC10907569 DOI: 10.1038/s41598-024-55891-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024] Open
Affiliation(s)
- Marilyn Horta
- Department of Psychology, University of Florida, Gainesville, FL, USA.
- Pain Research and Intervention Center of Excellence, University of Florida, Gainesville, FL, USA.
| | - Alayna Shoenfelt
- Department of Psychology, University of Florida, Gainesville, FL, USA
| | | | - Eliany Perez
- Department of Psychology, University of Florida, Gainesville, FL, USA
| | - Ian Frazier
- Department of Psychology, University of Florida, Gainesville, FL, USA
- Graduate School of Applied and Professional Psychology, Rutgers University, New Brunswick, NJ, USA
| | - Amber Heemskerk
- Department of Psychology, University of Florida, Gainesville, FL, USA
| | - Tian Lin
- Department of Psychology, University of Florida, Gainesville, FL, USA
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, AZ, USA
| | - Natalie C Ebner
- Department of Psychology, University of Florida, Gainesville, FL, USA.
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Haug LM, Wilson RC, Alm-Kristiansen AH. Epigenetic-related transcriptional reprogramming elucidated by identification and validation of a novel reference gene combination for RT-qPCR studies in porcine oocytes of contrasting quality. Mol Biol Rep 2024; 51:368. [PMID: 38411699 PMCID: PMC10899281 DOI: 10.1007/s11033-024-09319-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/05/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Reliable RT-qPCR results are dependent on appropriate normalisation. Oocyte maturation studies can be challenging in this respect, as the stage of development can distinctively affect reference gene transcript abundance. The aim of this study was to validate the use of reference genes in oocyte in vitro maturation RT-qPCR studies, and thereafter, examine the abundance of transcripts supporting histone modification during oocyte and early embryo development in oocytes of contrasting quality. METHODS AND RESULTS Total RNA from oocytes from prepubertal gilts and sows was extracted either directly succeeding follicle aspiration or after 44 h in vitro maturation, followed by RT-qPCR. The stability of YWHAG, HPRT1, ACTB, GAPDH, HMBS and PFKP, was analysed by NormFinder and further cross-validated by assessing results generated following application of different combinations of potential reference genes for normalisation of the RT-qPCR data. Combining ACTB and PFKP generated high stability according to NormFinder and concordant results. Applying this normalisation, gilt derived oocytes displayed significantly higher abundance than oocytes from sows of almost all the epigenetic-related transcripts studied (HDAC2, SIRT1, SALL4, KDM1A, KDM1B, KDM5A), both before and after maturation. CONCLUSIONS This study identified the combined use of ACTB and PFKP as the optimal normalisation for porcine oocyte RT-qPCR data. In oocytes collected from prepubertal gilts, transcription did not appear to be silenced at the time of aspiration, and accumulation of transcripts supporting histone modification facilitating proper fertilization and further embryo development seemed delayed. The results imply the epigenetic-related transcripts may have potential as markers of oocyte quality.
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Affiliation(s)
- Linda Marijke Haug
- CRESCO, Centre for Embryology and Healthy Development, Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Robert C Wilson
- CRESCO, Centre for Embryology and Healthy Development, Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Anne Hege Alm-Kristiansen
- CRESCO, Centre for Embryology and Healthy Development, Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.
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Mizell JM, Wang S, Frisvold A, Alvarado L, Farrell-Skupny A, Keung W, Phelps CE, Sundman MH, Franchetti MK, Chou YH, Alexander GE, Wilson RC. Differential impacts of healthy cognitive aging on directed and random exploration. Psychol Aging 2024; 39:88-101. [PMID: 38358695 PMCID: PMC10871551 DOI: 10.1037/pag0000791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Deciding whether to explore unknown opportunities or exploit well-known options is a ubiquitous part of our everyday lives. Extensive work in college students suggests that young people make explore-exploit decisions using a mixture of information seeking and random behavioral variability. Whether, and to what extent, older adults use the same strategies is unknown. To address this question, 51 older adults (ages 65-74) and 32 younger adults (ages 18-25) completed the Horizon Task, a gambling task that quantifies information seeking and behavioral variability as well as how these strategies are controlled for the purposes of exploration. Qualitatively, we found that older adults performed similar to younger adults on this task, increasing both their information seeking and behavioral variability when it was adaptive to explore. Quantitively, however, there were substantial differences between the age groups, with older adults showing less information seeking overall and less reliance on variability as a means to explore. In addition, we found a subset of approximately 26% of older adults whose information seeking was close to zero, avoiding informative options even when they were clearly the better choice. Unsurprisingly, these "information avoiders" performed worse on the task. In contrast, task performance in the remaining "information seeking" older adults was comparable to that of younger adults suggesting that age-related differences in explore-exploit decision making may be adaptive except when they are taken to extremes. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
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Affiliation(s)
| | - Siyu Wang
- University of Arizona, Department of Psychology
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5
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Horta M, Shoenfelt A, Lighthall NR, Perez E, Frazier I, Heemskerk A, Lin T, Wilson RC, Ebner NC. Age-group differences in trust-related decision-making and learning. Sci Rep 2024; 14:68. [PMID: 38167997 PMCID: PMC10762071 DOI: 10.1038/s41598-023-50500-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Facial impressions contribute to evaluations of trustworthiness. Older adults are especially vulnerable to trust violations, incurring risks for deception and exploitation. Using the newly developed social Iowa Gambling Task (S-IGT), we examined age-group differences in the impact of facial trustworthiness on decision-making and learning. In the congruent condition (CS-IGT), advantageous decks were paired with trustworthy faces and disadvantageous decks with untrustworthy faces. In the incongruent condition (IS-IGT), this pairing was reversed. Younger (n = 143) and older (n = 129) participants completed either the standard Iowa Gambling Task (IGT), CS-IGT, or IS-IGT. Both age groups preferred trustworthy faces in their initial choices. Older adults performed worse than younger adults across all tasks over time. Further, compared to younger adults, older adults performed worse on the IS-IGT, suggesting that incongruent facial cues interfered with older adults' performance, which aligns with reduced sensitivity to negative social reputations in aging. Multilevel modeling also indicated that age-group differences were most pronounced across all tasks in the last 40 trials. Together these findings suggest that differences between younger and older adults in experience-dependent decision-making are magnified in social contexts that involve a "wolf in sheep's clothing," which may reflect age-related difficulties in integrating incongruent information.
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Affiliation(s)
- Marilyn Horta
- Department of Psychology, University of Florida, Gainesville, FL, USA.
- Pain Research and Intervention Center of Excellence, University of Florida, Gainesville, FL, USA.
| | - Alayna Shoenfelt
- Department of Psychology, University of Florida, Gainesville, FL, USA
| | | | - Eliany Perez
- Department of Psychology, University of Florida, Gainesville, FL, USA
| | - Ian Frazier
- Department of Psychology, University of Florida, Gainesville, FL, USA
- Graduate School of Applied and Professional Psychology, Rutgers University, New Brunswick, NJ, USA
| | - Amber Heemskerk
- Department of Psychology, University of Florida, Gainesville, FL, USA
| | - Tian Lin
- Department of Psychology, University of Florida, Gainesville, FL, USA
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, AZ, USA
| | - Natalie C Ebner
- Department of Psychology, University of Florida, Gainesville, FL, USA.
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6
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Xu Y, Harms MB, Green CS, Wilson RC, Pollak SD. Childhood unpredictability and the development of exploration. Proc Natl Acad Sci U S A 2023; 120:e2303869120. [PMID: 38011553 DOI: 10.1073/pnas.2303869120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/12/2023] [Indexed: 11/29/2023] Open
Abstract
Early in development, the process of exploration helps children gather new information that fosters learning about the world. Yet, it is unclear how childhood experiences may influence the way humans approach new learning. What influences decisions to exploit known, familiar options versus trying a novel alternative? We found that childhood unpredictability, characterized by unpredictable caregiving and unstable living environments, was associated with reduced exploratory behavior. This effect holds while controlling for individual differences, including anxiety and stress. Individuals who perceived their childhoods as unpredictable explored less and were instead more likely to repeat previous choices (habitual responding). They were also more sensitive to uncertainty than to potential rewards, even when the familiar options yielded lower rewards. We examined these effects across multiple task contexts and via both in-person (N = 78) and online replication (N = 84) studies among 10- to 13-y-olds. Results are discussed in terms of the potential cascading effects of unpredictable environments on the development of decision-making and the effects of early experience on subsequent learning.
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Affiliation(s)
- Yuyan Xu
- Department of Psychology, University of Wisconsin-Madison, Madison, WI 53706
| | - Madeline B Harms
- Department of Psychology, University of Minnesota Duluth, Duluth, MN 55812
| | - C Shawn Green
- Department of Psychology, University of Wisconsin-Madison, Madison, WI 53706
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, AZ 85721
- Cognitive Science Program, University of Arizona, Tucson, AZ 85716
| | - Seth D Pollak
- Department of Psychology, University of Wisconsin-Madison, Madison, WI 53706
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Haug LM, Wilson RC, Gaustad AH, Jochems R, Kommisrud E, Grindflek E, Alm-Kristiansen AH. Cumulus Cell and Oocyte Gene Expression in Prepubertal Gilts and Sows Identifies Cumulus Cells as a Prime Informative Parameter of Oocyte Quality. Biology (Basel) 2023; 12:1484. [PMID: 38132310 PMCID: PMC10740982 DOI: 10.3390/biology12121484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
Cumulus cells (CCs) are pivotal during oocyte development. This study aimed to identify novel marker genes for porcine oocyte quality by examining the expression of selected genes in CCs and oocytes, employing the model of oocytes from prepubertal animals being of reduced quality compared to those from adult animals. Total RNA was extracted either directly after follicle aspiration or after in vitro maturation, followed by RT-qPCR. Immature gilt CCs accumulated BBOX1 transcripts, involved in L-carnitine biosynthesis, to a 14.8-fold higher level (p < 0.05) relative to sows, while for CPT2, participating in fatty acid oxidation, the level was 0.48 (p < 0.05). While showing no differences between gilt and sow CCs after maturation, CPT2 and BBOX1 levels in oocytes were higher in gilts at both time points. The apparent delayed lipid metabolism and reduced accumulation of ALDOA and G6PD transcripts in gilt CCs after maturation, implying downregulation of glycolysis and the pentose phosphate pathway, suggest gilt cumulus-oocyte complexes have inadequate ATP stores and oxidative stress balance compared to sows at the end of maturation. Reduced expression of BBOX1 and higher expression of CPT2 in CCs before maturation and higher expression of G6PD and ALDOA after maturation are new potential markers of oocyte quality.
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Affiliation(s)
- Linda Marijke Haug
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (L.M.H.); (R.C.W.); (R.J.); (E.K.)
| | - Robert C. Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (L.M.H.); (R.C.W.); (R.J.); (E.K.)
| | | | - Reina Jochems
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (L.M.H.); (R.C.W.); (R.J.); (E.K.)
- Norsvin SA, 2317 Hamar, Norway; (A.H.G.); (E.G.)
| | - Elisabeth Kommisrud
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (L.M.H.); (R.C.W.); (R.J.); (E.K.)
| | | | - Anne Hege Alm-Kristiansen
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (L.M.H.); (R.C.W.); (R.J.); (E.K.)
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8
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Du YK, Liang M, McAvan AS, Wilson RC, Ekstrom AD. Frontal-midline theta and posterior alpha oscillations index early processing of spatial representations during active navigation. Cortex 2023; 169:65-80. [PMID: 37862831 PMCID: PMC10841878 DOI: 10.1016/j.cortex.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/12/2023] [Accepted: 09/15/2023] [Indexed: 10/22/2023]
Abstract
Previous research has demonstrated that humans combine multiple sources of spatial information such as self-motion and landmark cues while navigating through an environment. However, it is unclear whether this involves comparing multiple representations obtained from different sources during navigation (parallel hypothesis) or building a representation first based on self-motion cues and then combining with landmarks later (serial hypothesis). We tested these two hypotheses (parallel vs serial) in an active navigation task using wireless mobile scalp EEG recordings. Participants walked through an immersive virtual hallway with or without conflicts between self-motion and landmarks (i.e., intersections) and pointed toward the starting position of the hallway. We employed the oscillatory signals recorded during mobile wireless scalp EEG as a means of identifying when participant representations based on self-motion versus landmark cues might have first emerged. We found that path segments, including intersections present early during navigation, were more strongly associated with later pointing error, regardless of when they appeared during encoding. We also found that there was sufficient information contained within the frontal-midline theta and posterior alpha oscillatory signals in the earliest segments of navigation involving intersections to decode condition (i.e., conflicting vs not conflicting). Together, these findings suggest that intersections play a pivotal role in the early development of spatial representations, suggesting that memory representations for the geometry of walked paths likely develop early during navigation, in support of the parallel hypothesis.
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Affiliation(s)
- Yu Karen Du
- Department of Psychology, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719, USA; Department of Psychology & Brain and Mind Institute, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Mingli Liang
- Department of Psychology, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719, USA
| | - Andrew S McAvan
- Department of Psychology, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719, USA; Department of Psychology, Vanderbilt University, Nashville, TN 37240, USA
| | - Robert C Wilson
- Department of Psychology, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719, USA
| | - Arne D Ekstrom
- Department of Psychology, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719, USA; Evelyn McKnight Brain Institute, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719, USA.
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9
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Narud B, Khezri A, Zeremichael TT, Eriksen AL, Grevle IS, Nordborg A, Klinkenberg G, Wilson RC, Kommisrud E. Sperm quality parameters, fertilizing potential, metabolites, and DNA methylation in cold-stored and cryopreserved milt from Atlantic salmon ( Salmo salar L.). Front Genet 2023; 14:1199681. [PMID: 37693310 PMCID: PMC10483119 DOI: 10.3389/fgene.2023.1199681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/25/2023] [Indexed: 09/12/2023] Open
Abstract
Cold storage and freezing/thawing of milt may affect sperm functionality and the subsequent fertilization ability of milt. This study aimed to investigate sperm quality parameters and fertilization potential of Atlantic salmon milt, stored cold and subsequently cryopreserved, using different storage conditions. The objective was also to assess if analysis of milt metabolites and sperm DNA methylation signatures could be applicable to further elucidate sperm quality and fertilization following preservation. Milt samples were collected from eight mature Atlantic salmon males and stored for 4 days at 2°C and 8°C. Samples were taken on day one of storage at 2°C and on day four of storage at 2°C and 8°C. Storage for 4 days at 8°C is expected to be detrimental to sperm quality, and was included to create contrasts. Correspondingly, aliquots of cold-stored milt were prepared for cryopreservation, resulting in a total of six experimental conditions. Samples from all six experimental conditions were used in fertilization trials and analyzed for sperm viability, motility, ATP content, DNA fragmentation index, and High DNA stainability. In addition, milt samples from four of the males were analyzed for targeted metabolites and DNA methylation signatures by reduced representation bisulfite sequencing. The fertilization trials were performed using sperm:egg ratios of 75 × 103 and 500 × 103, respectively. Storage duration, temperature, and cryopreservation of cold-stored milt influenced several sperm quality parameters, metabolites, and DNA methylation signatures. The total motility, progressive motility, ATP, and velocity parameters were the sperm parameters with the strongest correlation to fertilization rates (p < 0.01). Several metabolites were correlated with fertility rates in both cold-stored and cryopreserved samples (p < 0.05). The fertilizing capacity of cold-stored milt was significantly reduced after 4 days of storage at 8°C, while corresponding cryopreserved milt showed reduced fertilization at both storage temperatures (2°C and 8°C) (p < 0.05). The results indicate that cryopreservation of milt stored for 1 day does not compromise either fertilization ability or DNA methylation signatures.
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Affiliation(s)
- Birgitte Narud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Teklu T. Zeremichael
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | | | | | | | - Robert C. Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Elisabeth Kommisrud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
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10
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Du YK, Liang M, McAvan AS, Wilson RC, Ekstrom AD. Frontal-midline theta and posterior alpha oscillations index early processing of spatial representations during active navigation. bioRxiv 2023:2023.04.22.537940. [PMID: 37131721 PMCID: PMC10153283 DOI: 10.1101/2023.04.22.537940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Previous research has demonstrated that humans combine multiple sources of spatial information such as self-motion and landmark cues, while navigating through an environment. However, it is unclear whether this involves comparing multiple representations obtained from different sources during navigation (parallel hypothesis) or building a representation first based on self-motion cues and then combining with landmarks later (serial hypothesis). We tested these two hypotheses (parallel vs. serial) in an active navigation task using wireless mobile scalp EEG recordings. Participants walked through an immersive virtual hallway with or without conflicts between self-motion and landmarks (i.e., intersections) and pointed toward the starting position of the hallway. We employed the oscillatory signals recorded during mobile wireless scalp EEG as means of identifying when participant representations based on self-motion vs. landmark cues might have first emerged. We found that path segments, including intersections present early during navigation, were more strongly associated with later pointing error, regardless of when they appeared during encoding. We also found that there was sufficient information contained within the frontal-midline theta and posterior alpha oscillatory signals in the earliest segments of navigation involving intersections to decode condition (i.e., conflicting vs. not conflicting). Together, these findings suggest that intersections play a pivotal role in the early development of spatial representations, suggesting that memory representations for the geometry of walked paths likely develop early during navigation, in support of the parallel hypothesis.
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Affiliation(s)
- Yu Karen Du
- Department of Psychology, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719
- Department of Psychology & Brain and Mind Institute, University of Western Ontario, London, ON, Canada N6A 3K7
| | - Mingli Liang
- Department of Psychology, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719
| | - Andrew S McAvan
- Department of Psychology, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719
- Department of Psychology, Vanderbilt University, Vanderbilt University, Nashville, TN 37240
| | - Robert C Wilson
- Department of Psychology, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719
| | - Arne D Ekstrom
- Department of Psychology, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719
- Evelyn McKnight Brain Institute, University of Arizona, 1503 E. University Blvd., Tucson, AZ 85719
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11
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Wang S, Gerken B, Wieland JR, Wilson RC, Fellous JM. The effects of time horizon and guided choices on explore-exploit decisions in rodents. Behav Neurosci 2023; 137:127-142. [PMID: 36633987 PMCID: PMC10787949 DOI: 10.1037/bne0000549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Humans and animals have to balance the need for exploring new options with exploiting known options that yield good outcomes. This tradeoff is known as the explore-exploit dilemma. To better understand the neural mechanisms underlying how humans and animals address the explore-exploit dilemma, a good animal behavioral model is critical. Most previous rodents explore-exploit studies used ethologically unrealistic operant boxes and reversal learning paradigms in which the decision to abandon a bad option is confounded by the need for exploring a novel option for information collection, making it difficult to separate different drives and heuristics for exploration. In this study, we investigated how rodents make explore-exploit decisions using a spatial navigation horizon task (Wilson et al., 2014) adapted to rats to address the above limitations. We compared the rats' performance to that of humans using identical measures. We showed that rats use prior information to effectively guide exploration. In addition, rats use information-driven directed exploration like humans, but the extent to which they explore has the opposite dependance on time horizon than humans. Moreover, we found that free choices and guided choices have different influences on exploration in rodents, a finding that has not yet been tested in humans. This study reveals that the explore-exploit spatial behavior of rats is more complex than previously thought. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
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12
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Pehlivanoglu D, Lin T, Lighthall NR, Heemskerk A, Harber A, Wilson RC, Turner GR, Spreng RN, Ebner NC. Facial Trustworthiness Perception Across the Adult Life Span. J Gerontol B Psychol Sci Soc Sci 2023; 78:434-444. [PMID: 36242775 DOI: 10.1093/geronb/gbac166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Trust is crucial for successful social interaction across the life span. Perceiver age, facial age, and facial emotion have been shown to influence trustworthiness perception, but the complex interplay between these perceiver and facial characteristics has not been examined. METHOD Adopting an adult life-span developmental approach, 199 adults (aged 22-78 years) rated the trustworthiness of faces that systematically varied in age (young, middle-aged, and older) and emotion (neutral, happy, sad, fearful, angry, and disgusted) from the FACES Lifespan Database. RESULTS The study yielded three key results. First, on an aggregated level, facial trustworthiness perception did not differ by perceiver age. Second, all perceivers rated young faces as the most trustworthy, and middle-aged and older (but not young) perceivers rated older faces as least trustworthy. Third, facial emotions signaling threat (fear, anger, and disgust) relative to neutral, happy, and sad expressions moderated age effects on facial trustworthiness perception. DISCUSSION Findings from this study highlight the impact of perceiver and facial characteristics on facial trustworthiness perception in adulthood and aging and have potential to inform first impression formation, with effects on trait attributions and behavior. This publication also provides normative data on perceived facial trustworthiness for the FACES Lifespan Database.
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Affiliation(s)
- Didem Pehlivanoglu
- Department of Psychology, University of Florida, Gainesville, Florida, USA
| | - Tian Lin
- Department of Psychology, University of Florida, Gainesville, Florida, USA
| | - Nichole R Lighthall
- Department of Psychology, University of Central Florida, Orlando, Florida, USA
| | - Amber Heemskerk
- Department of Psychology, University of Florida, Gainesville, Florida, USA
| | - Alexandria Harber
- Department of Psychology, University of Florida, Gainesville, Florida, USA
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, Arizona, USA
| | - Gary R Turner
- Department of Psychology, York University, Toronto, Canada
| | - R Nathan Spreng
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Natalie C Ebner
- Department of Psychology, University of Florida, Gainesville, Florida, USA.,Institute on Aging, University of Florida, Gainesville, Florida, USA
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13
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Allen PC, Smith S, Wilson RC, Wirth JR, Wilson NH, Baker Frost D, Flume J, Gilkeson GS, Cunningham MA, Langefeld CD, Absher DM, Ramos PS. Distinct genome-wide DNA methylation and gene expression signatures in classical monocytes from African American patients with systemic sclerosis. Clin Epigenetics 2023; 15:25. [PMID: 36803404 PMCID: PMC9938585 DOI: 10.1186/s13148-023-01445-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a multisystem autoimmune disorder that has an unclear etiology and disproportionately affects women and African Americans. Despite this, African Americans are dramatically underrepresented in SSc research. Additionally, monocytes show heightened activation in SSc and in African Americans relative to European Americans. In this study, we sought to investigate DNA methylation and gene expression patterns in classical monocytes in a health disparity population. METHODS Classical monocytes (CD14+ + CD16-) were FACS-isolated from 34 self-reported African American women. Samples from 12 SSc patients and 12 healthy controls were hybridized on MethylationEPIC BeadChip array, while RNA-seq was performed on 16 SSc patients and 18 healthy controls. Analyses were computed to identify differentially methylated CpGs (DMCs), differentially expressed genes (DEGs), and CpGs associated with changes in gene expression (eQTM analysis). RESULTS We observed modest DNA methylation and gene expression differences between cases and controls. The genes harboring the top DMCs, the top DEGs, as well as the top eQTM loci were enriched for metabolic processes. Genes involved in immune processes and pathways showed a weak upregulation in the transcriptomic analysis. While many genes were newly identified, several other have been previously reported as differentially methylated or expressed in different blood cells from patients with SSc, supporting for their potential dysregulation in SSc. CONCLUSIONS While contrasting with results found in other blood cell types in largely European-descent groups, the results of this study support that variation in DNA methylation and gene expression exists among different cell types and individuals of different genetic, clinical, social, and environmental backgrounds. This finding supports the importance of including diverse, well-characterized patients to understand the different roles of DNA methylation and gene expression variability in the dysregulation of classical monocytes in diverse populations, which might help explaining the health disparities.
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Affiliation(s)
- Peter C Allen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sarah Smith
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Jena R Wirth
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Nathan H Wilson
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - DeAnna Baker Frost
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Jonathan Flume
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Gary S Gilkeson
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Melissa A Cunningham
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Paula S Ramos
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
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14
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Hiseni P, Snipen L, Wilson RC, Furu K, Hegge FT, Rudi K. Prediction of high fecal propionate-to-butyrate ratios using 16S rRNA-based detection of bacterial groups with liquid array diagnostics. Biotechniques 2023; 74:9-21. [PMID: 36601888 DOI: 10.2144/btn-2022-0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Butyrate and propionate represent two of three main short-chain fatty acids produced by the intestinal microbiota. In healthy populations, their levels are reportedly equimolar, whereas a deviation in their ratio has been observed in various diseased cohorts. Monitoring such a ratio represents a valuable metric; however, it remains a challenge to adopt short-chain fatty acid detection techniques in clinical settings because of the volatile nature of these acids. Here we aimed to estimate short-chain fatty acid information indirectly through a novel, simple quantitative PCR-compatible assay (liquid array diagnostics) targeting a limited number of microbiome 16S markers. Utilizing 15 liquid array diagnostics probes to target microbiome markers selected by a model that combines partial least squares and linear discriminant analysis, the classes (normal vs high propionate-to-butyrate ratio) separated at a threshold of 2.6 with a prediction accuracy of 96%.
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Affiliation(s)
- Pranvera Hiseni
- Genetic Analysis AS, Kabelgata 8, Oslo, 0580, Norway.,Department of Chemistry, Biotechnology & Food Sciences, Norwegian University of Life Sciences, PO Box 5003, Aas, 1432, Norway
| | - Lars Snipen
- Department of Chemistry, Biotechnology & Food Sciences, Norwegian University of Life Sciences, PO Box 5003, Aas, 1432, Norway
| | - Robert C Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, PO Box 400 Vestad, Elverum, 2418, Norway
| | - Kari Furu
- Genetic Analysis AS, Kabelgata 8, Oslo, 0580, Norway
| | | | - Knut Rudi
- Department of Chemistry, Biotechnology & Food Sciences, Norwegian University of Life Sciences, PO Box 5003, Aas, 1432, Norway.,Department of Biotechnology, Inland Norway University of Applied Sciences, PO Box 400 Vestad, Elverum, 2418, Norway
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15
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Xue J, Peterson MA, Wilson RC. A drift diffusion model of figure-ground perception. J Vis 2022. [DOI: 10.1167/jov.22.14.4205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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16
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Baker TG, Glen WB, Wilson RC, Batalis NI, Wolff DJ, Welsh CT. Postmortem Diagnosis of the Proteus Syndrome by Next Generation Sequencing of Affected Brain Tissue. Acad Forensic Pathol 2022; 12:52-57. [PMID: 35799996 PMCID: PMC9254014 DOI: 10.1177/19253621221097294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/08/2022] [Indexed: 11/15/2022]
Abstract
We report a case of a somatic overgrowth syndrome diagnosed at forensic autopsy with the aid of next generation sequencing as Proteus syndrome. Somatic overgrowth syndromes result from spontaneous somatic mutations that arise early in development and display a mosaic pattern of expression in patient tissues. Due to the temporal and anatomic heterogeneity of these syndromes, phenotypes vary widely, resulting in clinical overlap. Furthermore, the variable ratio of mutated to nonmutated cells in patient tissue can result in low-level mutations that could be missed using Sanger sequencing. Due to these factors, recent literature points to next generation sequencing (NGS) as an adjunct to diagnosis of these rare entities. A male in his fourth decade of life presented to our forensic autopsy service with physical features suggestive of a somatic overgrowth syndrome. Due to the paucity of clinical information accompanying the individual, a definitive diagnosis based on physical characteristics, alone, was not possible. Next generation sequencing of affected formalin-fixed and paraffin-embedded brain tissue confirmed the presence of the variant in AKT1 (c.49G>A, p.Glu17Lys, in 14.13% of reads) found in Proteus syndrome. To our knowledge, this is the first report of the mosaic variant of AKT1 detected in brain tissue and the first reported case of a postmortem diagnosis of Proteus syndrome with the aid of NGS. We conclude that NGS can be used as an adjunctive method to support a specific diagnosis among the somatic overgrowth syndromes postmortem in the absence of sufficient clinical history.
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Affiliation(s)
- Tiffany G. Baker
- Tiffany G. Baker, MD, PhD,
Department of Pathology and Laboratory Medicine, Medical University of
South Carolina, Charleston, SC;
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17
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Hiseni P, Snipen L, Wilson RC, Furu K, Rudi K. Questioning the Quality of 16S rRNA Gene Sequences Derived From Human Gut Metagenome-Assembled Genomes. Front Microbiol 2022; 12:822301. [PMID: 35185835 PMCID: PMC8855107 DOI: 10.3389/fmicb.2021.822301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/28/2021] [Indexed: 12/04/2022] Open
Affiliation(s)
- Pranvera Hiseni
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
- Genetic Analysis AS, Oslo, Norway
- *Correspondence: Pranvera Hiseni
| | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Robert C. Wilson
- Department of Biotechnology, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
- Department of Biotechnology, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
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18
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Smith R, Taylor S, Wilson RC, Chuning AE, Persich MR, Wang S, Killgore WDS. Lower Levels of Directed Exploration and Reflective Thinking Are Associated With Greater Anxiety and Depression. Front Psychiatry 2022; 12:782136. [PMID: 35126200 PMCID: PMC8808291 DOI: 10.3389/fpsyt.2021.782136] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/07/2021] [Indexed: 01/15/2023] Open
Abstract
Anxiety and depression are often associated with strong beliefs that entering specific situations will lead to aversive outcomes - even when these situations are objectively safe and avoiding them reduces well-being. A possible mechanism underlying this maladaptive avoidance behavior is a failure to reflect on: (1) appropriate levels of uncertainty about the situation, and (2) how this uncertainty could be reduced by seeking further information (i.e., exploration). To test this hypothesis, we asked a community sample of 416 individuals to complete measures of reflective cognition, exploration, and symptoms of anxiety and depression. Consistent with our hypotheses, we found significant associations between each of these measures in expected directions (i.e., positive relationships between reflective cognition and strategic information-seeking behavior or "directed exploration", and negative relationships between these measures and anxiety/depression symptoms). Further analyses suggested that the relationship between directed exploration and depression/anxiety was due in part to an ambiguity aversion promoting exploration in conditions where information-seeking was not beneficial (as opposed to only being due to under-exploration when more information would aid future choices). In contrast, reflectiveness was associated with greater exploration in appropriate settings and separately accounted for differences in reaction times, decision noise, and choice accuracy in expected directions. These results shed light on the mechanisms underlying information-seeking behavior and how they may contribute to symptoms of emotional disorders. They also highlight the potential clinical relevance of individual differences in reflectiveness and exploration and should motivate future research on their possible contributions to vulnerability and/or maintenance of affective disorders.
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Affiliation(s)
- Ryan Smith
- Laureate Institute for Brain Research, Tulsa, OK, United States
| | - Samuel Taylor
- Laureate Institute for Brain Research, Tulsa, OK, United States
| | - Robert C. Wilson
- Department of Psychology, University of Arizona, Tucson, AZ, United States
| | - Anne E. Chuning
- Laureate Institute for Brain Research, Tulsa, OK, United States
| | | | - Siyu Wang
- Department of Psychology, University of Arizona, Tucson, AZ, United States
| | - William D. S. Killgore
- Department of Psychology, University of Arizona, Tucson, AZ, United States
- Department of Psychiatry, University of Arizona, Tucson, AZ, United States
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19
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Chase HW, Wilson RC, Waltz JA. Editorial: Computational accounts of reinforcement learning and decision making in psychiatric disorders. Front Psychiatry 2022; 13:966369. [PMID: 35958661 PMCID: PMC9358282 DOI: 10.3389/fpsyt.2022.966369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Henry W Chase
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, AZ, United States
| | - James A Waltz
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, United States
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20
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Grilli MD, McVeigh KS, Hakim ZM, Wank AA, Getz SJ, Levin BE, Ebner NC, Wilson RC. Is This Phishing? Older Age Is Associated With Greater Difficulty Discriminating Between Safe and Malicious Emails. J Gerontol B Psychol Sci Soc Sci 2021; 76:1711-1715. [PMID: 33378418 DOI: 10.1093/geronb/gbaa228] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES As our social worlds become increasingly digitally connected, so too has concern about older adults falling victim to "phishing" emails, which attempt to deceive a person into identity theft and fraud. In the present study, we investigated whether older age is associated with differences in perceived suspiciousness of phishing emails. METHODS Sixty-five cognitively normal middle-aged to older adults rated a series of genuine and phishing emails on a scale from definitely safe to definitely suspicious. RESULTS Although older age was not related to a shift in overall perception of email safety, older age was related to worse discrimination between genuine and phishing emails, according to perceived suspiciousness. DISCUSSION These findings suggest that cognitively normal older adults may be at particular risk for online fraud because of an age-associated reduction in their sensitivity to the credibility of emails.
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Affiliation(s)
- Matthew D Grilli
- Department of Psychology, University of Arizona, Tucson, USA.,Department of Neurology, University of Arizona, Tucson, USA
| | | | - Ziad M Hakim
- Department of Psychology, University of Arizona, Tucson, USA.,Department of Psychology, University of Florida, Gainesville, USA
| | - Aubrey A Wank
- Department of Psychology, University of Arizona, Tucson, USA
| | - Sarah J Getz
- Evelyn F. McKnight Brain Institute, University of Miami, Miami, Florida, USA.,Department of Neurology, Miller School of Medicine, University of Miami, Florida, USA
| | - Bonnie E Levin
- Evelyn F. McKnight Brain Institute, University of Miami, Miami, Florida, USA.,Department of Neurology, Miller School of Medicine, University of Miami, Florida, USA
| | - Natalie C Ebner
- Evelyn F. McKnight Brain Institute, University of Miami, Miami, Florida, USA.,Department of Aging and Geriatric Research, Institute on Aging, University of Florida, Gainesville, USA
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, USA.,Cognitive Science Program, University of Arizona, Tucson, USA
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21
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Abstract
To make informed decisions in natural environments that change over time, humans must update their beliefs as new observations are gathered. Studies exploring human inference as a dynamical process that unfolds in time have focused on situations in which the statistics of observations are history-independent. Yet, temporal structure is everywhere in nature and yields history-dependent observations. Do humans modify their inference processes depending on the latent temporal statistics of their observations? We investigate this question experimentally and theoretically using a change-point inference task. We show that humans adapt their inference process to fine aspects of the temporal structure in the statistics of stimuli. As such, humans behave qualitatively in a Bayesian fashion but, quantitatively, deviate away from optimality. Perhaps more importantly, humans behave suboptimally in that their responses are not deterministic, but variable. We show that this variability itself is modulated by the temporal statistics of stimuli. To elucidate the cognitive algorithm that yields this behavior, we investigate a broad array of existing and new models that characterize different sources of suboptimal deviations away from Bayesian inference. While models with "output noise" that corrupts the response-selection process are natural candidates, human behavior is best described by sampling-based inference models, in which the main ingredient is a compressed approximation of the posterior, represented through a modest set of random samples and updated over time. This result comes to complement a growing literature on sample-based representation and learning in humans. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
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22
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Abstract
People use information flexibly. They often combine multiple sources of relevant information over time in order to inform decisions with little or no interference from intervening irrelevant sources. They adjust the degree to which they use new information over time rationally in accordance with environmental statistics and their own uncertainty. They can even use information gained in one situation to solve a problem in a very different one. Learning flexibly rests on the ability to infer the context at a given time, and therefore knowing which pieces of information to combine and which to separate. We review the psychological and neural mechanisms behind adaptive learning and structure learning to outline how people pool together relevant information, demarcate contexts, prevent interference between information collected in different contexts, and transfer information from one context to another. By examining all of these processes through the lens of optimal inference we bridge concepts from multiple fields to provide a unified multi-system view of how the brain exploits structure in time to optimize learning.
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Affiliation(s)
- Linda Q Yu
- Carney Institute for Brain Sciences, Brown University, 164 Angell Street, Providence, RI, 02912, USA.
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, AZ, 85721, USA
| | - Matthew R Nassar
- Carney Institute for Brain Sciences, Brown University, 164 Angell Street, Providence, RI, 02912, USA
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23
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Hiseni P, Rudi K, Wilson RC, Hegge FT, Snipen L. HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data. Microbiome 2021; 9:165. [PMID: 34330336 PMCID: PMC8325300 DOI: 10.1186/s40168-021-01114-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/18/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND A major bottleneck in the use of metagenome sequencing for human gut microbiome studies has been the lack of a comprehensive genome collection to be used as a reference database. Several recent efforts have been made to re-construct genomes from human gut metagenome data, resulting in a huge increase in the number of relevant genomes. In this work, we aimed to create a collection of the most prevalent healthy human gut prokaryotic genomes, to be used as a reference database, including both MAGs from the human gut and ordinary RefSeq genomes. RESULTS We screened > 5,700 healthy human gut metagenomes for the containment of > 490,000 publicly available prokaryotic genomes sourced from RefSeq and the recently announced UHGG collection. This resulted in a pool of > 381,000 genomes that were subsequently scored and ranked based on their prevalence in the healthy human metagenomes. The genomes were then clustered at a 97.5% sequence identity resolution, and cluster representatives (30,691 in total) were retained to comprise the HumGut collection. Using the Kraken2 software for classification, we find superior performance in the assignment of metagenomic reads, classifying on average 94.5% of the reads in a metagenome, as opposed to 86% with UHGG and 44% when using standard Kraken2 database. A coarser HumGut collection, consisting of genomes dereplicated at 95% sequence identity-similar to UHGG, classified 88.25% of the reads. HumGut, half the size of standard Kraken2 database and directly comparable to the UHGG size, outperforms them both. CONCLUSIONS The HumGut collection contains > 30,000 genomes clustered at a 97.5% sequence identity resolution and ranked by human gut prevalence. We demonstrate how metagenomes from IBD-patients map equally well to this collection, indicating this reference is relevant also for studies well outside the metagenome reference set used to obtain HumGut. All data and metadata, as well as helpful code, are available at http://arken.nmbu.no/~larssn/humgut/ . Video Abstract.
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Affiliation(s)
- Pranvera Hiseni
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
- Genetic Analysis AS, Kabelgaten 8, 0580 Oslo, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway
| | - Robert C. Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway
| | | | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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24
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Davik J, Wilson RC, Njah RG, Grini PE, Randall SK, Alsheik MK, Sargent DJ. Genetic mapping and identification of a QTL determining tolerance to freezing stress in Fragaria vesca L. PLoS One 2021; 16:e0248089. [PMID: 34019543 PMCID: PMC8139484 DOI: 10.1371/journal.pone.0248089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/05/2021] [Indexed: 11/22/2022] Open
Abstract
Extreme cold and frost cause significant stress to plants which can potentially be lethal. Low temperature freezing stress can cause significant and irreversible damage to plant cells and can induce physiological and metabolic changes that impact on growth and development. Low temperatures cause physiological responses including winter dormancy and autumn cold hardening in strawberry (Fragaria) species, and some diploid F. vesca accessions have been shown to have adapted to low-temperature stresses. To study the genetics of freezing tolerance, a F. vesca mapping population of 143 seedlings segregating for differential responses to freezing stress was raised. The progeny was mapped using ‘Genotyping-by-Sequencing’ and a linkage map of 2,918 markers at 851 loci was resolved. The mapping population was phenotyped for freezing tolerance response under controlled and replicated laboratory conditions and subsequent quantitative trait loci analysis using interval mapping revealed a single significant quantitative trait locus on Fvb2 in the physical interval 10.6 Mb and 15.73 Mb on the F. vesca v4.0 genome sequence. This physical interval contained 896 predicted genes, several of which had putative roles associated with tolerance to abiotic stresses including freezing. Differential expression analysis of the 896 QTL-associated gene predictions in the leaves and crowns from ‘Alta’ and ‘NCGR1363’ parental genotypes revealed genotype-specific changes in transcript accumulation in response to low temperature treatment as well as expression differences between genotypes prior to treatment for many of the genes. The putative roles, and significant interparental differential expression levels of several of the genes reported here identified them as good candidates for the control of the effects of freezing tolerance at the QTL identified in this investigation and the possible role of these candidate genes in response to freezing stress is discussed.
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Affiliation(s)
- Jahn Davik
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
- * E-mail:
| | - Robert C. Wilson
- Department of Biotechnology, Faculty of Applied Ecology, Agricultural Sciences & Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Relindis G. Njah
- Department of Biotechnology, Faculty of Applied Ecology, Agricultural Sciences & Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Paul E. Grini
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Stephen K. Randall
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Muath K. Alsheik
- Graminor Breeding Ltd., Ridabu, Norway
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Daniel James Sargent
- Department of Genetics, Genomics and Breeding, NIAB-EMR, East Malling, Kent, United Kingdom
- Natural Resources Institute, University of Greenwich, Medway Campus, Chatham Maritime, Kent, United Kingdom
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25
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Abstract
Explore-exploit decisions require us to trade off the benefits of exploring unknown options to learn more about them, with exploiting known options, for immediate reward. Such decisions are ubiquitous in nature, but from a computational perspective, they are notoriously hard. There is therefore much interest in how humans and animals make these decisions and recently there has been an explosion of research in this area. Here we provide a biased and incomplete snapshot of this field focusing on the major finding that many organisms use two distinct strategies to solve the explore-exploit dilemma: a bias for information ('directed exploration') and the randomization of choice ('random exploration'). We review evidence for the existence of these strategies, their computational properties, their neural implementations, as well as how directed and random exploration vary over the lifespan. We conclude by highlighting open questions in this field that are ripe to both explore and exploit.
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Affiliation(s)
- Robert C. Wilson
- Department of Psychology, University of Arizona, Tucson AZ USA
- Cognitive Science Program, University of Arizona, Tucson AZ USA
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson AZ USA
| | | | - Vincent D. Costa
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland OR USA
| | - R. Becket Ebitz
- Department of Neuroscience, University of Montréal, Montréal, Québec, Canada
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Longo JF, Brosius SN, Znoyko I, Alers VA, Jenkins DP, Wilson RC, Carroll AJ, Wolff DJ, Roth KA, Carroll SL. Establishment and genomic characterization of a sporadic malignant peripheral nerve sheath tumor cell line. Sci Rep 2021; 11:5690. [PMID: 33707600 PMCID: PMC7952412 DOI: 10.1038/s41598-021-85055-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 02/17/2021] [Indexed: 12/19/2022] Open
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive Schwann cell-derived neoplasms that occur sporadically or in patients with neurofibromatosis type 1 (NF1). Preclinical research on sporadic MPNSTs has been limited as few cell lines exist. We generated and characterized a new sporadic MPNST cell line, 2XSB, which shares the molecular and genomic features of the parent tumor. These cells have a highly complex karyotype with extensive chromothripsis. 2XSB cells show robust invasive 3-dimensional and clonogenic culture capability and form solid tumors when xenografted into immunodeficient mice. High-density single nucleotide polymorphism array and whole exome sequencing analyses indicate that, unlike NF1-associated MPNSTs, 2XSB cells have intact, functional NF1 alleles with no evidence of mutations in genes encoding components of Polycomb Repressor Complex 2. However, mutations in other genes implicated in MPNST pathogenesis were identified in 2XSB cells including homozygous deletion of CDKN2A and mutations in TP53 and PTEN. We also identified mutations in genes not previously associated with MPNSTs but associated with the pathogenesis of other human cancers. These include DNMT1, NUMA1, NTRK1, PDE11A, CSMD3, LRP5 and ACTL9. This sporadic MPNST-derived cell line provides a useful tool for investigating the biology and potential treatment regimens for sporadic MPNSTs.
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Affiliation(s)
- Jody Fromm Longo
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Stephanie N Brosius
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA.,Medical Scientist Training Program, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA.,Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Iya Znoyko
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Victoria A Alers
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Dorea P Jenkins
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA.,Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC, 29425-9080, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA
| | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Kevin A Roth
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Steven L Carroll
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA. .,Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC, 29425-9080, USA. .,Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA.
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Feng SF, Wang S, Zarnescu S, Wilson RC. The dynamics of explore-exploit decisions reveal a signal-to-noise mechanism for random exploration. Sci Rep 2021; 11:3077. [PMID: 33542333 PMCID: PMC7862437 DOI: 10.1038/s41598-021-82530-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 12/16/2020] [Indexed: 12/29/2022] Open
Abstract
Growing evidence suggests that behavioral variability plays a critical role in how humans manage the tradeoff between exploration and exploitation. In these decisions a little variability can help us to overcome the desire to exploit known rewards by encouraging us to randomly explore something else. Here we investigate how such 'random exploration' could be controlled using a drift-diffusion model of the explore-exploit choice. In this model, variability is controlled by either the signal-to-noise ratio with which reward is encoded (the 'drift rate'), or the amount of information required before a decision is made (the 'threshold'). By fitting this model to behavior, we find that while, statistically, both drift and threshold change when people randomly explore, numerically, the change in drift rate has by far the largest effect. This suggests that random exploration is primarily driven by changes in the signal-to-noise ratio with which reward information is represented in the brain.
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Affiliation(s)
- Samuel F Feng
- Department of Mathematics, Khalifa University of Science and Technology, Abu Dhabi, UAE
- Khalifa University Centre for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE
| | - Siyu Wang
- Department of Psychology, University of Arizona, Tucson, AZ, USA
| | - Sylvia Zarnescu
- Department of Psychology, University of Arizona, Tucson, AZ, USA
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, AZ, USA.
- Cognitive Science Program, University of Arizona, Tucson, AZ, USA.
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Baker Frost D, da Silveira W, Hazard ES, Atanelishvili I, Wilson RC, Flume J, Day KL, Oates JC, Bogatkevich GS, Feghali-Bostwick C, Hardiman G, Ramos PS. Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis. Genes (Basel) 2021; 12:129. [PMID: 33498390 PMCID: PMC7909410 DOI: 10.3390/genes12020129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/20/2023] Open
Abstract
The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc and yet are underrepresented in research. The aim of this study was to comprehensively investigate the association of DNA methylation levels with SSc in dermal fibroblasts from patients of African ancestry. Reduced representation bisulfite sequencing (RRBS) was performed on primary dermal fibroblasts from 15 SSc patients and 15 controls of African ancestry, and over 3.8 million CpG sites were tested for differential methylation patterns between cases and controls. The dermal fibroblasts from African American patients exhibited widespread reduced DNA methylation. Differentially methylated CpG sites were most enriched in introns and intergenic regions while depleted in 5' UTR, promoters, and CpG islands. Seventeen genes and eleven promoters showed significant differential methylation, mostly in non-coding RNA genes and pseudogenes. Gene set enrichment analysis (GSEA) and gene ontology (GO) analyses revealed an enrichment of pathways related to interferon signaling and mesenchymal differentiation. The hypomethylation of DLX5 and TMEM140 was accompanied by these genes' overexpression in patients but underexpression for lncRNA MGC12916. These data show that differential methylation occurs in dermal fibroblasts from African American patients with SSc and identifies novel coding and non-coding genes.
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Affiliation(s)
- DeAnna Baker Frost
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Willian da Silveira
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast BT9 5DL, UK; (W.d.S.); (G.H.)
| | - E. Starr Hazard
- Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Ilia Atanelishvili
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Robert C. Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Jonathan Flume
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | | | - James C. Oates
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
- Rheumatology Section, Ralph H. Johnson VA Medical Center, Charleston, SC 29425, USA
| | - Galina S. Bogatkevich
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Carol Feghali-Bostwick
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Gary Hardiman
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast BT9 5DL, UK; (W.d.S.); (G.H.)
| | - Paula S. Ramos
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
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Sadeghiyeh H, Wang S, Kyllo HM, Alberhasky MR, Savita S, Kellohen KL, Wilson RC. On the Psychology of the Psychology Subject Pool. Journal of Individual Differences 2021. [DOI: 10.1027/1614-0001/a000327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract. Many psychology researches are performed through “psychology subject pools” which give participants considerable flexibility when they participate. This “participant degree-of-freedom” has led to concern that the characteristics of subject pool participants may change with time, with the most engaged students signing up at the start of the semester and the least engaged students leaving it all to the end. In this paper, we performed an exploratory analysis to look for evidence of this “good student effect.” Consistent with previous work, we find support for the good student effect with earlier participants scoring higher on the Big-Five subscales of Achievement-Striving and Cooperation, as well as Grit and Empathic-Concern. In addition, we found a non-linear effect of time-of-semester on Sensation-Seeking, with this measure peaking in the middle of the semester as well as the end. However, the vast majority of the measures we tested, including measures of personality, cognition, decision-making, and social interaction, did not correlate with time-of-semester or time-of-day at all. Thus, we conclude that, while some studies directly related to measures of Grit and Sensation-Seeking would do well to recruit throughout the semester, in most cases any bias introduced by the good student effect is likely to be small.
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Affiliation(s)
| | - Siyu Wang
- Department of Psychology, University of Arizona, Tucson, AZ, USA
| | - Hannah M. Kyllo
- Department of Psychology, University of Arizona, Tucson, AZ, USA
| | | | - Shlishaa Savita
- Department of Psychology, University of Arizona, Tucson, AZ, USA
| | | | - Robert C. Wilson
- Department of Psychology, University of Arizona, Tucson, AZ, USA
- Cognitive Science Program, University of Arizona, Tucson, AZ, USA
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
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Arbizu RA, Collins D, Wilson RC, Alekseyenko AV. Evidence for Differentiation of Colon Tissue Microbiota in Patients with and without Postoperative Hirschsprung's Associated Enterocolitis: A Pilot Study. Pediatr Gastroenterol Hepatol Nutr 2021; 24:30-37. [PMID: 33505891 PMCID: PMC7813566 DOI: 10.5223/pghn.2021.24.1.30] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/25/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
PURPOSE To investigate the differences in the colon microbiota composition of Hirschsprung's disease (HSCR) patients with and without a history of postoperative Hirschsprung's associated enterocolitis (HAEC). METHODS Colon tissue microbiota was characterized by bacterial deoxyribonucleic acid (DNA) extraction and 16S rDNA sequencing for taxonomic classification and comparison. RESULTS The sequence diversity richness within samples was significantly higher in samples from patients with a history of postoperative HAEC. We observed an increased relative abundance of the phyla Bacteroidetes, Firmicutes and Cyanobacteria in HAEC patients and Fusobacteria, Actinobacteria and Proteobacteria in HSCR patients and, an increased relative abundance of the genera Dolosigranulum, Roseouria and Streptococcus in HAEC patients and Propionibacterium and Delftia in HSCR patients. CONCLUSION Our findings provide evidence that the colon tissue microbiota composition is different in HSCR patients with and without postoperative HAEC.
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Affiliation(s)
- Ricardo A Arbizu
- Division of Pediatric Gastroenterology, Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - David Collins
- South Carolina Clinical and Translational Research Institute, Charleston, SC, USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Alexander V Alekseyenko
- Program for Human Microbiome Research, Biomedical Informatics Center, Departments of Public Health Sciences in College of Medicine; Oral Health Sciences in College of Dental Medicine; and Healthcare Leadership and Management in College of Health Professions, Medical University of South Carolina, Charleston, SC, USA
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31
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Sundman MH, Lim K, Ton That V, Mizell JM, Ugonna C, Rodriguez R, Chen NK, Fuglevand AJ, Liu Y, Wilson RC, Fellous JM, Rapcsak S, Chou YH. Transcranial magnetic stimulation reveals diminished homoeostatic metaplasticity in cognitively impaired adults. Brain Commun 2020; 2:fcaa203. [PMID: 33376989 PMCID: PMC7750948 DOI: 10.1093/braincomms/fcaa203] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/22/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Homoeostatic metaplasticity is a neuroprotective physiological feature that counterbalances Hebbian forms of plasticity to prevent network destabilization and hyperexcitability. Recent animal models highlight dysfunctional homoeostatic metaplasticity in the pathogenesis of Alzheimer's disease. However, the association between homoeostatic metaplasticity and cognitive status has not been systematically characterized in either demented or non-demented human populations, and the potential value of homoeostatic metaplasticity as an early biomarker of cognitive impairment has not been explored in humans. Here, we report that, through pre-conditioning the synaptic activity prior to non-invasive brain stimulation, the association between homoeostatic metaplasticity and cognitive status could be established in a population of non-demented human subjects (older adults across cognitive spectrums; all within the non-demented range). All participants (n = 40; age range, 65-74, 47.5% female) underwent a standardized neuropsychological battery, magnetic resonance imaging and a transcranial magnetic stimulation protocol. Specifically, we sampled motor-evoked potentials with an input/output curve immediately before and after repetitive transcranial magnetic stimulation to assess neural plasticity with two experimental paradigms: one with voluntary muscle contraction (i.e. modulated synaptic activity history) to deliberately introduce homoeostatic interference, and one without to serve as a control condition. From comparing neuroplastic responses across these experimental paradigms and across cohorts grouped by cognitive status, we found that (i) homoeostatic metaplasticity is diminished in our cohort of cognitively impaired older adults and (ii) this neuroprotective feature remains intact in cognitively normal participants. This novel finding suggests that (i) future studies should expand their scope beyond just Hebbian forms of plasticity that are traditionally assessed when using non-invasive brain stimulation to investigate cognitive ageing and (ii) the potential value of homoeostatic metaplasticity in serving as a biomarker for cognitive impairment should be further explored.
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Affiliation(s)
- Mark H Sundman
- Department of Psychology, University of Arizona, Tucson, AZ 85721, USA
| | - Koeun Lim
- Department of Psychology, University of Arizona, Tucson, AZ 85721, USA
| | - Viet Ton That
- Department of Psychology, University of Arizona, Tucson, AZ 85721, USA
| | | | - Chidi Ugonna
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ 85721, USA
- Department of Medical Imaging, University of Arizona, Tucson, AZ 85721, USA
| | - Rudolph Rodriguez
- Department of Psychology, University of Arizona, Tucson, AZ 85721, USA
| | - Nan-Kuei Chen
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ 85721, USA
- Department of Medical Imaging, University of Arizona, Tucson, AZ 85721, USA
| | - Andrew J Fuglevand
- Department of Physiology, College of Medicine, University of Arizona, Tucson, AZ 85721, USA
- Department of Neuroscience, College of Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Yilin Liu
- Department of Psychology, University of Arizona, Tucson, AZ 85721, USA
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, AZ 85721, USA
| | - Jean-Marc Fellous
- Department of Psychology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ 85721, USA
| | - Steven Rapcsak
- Department of Psychology, University of Arizona, Tucson, AZ 85721, USA
- Department of Neurology, University of Arizona, Tucson, AZ 85721, USA
| | - Ying-Hui Chou
- Department of Psychology, University of Arizona, Tucson, AZ 85721, USA
- Evelyn F. McKnight Brain Institute, Arizona Center on Aging, and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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Runyon JR, Hyde JN, Staroschak C, Kromenacker B, Wilson RC, Sternberg EM. LCMS Measurement of Steroid Biomarkers Collected from Palmar Sweat. ChemRxiv 2020:12931769. [PMID: 32935082 PMCID: PMC7491523 DOI: 10.26434/chemrxiv.12931769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 09/09/2020] [Indexed: 11/20/2022]
Abstract
Human eccrine sweat contains numerous biomarkers which can provide information on health, performance, and aging. Non-invasive collection and measurement of biomarkers has become especially important in recent times given viral outbreaks like SARS-CoV-2. In the current study we describe a method of sweat collection from palmar surfaces in participants via surface capture using glass beads and the resulting analysis of biomarkers from very low volumes of sweat using liquid chromatography mass spectrometry with selected ion monitoring. Study participants underwent a cognitive and physical stress task with easy and hard conditions with sweat being collected after each task. Resulting analysis found a signal for 22 steroid biomarkers and we report detailed information on selected biomarkers, given their applicability to timely real-world exemplars, including cortisol, dehydroepiandrosterone, allopregnanolone, estrone, aldosterone, and 20α/β-dihydrocortisone.
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Affiliation(s)
- J. Ray Runyon
- Andrew Weil Center for Integrative Medicine, University of Arizona, Tucson, Arizona, United States of America
- Department of Environmental Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Jacob N. Hyde
- Andrew Weil Center for Integrative Medicine, University of Arizona, Tucson, Arizona, United States of America
- Department of Family & Community Medicine, College of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Christina Staroschak
- Department of Family & Community Medicine, College of Medicine, University of Arizona, Tucson, Arizona, United States of America
- College of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Bryan Kromenacker
- College of Medicine, University of Arizona, Tucson, Arizona, United States of America
- Department of Psychology, College of Science, University of Arizona, Tucson, Arizona, United States of America
| | - Robert C. Wilson
- Department of Psychology, College of Science, University of Arizona, Tucson, Arizona, United States of America
| | - Esther M. Sternberg
- Andrew Weil Center for Integrative Medicine, University of Arizona, Tucson, Arizona, United States of America
- College of Medicine, University of Arizona, Tucson, Arizona, United States of America
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Linløkken AN, Garlie S, Johansen W, Wilson RC. Assessing Evolutionary Significant Units (ESU) of the Endangered Freshwater Pearl Mussel ( Margaritifera margaritifera) in Southeast Norway on the Basis of Genetic Analysis. Genes (Basel) 2020; 11:E1061. [PMID: 32911821 PMCID: PMC7565849 DOI: 10.3390/genes11091061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 11/16/2022] Open
Abstract
A total of 312 specimens of freshwater pearl mussel (Margaritifera margaritifera) were sampled from 11 populations, located in four different river systems in Southeast Norway, and analyzed for 11 simple sequence repeat (SSR) (microsatellite) markers. All study populations have landlocked brown trout (Salmo trutta) as the only possible host. Several populations had experienced recruitment failure, probably due to low pH (about 6.0) and calcium concentration. STRUCTURE clustering analysis revealed two genetic clusters, of which one cluster occurred mainly in the western river systems, and totally dominated in one population (Fallselva (A-FAL)) that had higher genetic diversity than the others. Cluster 2 completely dominated in the populations of the eastern river systems, and all of them had low genetic diversity. Bottleneck events were indicated in all populations and the inbreeding coefficient FIS was significant in all populations, except for the southernmost population (Sørkedalselva (B-SØR)), which was the only population with genotypes in Hardy-Weinberg equilibrium. FIS were especially high in the populations of the eastern river systems, and maximum shell length was negatively correlated to FIS. If artificially breeding and stocking should become necessary for future preservation, it should be based on single populations; alternatively, the eastern populations should be based on cross-breeding of populations within the cluster to increase their genetic diversity.
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Affiliation(s)
- Arne N. Linløkken
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Inland Norway University of Applied Sciences, N-2418 Elverum, Norway; (S.G.); (W.J.); (R.C.W.)
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Khezri A, Narud B, Stenseth EB, Zeremichael TT, Myromslien FD, Wilson RC, Ahmad R, Kommisrud E. Sperm DNA Hypomethylation Proximal to Reproduction Pathway Genes in Maturing Elite Norwegian Red Bulls. Front Genet 2020; 11:922. [PMID: 32849856 PMCID: PMC7431628 DOI: 10.3389/fgene.2020.00922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/24/2020] [Indexed: 01/08/2023] Open
Abstract
Genomic selection in modern farming demands sufficient semen production in young bulls. Factors affecting semen quality and production capacity in young bulls are not well understood; DNA methylation, a complicated phenomenon in sperm cells, is one such factors. In this study, fresh and frozen-thawed semen samples from the same Norwegian Red (NR) bulls at both 14 and 17 months of age were examined for sperm chromatin integrity parameters, ATP content, viability, and motility. Furthermore, reduced representation bisulfite libraries constructed according to two protocols, the Ovation® RRBS Methyl-Seq System (Ovation method) and a previously optimized gel-free method and were sequenced to study the sperm DNA methylome in frozen-thawed semen samples. Sperm quality analyses indicated that sperm concentration, total motility and progressivity in fresh semen from 17 months old NR bulls were significantly higher compared to individuals at 14 months of age. The percentage of DNA fragmented sperm cells significantly decreased in both fresh and frozen-thawed semen samples in bulls with increasing age. Libraries from the Ovation method exhibited a greater percentage of read loss and shorter read size following trimming. Downstream analyses for reads obtained from the gel-free method revealed similar global sperm DNA methylation but differentially methylated regions (DMRs) between 14- and 17 months old NR bulls. The majority of identified DMRs were hypomethylated in 14 months old bulls. Most of the identified DMRs (69%) exhibited a less than 10% methylation difference while only 1.5% of DMRs exceeded a 25% methylation difference. Pathway analysis showed that genes annotated with DMRs having low methylation differences (less than 10%) and DMRs having between 10 and 25% methylation differences, could be associated with important hormonal signaling and sperm function relevant pathways, respectively. The current research shows that RRBS in parallel with routine sperm quality analyses could be informative in reproductive capacity of young NR bulls. Although global sperm DNA methylation levels in 14 and 17 months old NR bulls were similar, regions with low and varying levels of DNA methylation differences can be identified and linked with important sperm function and hormonal pathways.
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Affiliation(s)
- Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Birgitte Narud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Else-Berit Stenseth
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | | | - Robert C Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Elisabeth Kommisrud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
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35
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Waltz JA, Wilson RC, Albrecht MA, Frank MJ, Gold JM. Differential Effects of Psychotic Illness on Directed and Random Exploration. Comput Psychiatr 2020; 4:18-39. [PMID: 33768158 PMCID: PMC7990386 DOI: 10.1162/cpsy_a_00027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 04/27/2020] [Indexed: 12/25/2022]
Abstract
Schizophrenia is associated with a number of deficits in decision-making, but the scope, nature, and cause of these deficits are not completely understood. Here we focus on a particular type of decision, known as the explore/exploit dilemma, in which people must choose between exploiting options that yield relatively known rewards and exploring more ambiguous options of uncertain reward probability or magnitude. Previous work has shown that healthy people use two distinct strategies to decide when to explore: directed exploration, which involves choosing options that would reduce uncertainty about the reward values (information seeking), and random exploration (exploring by chance), which describes behavioral variability that is not goal directed. We administered a recently developed gambling task designed to quantify both directed and random exploration to 108 patients with schizophrenia (PSZ) and 33 healthy volunteers (HVs). We found that PSZ patients show reduced directed exploration relative to HVs, but no difference in random exploration. Moreover, patients' directed exploration behavior clusters into two qualitatively different behavioral phenotypes. In the first phenotype, which accounts for the majority of the patients (79%) and is consistent with previously reported behavior, directed exploration is only marginally (but significantly) reduced, suggesting that these patients can use directed exploration, but at a slightly lower level than community controls. In contrast, the second phenotype, comprising 21% of patients, exhibit a form of "extreme ambiguity aversion," in which they almost never choose more informative options, even when they are clearly of higher value. Moreover, in PSZ, deficits in directed exploration were related to measures of intellectual function, whereas random exploration was related to positive symptoms. Taken together, our results suggest that schizophrenia has differential effects on directed and random exploration and that investigating the explore/exploit dilemma in psychosis patients may reveal subgroups of patients with qualitatively different patterns of exploration.
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Affiliation(s)
- James A. Waltz
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Robert C. Wilson
- Department of Psychology and Cognitive Science Program, University of Arizona, Tucson, Arizona, USA
| | - Matthew A. Albrecht
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
- School of Public Health, Curtin Health Innovation Research Institute, Curtin University, Perth, Western Australia, Australia
| | - Michael J. Frank
- Department of Cognitive, Linguistic, and Psychological Sciences, Brown University, Providence, Rhode Island, USA
- Department of Psychiatry and Brown Institute for Brain Science, Brown University, Providence, Rhode Island, USA
| | - James M. Gold
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Ethier SP, Guest ST, Garrett-Mayer E, Armeson K, Wilson RC, Duchinski K, Couch D, Gray JW, Kappler C. Development and implementation of the SUM breast cancer cell line functional genomics knowledge base. NPJ Breast Cancer 2020; 6:30. [PMID: 32715085 PMCID: PMC7374090 DOI: 10.1038/s41523-020-0173-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/23/2020] [Indexed: 12/24/2022] Open
Abstract
Several years ago, the SUM panel of human breast cancer cell lines was developed, and these cell lines have been distributed to hundreds of labs worldwide. Our lab and others have developed extensive omics data sets from these cells. More recently, we performed genome-scale shRNA essentiality screens on the entire SUM line panel, as well as on MCF10A cells, MCF-7 cells, and MCF-7LTED cells. These gene essentiality data sets allowed us to perform orthogonal analyses that functionalize the otherwise descriptive genomic data obtained from traditional genomics platforms. To make these omics data sets available to users of the SUM lines, and to allow users to mine these data sets, we developed the SUM Breast Cancer Cell Line Knowledge Base. This knowledge base provides information on the derivation of each cell line, provides protocols for the proper maintenance of the cells, and provides a series of data mining tools that allow rapid identification of the oncogene signatures for each line, the enrichment of KEGG pathways with screen hit and gene expression data, an analysis of protein and phospho-protein expression for the cell lines, as well as a gene search tool and a functional-druggable signature tool. Recently, we expanded our database to include genomic data for an additional 27 commonly used breast cancer cell lines. Thus, the SLKBase provides users with deep insights into the biology of human breast cancer cell lines that can be used to develop strategies for the reverse engineering of individual breast cancer cell lines.
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Affiliation(s)
- Stephen P Ethier
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
| | - Stephen T Guest
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
- Present Address: Department of Biomedical Informatics, University of Michigan Medical School, Ann Arbor, MI USA
| | - Elizabeth Garrett-Mayer
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
- Present Address: American Society for Clinical Oncology, Charleston, SC USA
| | - Kent Armeson
- Biostatistics Core, Hollings Cancer Center, Charleston, SC USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
| | - Kathryn Duchinski
- Department of Computer Science, The College of Charleston, Charleston, SC USA
- Present Address: Program in Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA USA
| | - Daniel Couch
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health and Sciences University, Portland, OR USA
| | - Christiana Kappler
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
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Harootonian SK, Wilson RC, Hejtmánek L, Ziskin EM, Ekstrom AD. Path integration in large-scale space and with novel geometries: Comparing vector addition and encoding-error models. PLoS Comput Biol 2020; 16:e1007489. [PMID: 32379824 PMCID: PMC7244182 DOI: 10.1371/journal.pcbi.1007489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 05/22/2020] [Accepted: 03/24/2020] [Indexed: 11/19/2022] Open
Abstract
Path integration is thought to rely on vestibular and proprioceptive cues yet most studies in humans involve primarily visual input, providing limited insight into their respective contributions. We developed a paradigm involving walking in an omnidirectional treadmill in which participants were guided on two sides of a triangle and then found their back way to origin. In Experiment 1, we tested a range of different triangle types while keeping the distance of the unguided side constant to determine the influence of spatial geometry. Participants overshot the angle they needed to turn and undershot the distance they needed to walk, with no consistent effect of triangle type. In Experiment 2, we manipulated distance while keeping angle constant to determine how path integration operated over both shorter and longer distances. Participants underestimated the distance they needed to walk to the origin, with error increasing as a function of the walked distance. To attempt to account for our findings, we developed configural-based computational models involving vector addition, the second of which included terms for the influence of past trials on the current one. We compared against a previously developed configural model of human path integration, the Encoding-Error model. We found that the vector addition models captured the tendency of participants to under-encode guided sides of the triangles and an influence of past trials on current trials. Together, our findings expand our understanding of body-based contributions to human path integration, further suggesting the value of vector addition models in understanding these important components of human navigation. How do we remember where we have been? One important mechanism for doing so is called path integration, which refers to the computation of one’s position in space with only self-motion cues. By tracking the direction and distance we have walked, we can create a mental arrow from the current location to the origin, termed the homing vector. Previous studies have shown that the homing vector is subject to systematic distortions depending on previously experienced paths, yet what influences these patterns of errors, particularly in humans, remains uncertain. In this study, we compare two models of path integration based on participants walking two sides of a triangle without vision and then completing the third side based on their estimate of the homing vector. We found no effect of triangle shape on systematic errors, while the systematic errors scaled with path length logarithmically, similar to Weber-Fechner law. While we show that both models captured participants’ behavior, a model based on vector addition best captured the patterns of error in the homing vector. Our study therefore has important implications for how humans track their location, suggesting that vector-based models provide a reasonable and simple explanation for how we do so.
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Affiliation(s)
- Sevan K. Harootonian
- Center for Neuroscience, University of California Davis, Davis, California, United States of America
- Psychology Department, University of Arizona, Tucson, Arizona, United States of America
| | - Robert C. Wilson
- Psychology Department, University of Arizona, Tucson, Arizona, United States of America
- Cognitive Science Program, University of Arizona, Tucson, Arizona, United States of America
- Evelyn McKnight Brain Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Lukáš Hejtmánek
- Center for Neuroscience, University of California Davis, Davis, California, United States of America
- Third Faculty of Medicine, Charles University, Ruská, Prague, Czech Republic
| | - Eli M. Ziskin
- Center for Neuroscience, University of California Davis, Davis, California, United States of America
- Psychology Department, University of Arizona, Tucson, Arizona, United States of America
| | - Arne D. Ekstrom
- Center for Neuroscience, University of California Davis, Davis, California, United States of America
- Psychology Department, University of Arizona, Tucson, Arizona, United States of America
- Evelyn McKnight Brain Institute, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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Keung W, Hagen TA, Wilson RC. A divisive model of evidence accumulation explains uneven weighting of evidence over time. Nat Commun 2020; 11:2160. [PMID: 32358501 PMCID: PMC7195479 DOI: 10.1038/s41467-020-15630-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 03/12/2020] [Indexed: 12/21/2022] Open
Abstract
Divisive normalization has long been used to account for computations in various neural processes and behaviours. The model proposes that inputs into a neural system are divisively normalized by the system’s total activity. More recently, dynamical versions of divisive normalization have been shown to account for how neural activity evolves over time in value-based decision making. Despite its ubiquity, divisive normalization has not been studied in decisions that require evidence to be integrated over time. Such decisions are important when the information is not all available at once. A key feature of such decisions is how evidence is weighted over time, known as the integration kernel. Here, we provide a formal expression for the integration kernel in divisive normalization, and show that divisive normalization quantitatively accounts for 133 human participants’ perceptual decision making behaviour, performing as well as the state-of-the-art Drift Diffusion Model, the predominant model for perceptual evidence accumulation. Divisive normalization is thought to be a ubiquitous computation in the brain, but has not been studied in decisions that require integrating evidence over time. Here, the authors show in humans that dynamic divisive normalization accounts for the uneven weighting of perceptual evidence over time.
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Affiliation(s)
- Waitsang Keung
- Department of Psychology, University of Arizona, Tucson, AZ, 85719, USA.
| | - Todd A Hagen
- Department of Psychology, University of Arizona, Tucson, AZ, 85719, USA
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, AZ, 85719, USA.,Cognitive Science Program, University of Arizona, Tucson, AZ, 85719, USA
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Sadeghiyeh H, Wang S, Alberhasky MR, Kyllo HM, Shenhav A, Wilson RC. Temporal discounting correlates with directed exploration but not with random exploration. Sci Rep 2020; 10:4020. [PMID: 32132573 PMCID: PMC7055215 DOI: 10.1038/s41598-020-60576-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/12/2020] [Indexed: 11/09/2022] Open
Abstract
The explore-exploit dilemma describes the trade off that occurs any time we must choose between exploring unknown options and exploiting options we know well. Implicit in this trade off is how we value future rewards - exploiting is usually better in the short term, but in the longer term the benefits of exploration can be huge. Thus, in theory there should be a tight connection between how much people value future rewards, i.e. how much they discount future rewards relative to immediate rewards, and how likely they are to explore, with less 'temporal discounting' associated with more exploration. By measuring individual differences in temporal discounting and correlating them with explore-exploit behavior, we tested whether this theoretical prediction holds in practice. We used the 27-item Delay-Discounting Questionnaire to estimate temporal discounting and the Horizon Task to quantify two strategies of explore-exploit behavior: directed exploration, where information drives exploration by choice, and random exploration, where behavioral variability drives exploration by chance. We find a clear correlation between temporal discounting and directed exploration, with more temporal discounting leading to less directed exploration. Conversely, we find no relationship between temporal discounting and random exploration. Unexpectedly, we find that the relationship with directed exploration appears to be driven by a correlation between temporal discounting and uncertainty seeking at short time horizons, rather than information seeking at long horizons. Taken together our results suggest a nuanced relationship between temporal discounting and explore-exploit behavior that may be mediated by multiple factors.
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Affiliation(s)
- Hashem Sadeghiyeh
- Department of Psychology, University of Arizona, Tucson, USA. .,Department of Psychological Science, Missouri University of Science and Technology, Rolla, USA.
| | - Siyu Wang
- Department of Psychology, University of Arizona, Tucson, USA
| | | | - Hannah M Kyllo
- Department of Psychology, University of Arizona, Tucson, USA
| | - Amitai Shenhav
- Department of Cognitive, Linguistic, & Psychological Sciences, Brown University, Providence, USA
| | - Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, USA.,Cognitive Science Program, University of Arizona, Tucson, USA
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40
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Bisese EC, Ciuba CM, Davidson AL, Kaushik A, Mullen SM, Barth JL, Hazard ES, Wilson RC, Hardiman G, Hollis DM. The acute transcriptome response of the midbrain/diencephalon to injury in the adult mummichog (Fundulus heteroclitus). Mol Brain 2019; 12:119. [PMID: 31888716 PMCID: PMC6937918 DOI: 10.1186/s13041-019-0542-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/23/2019] [Indexed: 11/18/2022] Open
Abstract
Adult fish produce new cells throughout their central nervous system during the course of their lives and maintain a tremendous capacity to repair damaged neural tissue. Much of the focus on understanding brain repair and regeneration in adult fish has been directed at regions of the brainstem and forebrain; however, the mesencephalon (midbrain) and diencephalon have received little attention. We sought to examine differential gene expression in the midbrain/diencephalon in response to injury in the adult fish using RNA-seq. Using the mummichog (Fundulus heteroclitus), we administered a mechanical lesion to the midbrain/diencephalon and examined differentially expressed genes (DEGs) at an acute recovery time of 1 h post-injury. Comparisons of whole transcriptomes derived from isolated RNA of intact and injured midbrain/diencephalic tissue identified 404 DEGs with the vast majority being upregulated. Using qPCR, we validated the upregulation of DEGs pim-2-like, syndecan-4-like, and cd83. Based on genes both familiar and novel regarding the adult brain response to injury, these data provide an extensive molecular profile giving insight into a range of cellular processes involved in the injury response of a brain regenerative-capable vertebrate.
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Affiliation(s)
- Eleanor C Bisese
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA
| | - Chandler M Ciuba
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA
| | - Amelia L Davidson
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA
| | - Akanksha Kaushik
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA
| | - Sabrina M Mullen
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA
| | - Jeremy L Barth
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC, 29425, USA
| | - E Starr Hazard
- Computational Biology Resource Center, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC, 29425, USA
| | - Robert C Wilson
- Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC, 29425, USA
| | - Gary Hardiman
- Department of Medicine, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC, 29425, USA.,School of Biological Sciences & Institute for Global Food Security, Queen's University Belfast, Belfast, Northern Ireland, BT9 5DL, UK
| | - David M Hollis
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA.
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Khezri A, Narud B, Stenseth EB, Johannisson A, Myromslien FD, Gaustad AH, Wilson RC, Lyle R, Morrell JM, Kommisrud E, Ahmad R. DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation. BMC Genomics 2019; 20:897. [PMID: 31775629 PMCID: PMC6880426 DOI: 10.1186/s12864-019-6307-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Sperm DNA integrity is considered essential for successful transmission of the paternal genome, fertilization and normal embryo development. DNA fragmentation index (DFI, %) has become a key parameter in the swine artificial insemination industry to assess sperm DNA integrity. Recently, in some elite Norwegian Landrace boars (boars with excellent field fertility records), a higher level of sperm DFI has been observed. In order to obtain a better understanding of this, and to study the complexity of sperm DNA integrity, liquid preserved semen samples from elite boars with contrasting DFI levels were examined for protamine deficiency, thiol profile and disulphide bonds. Additionally, the DNA methylation profiles of the samples were determined by reduced representation bisulphite sequencing (RRBS). RESULTS In this study, different traits related to sperm DNA integrity were investigated (n = 18 ejaculates). Upon liquid storage, the levels of total thiols and disulphide bonds decreased significantly, while the DFI and protamine deficiency level increased significantly. The RRBS results revealed similar global patterns of low methylation from semen samples with different levels of DFI (low, medium and high). Differential methylation analyses indicated that the number of differentially methylated cytosines (DMCs) increased in the low-high compared to the low-medium and the medium-high DFI groups. Annotating the DMCs with gene and CpG features revealed clear differences between DFI groups. In addition, the number of annotated transcription starting sites (TSS) and associated pathways in the low-high comparison was greater than the other two groups. Pathway analysis showed that genes (based on the closest TSS to DMCs) corresponding to low-high DFI comparison were associated with important processes such as membrane function, metabolic cascade and antioxidant defence system. CONCLUSION To our knowledge, this is the first study evaluating DNA methylation in boar sperm cells with different levels of DFI. The present study shows that sperm cells with varying levels of DNA fragmentation exhibit similar global methylation, but different site-specific DNA methylation signatures. Moreover, with increasing DNA fragmentation in spermatozoa, there is an increase in the number of potentially affected downstream genes and their respective regulatory pathways.
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Affiliation(s)
- Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Birgitte Narud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Else-Berit Stenseth
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Anders Johannisson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Ann Helen Gaustad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
- Topigs Norsvin, Hamar, Norway
| | - Robert C Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Robert Lyle
- Department of Medical Genetics and Norwegian Sequencing Centre, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Jane M Morrell
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Elisabeth Kommisrud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.
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Abstract
Computational modeling of behavior has revolutionized psychology and neuroscience. By fitting models to experimental data we can probe the algorithms underlying behavior, find neural correlates of computational variables and better understand the effects of drugs, illness and interventions. But with great power comes great responsibility. Here, we offer ten simple rules to ensure that computational modeling is used with care and yields meaningful insights. In particular, we present a beginner-friendly, pragmatic and details-oriented introduction on how to relate models to data. What, exactly, can a model tell us about the mind? To answer this, we apply our rules to the simplest modeling techniques most accessible to beginning modelers and illustrate them with examples and code available online. However, most rules apply to more advanced techniques. Our hope is that by following our guidelines, researchers will avoid many pitfalls and unleash the power of computational modeling on their own data.
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Affiliation(s)
- Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, United States.,Cognitive Science Program, University of Arizona, Tucson, United States
| | - Anne Ge Collins
- Department of Psychology, University of California, Berkeley, Berkeley, United States.,Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, United States
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43
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Abstract
Researchers and educators have long wrestled with the question of how best to teach their clients be they humans, non-human animals or machines. Here, we examine the role of a single variable, the difficulty of training, on the rate of learning. In many situations we find that there is a sweet spot in which training is neither too easy nor too hard, and where learning progresses most quickly. We derive conditions for this sweet spot for a broad class of learning algorithms in the context of binary classification tasks. For all of these stochastic gradient-descent based learning algorithms, we find that the optimal error rate for training is around 15.87% or, conversely, that the optimal training accuracy is about 85%. We demonstrate the efficacy of this ‘Eighty Five Percent Rule’ for artificial neural networks used in AI and biologically plausible neural networks thought to describe animal learning. Is there an optimum difficulty level for training? In this paper, the authors show that for the widely-used class of stochastic gradient-descent based learning algorithms, learning is fastest when the accuracy during training is 85%.
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Affiliation(s)
- Robert C Wilson
- Department of Psychology, University of Arizona, Tucson, AZ, USA. .,Cognitive Science Program, University of Arizona, Tucson, AZ, USA.
| | - Amitai Shenhav
- Cognitive, Linguistic, & Psychological Sciences, Brown University, Providence, RI, USA.,Brown Institute for Brain Science, Brown University, Providence, RI, USA
| | - Mark Straccia
- Department of Psychology, UCLA, Los Angeles, CA, USA
| | - Jonathan D Cohen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
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Kane GA, Bornstein AM, Shenhav A, Wilson RC, Daw ND, Cohen JD. Rats exhibit similar biases in foraging and intertemporal choice tasks. eLife 2019; 8:48429. [PMID: 31532391 PMCID: PMC6794087 DOI: 10.7554/elife.48429] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/17/2019] [Indexed: 12/05/2022] Open
Abstract
Animals, including humans, consistently exhibit myopia in two different contexts: foraging, in which they harvest locally beyond what is predicted by optimal foraging theory, and intertemporal choice, in which they exhibit a preference for immediate vs. delayed rewards beyond what is predicted by rational (exponential) discounting. Despite the similarity in behavior between these two contexts, previous efforts to reconcile these observations in terms of a consistent pattern of time preferences have failed. Here, via extensive behavioral testing and quantitative modeling, we show that rats exhibit similar time preferences in both contexts: they prefer immediate vs. delayed rewards and they are sensitive to opportunity costs of delays to future decisions. Further, a quasi-hyperbolic discounting model, a form of hyperbolic discounting with separate components for short- and long-term rewards, explains individual rats’ time preferences across both contexts, providing evidence for a common mechanism for myopic behavior in foraging and intertemporal choice. Often decisions have to be made on whether to stick with a resource or leave it behind to search for a better alternative. Should you book that hotel room or continue looking at others? Is it time to start searching for a new job, or even for a new partner? Animals face similar 'stick or twist' decisions when foraging for food. Knowing how to maximize the amount of food you obtain is key to survival. Studies have shown that most animals tend to stick with a food source for a little too long, a phenomenon known as 'overharvesting'. To find out why, Kane et al. designed carefully controlled experiments to compare foraging behavior in rats to another form of decision-making, known as intertemporal choice. The latter involves choosing between a small reward now versus a larger reward later. Given this choice, most rats opt to receive a smaller reward now rather than wait for the larger reward. This suggests that rats value rewards available in the future less than rewards they can get immediately. Kane et al. showed that this preference for short-term rewards can also explain why rats overharvest in foraging scenarios. By leaving one food source to go in search of another, rats must put up with a delay before they can access the new food supply. This delay, due to the time required to travel and search, reduces the value of the future reward. As a result, rats are more likely to stick with their current food source, even though leaving it would yield a greater reward in the long run. These findings in rats raise important questions about the mechanisms that lead to biases in thinking, and how factors like changes in the environment or specific disease states can influence these biases.
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Affiliation(s)
- Gary A Kane
- Department of Psychology, Princeton Neuroscience Institute, Princeton University, Princeton, United States.,Rowland Institute at Harvard, Harvard University, Cambridge, United States
| | - Aaron M Bornstein
- Department of Psychology, Princeton Neuroscience Institute, Princeton University, Princeton, United States.,Department of Cognitive Sciences, Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, United States
| | - Amitai Shenhav
- Department of Cognitive, Linguistic and Psychological Sciences, Carney Institute for Brain Science, Brown University, Providence, United States
| | - Robert C Wilson
- Department of Psychology, Cognitive Science Program, University of Arizona, Tucson, United States
| | - Nathaniel D Daw
- Department of Psychology, Princeton Neuroscience Institute, Princeton University, Princeton, United States
| | - Jonathan D Cohen
- Department of Psychology, Princeton Neuroscience Institute, Princeton University, Princeton, United States
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45
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Sun B, Mason S, Wilson RC, Hazard SE, Wang Y, Fang R, Wang Q, Yeh ES, Yang M, Roberts TM, Zhao JJ, Wang Q. Inhibition of the transcriptional kinase CDK7 overcomes therapeutic resistance in HER2-positive breast cancers. Oncogene 2019; 39:50-63. [PMID: 31462705 PMCID: PMC6937212 DOI: 10.1038/s41388-019-0953-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/04/2019] [Accepted: 05/13/2019] [Indexed: 12/16/2022]
Abstract
Resistance of breast cancer to human epidermal growth factor receptor 2 (HER2) inhibitors involves reprogramming of the kinome through HER2/HER3 signaling via the activation of multiple tyrosine kinases and transcriptional upregulation. The heterogeneity of induced kinases prevents kinase targeting by a single kinase inhibitor and presents a major challenge to the treatment of therapeutically recalcitrant HER2-positive breast cancers (HER2+ BCs). As a result, there is a critical need for effective treatment that attacks the aberrant kinome activation associated with resistance to HER2-targeted therapy. Here, we describe a novel treatment strategy that targets cyclin-dependent kinase 7 (CDK7) in HER2 inhibitor-resistant (HER2iR) breast cancer. We show that both HER2 inhibitor-sensitive (HER2iS) and HER2iR breast cancer cell lines exhibit high sensitivity to THZ1, a newly identified covalent inhibitor of the transcription regulatory kinase CDK7. CDK7 promotes cell cycle progression through inhibition of transcription, rather than via direct phosphorylation of classical CDK targets. The transcriptional kinase activity of CDK7 is regulated by HER2, and by the receptor tyrosine kinases activated in response to HER2 inhibition, as well as by the downstream SHP2 and PI3K/AKT pathways. A low dose of THZ1 displayed potent synergy with the HER2 inhibitor lapatinib in HER2iR BC cells in vitro. Dual HER2 and CDK7 inhibition induced tumor regression in two HER2iR BC xenograft models in vivo. Our data support the utilization of CDK7 inhibition as an additional therapeutic avenue that blocks the activation of genes engaged by multiple HER2iR kinases.
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Affiliation(s)
- Bowen Sun
- The First Affiliated Hospital, Biomedical Translational Research Institute and School of Pharmacy, Jinan University, Guangzhou, 510632, China.,Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Seth Mason
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Starr E Hazard
- Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Yubao Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Rong Fang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Pathology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Qiwei Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Elizabeth S Yeh
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Meixiang Yang
- The First Affiliated Hospital, Biomedical Translational Research Institute and School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Thomas M Roberts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jean J Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Qi Wang
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA.
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Longo JF, Brosius SN, Black L, Worley SH, Wilson RC, Roth KA, Carroll SL. ErbB4 promotes malignant peripheral nerve sheath tumor pathogenesis via Ras-independent mechanisms. Cell Commun Signal 2019; 17:74. [PMID: 31291965 PMCID: PMC6621970 DOI: 10.1186/s12964-019-0388-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/02/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND We have found that erbB receptor tyrosine kinases drive Ras hyperactivation and growth in NF1-null malignant peripheral nerve sheath tumors (MPNSTs). However, MPNSTs variably express multiple erbB receptors with distinct functional characteristics and it is not clear which of these receptors drive MPNST pathogenesis. Here, we test the hypothesis that altered erbB4 expression promotes MPNST pathogenesis by uniquely activating key cytoplasmic signaling cascades. METHODS ErbB4 expression was assessed using immunohistochemistry, immunocytochemistry, immunoblotting and real-time PCR. To define erbB4 functions, we generated mice that develop MPNSTs with floxed Erbb4 alleles (P0-GGFβ3;Trp53+/-;Erbb4flox/flox mice) and ablated Erbb4 in these tumors. MPNST cell proliferation and survival was assessed using 3H-thymidine incorporation, MTT assays, Real-Time Glo and cell count assays. Control and Erbb4-null MPNST cells were orthotopically xenografted in immunodeficient mice and the growth, proliferation (Ki67 labeling), apoptosis (TUNEL labeling) and angiogenesis of these grafts was analyzed. Antibody arrays querying cytoplasmic kinases were used to identify erbB4-responsive kinases. Pharmacologic or genetic inhibition was used to identify erbB4-responsive kinases that drive proliferation. RESULTS Aberrant erbB4 expression was evident in 25/30 surgically resected human MPNSTs and in MPNSTs from genetically engineered mouse models (P0-GGFβ3 and P0-GGFβ3;Trp53+/- mice); multiple erbB4 splice variants that differ in their ability to activate PI3 kinase and nuclear signaling were present in MPNST-derived cell lines. Erbb4-null MPNST cells demonstrated decreased proliferation and survival and altered morphology relative to non-ablated controls. Orthotopic allografts of Erbb4-null cells were significantly smaller than controls, with reduced proliferation, survival and vascularization. ERBB4 knockdown in human MPNST cells similarly inhibited DNA synthesis and viability. Although we have previously shown that broad-spectrum erbB inhibitors inhibit Ras activation, Erbb4 ablation did not affect Ras activation, suggesting that erbB4 drives neoplasia via non-Ras dependent pathways. An analysis of 43 candidate kinases identified multiple NRG1β-responsive and erbB4-dependent signaling cascades including the PI3K, WNK1, STAT3, STAT5 and phospholipase-Cγ pathways. Although WNK1 inhibition did not alter proliferation, inhibition of STAT3, STAT5 and phospholipase-Cγ markedly reduced proliferation. CONCLUSIONS ErbB4 promotes MPNST growth by activating key non-Ras dependent signaling cascades including the STAT3, STAT5 and phospholipase-Cγ pathways. ErbB4 and its effector pathways are thus potentially useful therapeutic targets in MPNSTs.
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Affiliation(s)
- Jody Fromm Longo
- Department of Pathology and Laboratory Medicine (JFL, LB, RCW, SJW, SLC), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC 29425-9080 USA
| | - Stephanie N. Brosius
- Department of Pathology (SNB, KAR) and the Medical Scientist Training Program (SNB), University of Alabama at Birmingham, Birmingham, AL 35294-0017 USA
- Present address: Department of Pediatrics at The Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Laurel Black
- Department of Pathology and Laboratory Medicine (JFL, LB, RCW, SJW, SLC), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC 29425-9080 USA
| | - Stuart H. Worley
- Department of Pathology and Laboratory Medicine (JFL, LB, RCW, SJW, SLC), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC 29425-9080 USA
| | - Robert C. Wilson
- Department of Pathology and Laboratory Medicine (JFL, LB, RCW, SJW, SLC), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC 29425-9080 USA
| | - Kevin A. Roth
- Department of Pathology (SNB, KAR) and the Medical Scientist Training Program (SNB), University of Alabama at Birmingham, Birmingham, AL 35294-0017 USA
- Present address: Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY USA
| | - Steven L. Carroll
- Department of Pathology and Laboratory Medicine (JFL, LB, RCW, SJW, SLC), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC 29425-9080 USA
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47
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Zhang F, Jaffe-Dax S, Wilson RC, Emberson LL. Prediction in infants and adults: A pupillometry study. Dev Sci 2019; 22:e12780. [PMID: 30506618 PMCID: PMC7294578 DOI: 10.1111/desc.12780] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 08/29/2018] [Accepted: 11/26/2018] [Indexed: 11/30/2022]
Abstract
Adults use both bottom-up sensory inputs and top-down signals to generate predictions about future sensory inputs. Infants have also been shown to make predictions with simple stimuli and recent work has suggested top-down processing is available early in infancy. However, it is unknown whether this indicates that top-down prediction is an ability that is continuous across the lifespan or whether an infant's ability to predict is different from an adult's, qualitatively or quantitatively. We employed pupillometry to provide a direct comparison of prediction abilities across these disparate age groups. Pupil dilation response (PDR) was measured in 6-month olds and adults as they completed an identical implicit learning task designed to help learn associations between sounds and pictures. We found significantly larger PDR for visual omission trials (i.e. trials that violated participants' predictions without the presentation of new stimuli to control for bottom-up signals) compared to visual present trials (i.e. trials that confirmed participants' predictions) in both age groups. Furthermore, a computational learning model that is closely linked to prediction error (Rescorla-Wagner model) demonstrated similar learning trajectories suggesting a continuity of predictive capacity and learning across the two age groups.
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Affiliation(s)
- Felicia Zhang
- Department of Psychology, Princeton University, Princeton, New Jersey
| | - Sagi Jaffe-Dax
- Department of Psychology, Princeton University, Princeton, New Jersey
| | - Robert C. Wilson
- Department of Psychology, University of Arizona, Tucson, Arizona
- Cognitive Science Program, University of Arizona, Tucson, Arizona
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O'Brien ME, Chandra D, Wilson RC, Karoleski CM, Fuhrman CR, Leader JK, Pu J, Zhang Y, Morris A, Nouraie S, Bon J, Urban Z, Sciurba FC. Loss of skin elasticity is associated with pulmonary emphysema, biomarkers of inflammation, and matrix metalloproteinase activity in smokers. Respir Res 2019; 20:128. [PMID: 31234847 PMCID: PMC6591816 DOI: 10.1186/s12931-019-1098-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Elastin breakdown and the resultant loss of lung elastic recoil is a hallmark of pulmonary emphysema in susceptible individuals as a consequence of tobacco smoke exposure. Systemic alterations to the synthesis and degradation of elastin may be important to our understanding of disease phenotypes in chronic obstructive pulmonary disease. We investigated the association of skin elasticity with pulmonary emphysema, obstructive lung disease, and blood biomarkers of inflammation and tissue protease activity in tobacco-exposed individuals. METHODS Two hundred and thirty-six Caucasian individuals were recruited into a sub-study of the University of Pittsburgh Specialized Center for Clinically Orientated Research in chronic obstructive pulmonary disease, a prospective cohort study of current and former smokers. The skin viscoelastic modulus (VE), a determinant of skin elasticity, was recorded from the volar forearm and facial wrinkling severity was determined using the Daniell scoring system. RESULTS In a multiple regression analysis, reduced VE was significantly associated with cross-sectional measurement of airflow obstruction (FEV1/FVC) and emphysema quantified from computed tomography (CT) images, β = 0.26, p = 0.001 and β = 0.24, p = 0.001 respectively. In emphysema-susceptible individuals, elasticity-determined skin age was increased (median 4.6 years) compared to the chronological age of subjects without emphysema. Plasma biomarkers of inflammation (TNFR1, TNFR2, CRP, PTX3, and SAA) and matrix metalloproteinase activity (MMP1, TIMP1, TIMP2, and TIMP4) were inversely associated with skin elasticity. CONCLUSIONS We report that an objective non-invasive determinant of skin elasticity is independently associated with measures of lung function, pulmonary emphysema, and biomarkers of inflammation and tissue proteolysis in tobacco-exposed individuals. Loss of skin elasticity is a novel observation that may link the common pathological processes that drive tissue elastolysis in the extracellular matrix of the skin and lung in emphysema-susceptible individuals.
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Affiliation(s)
- Michael E O'Brien
- Division of Pulmonary Allergy and Critical Care Medicine Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Kaufmann Building, Suite 1211, 3471 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Divay Chandra
- Division of Pulmonary Allergy and Critical Care Medicine Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Kaufmann Building, Suite 1211, 3471 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Robert C Wilson
- Division of Pulmonary Allergy and Critical Care Medicine Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Kaufmann Building, Suite 1211, 3471 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Chad M Karoleski
- Division of Pulmonary Allergy and Critical Care Medicine Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Kaufmann Building, Suite 1211, 3471 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Carl R Fuhrman
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joseph K Leader
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jiantao Pu
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary Allergy and Critical Care Medicine Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Kaufmann Building, Suite 1211, 3471 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Alison Morris
- Division of Pulmonary Allergy and Critical Care Medicine Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Kaufmann Building, Suite 1211, 3471 Fifth Ave, Pittsburgh, PA, 15213, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Seyed Nouraie
- Division of Pulmonary Allergy and Critical Care Medicine Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Kaufmann Building, Suite 1211, 3471 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Jessica Bon
- Division of Pulmonary Allergy and Critical Care Medicine Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Kaufmann Building, Suite 1211, 3471 Fifth Ave, Pittsburgh, PA, 15213, USA.,Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Zsolt Urban
- Department of Human Genetics Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Frank C Sciurba
- Division of Pulmonary Allergy and Critical Care Medicine Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Kaufmann Building, Suite 1211, 3471 Fifth Ave, Pittsburgh, PA, 15213, USA.
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Pastorino S, Bishop T, Crozier SR, Granström C, Kordas K, Küpers LK, O'Brien EC, Polanska K, Sauder KA, Zafarmand MH, Wilson RC, Agyemang C, Burton PR, Cooper C, Corpeleijn E, Dabelea D, Hanke W, Inskip HM, McAuliffe FM, Olsen SF, Vrijkotte TG, Brage S, Kennedy A, O'Gorman D, Scherer P, Wijndaele K, Wareham NJ, Desoye G, Ong KK. Associations between maternal physical activity in early and late pregnancy and offspring birth size: remote federated individual level meta-analysis from eight cohort studies. BJOG 2019; 126:459-470. [PMID: 30230190 PMCID: PMC6330060 DOI: 10.1111/1471-0528.15476] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2018] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Evidence on the impact of leisure time physical activity (LTPA) in pregnancy on birth size is inconsistent. We aimed to examine the association between LTPA during early and late pregnancy and newborn anthropometric outcomes. DESIGN Individual level meta-analysis, which reduces heterogeneity across studies. SETTING A consortium of eight population-based studies (seven European and one US) comprising 72 694 participants. METHODS Generalised linear models with consistent inclusion of confounders (gestational age, sex, parity, maternal age, education, ethnicity, BMI, smoking, and alcohol intake) were used to test associations between self-reported LTPA at either early (8-18 weeks gestation) or late pregnancy (30+ weeks) and the outcomes. Results were pooled using random effects meta-analyses. MAIN OUTCOME MEASURES Birth weight, large-for-gestational age (LGA), macrosomia, small-for-gestational age (SGA), % body fat, and ponderal index at birth. RESULTS Late, but not early, gestation maternal moderate to vigorous physical activity (MVPA), vigorous activity, and LTPA energy expenditure were modestly inversely associated with BW, LGA, macrosomia, and ponderal index, without heterogeneity (all: I2 = 0%). For each extra hour/week of MVPA, RR for LGA and macrosomia were 0.97 (95% CI: 0.96, 0.98) and 0.96 (95% CI: 0.94, 0.98), respectively. Associations were only modestly reduced after additional adjustments for maternal BMI and gestational diabetes. No measure of LTPA was associated with risk for SGA. CONCLUSIONS Physical activity in late, but not early, pregnancy is consistently associated with modestly lower risk of LGA and macrosomia, but not SGA. TWEETABLE ABSTRACT In an individual participant meta-analysis, late pregnancy moderate to vigorous physical activity modestly reduced birth size outcomes.
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Affiliation(s)
- S Pastorino
- MRC Epidemiology UnitUniversity of CambridgeCambridgeUK
| | - T Bishop
- MRC Epidemiology UnitUniversity of CambridgeCambridgeUK
| | - SR Crozier
- MRC Lifecourse Epidemiology Unit (University of Southampton)Southampton General HospitalSouthamptonUK
| | - C Granström
- Department of Epidemiology ResearchCentre for Fetal ProgrammingState Serum InstituteCopenhagenDenmark
| | - K Kordas
- Epidemiology and Environmental HealthSchool of Public Health and Health ProfessionsUniversity at BuffaloBuffaloNYUSA
| | - LK Küpers
- Department of EpidemiologyUniversity Medical Center GroningenUniversity of GroningenGroningenthe Netherlands
- MRC Integrative Epidemiology UnitSchool of Social and Community MedicineUniversity of BristolBristolUK
| | - EC O'Brien
- Obstetrics & GynaecologyUCD Perinatal Research CentreSchool of MedicineUniversity College DublinNational Maternity HospitalDublinIreland
| | - K Polanska
- Department of Environmental EpidemiologyNofer Institute of Occupational MedicineLodzPoland
| | - KA Sauder
- Department of PediatricsUniversity of Colorado School of MedicineAuroraCOUSA
| | - MH Zafarmand
- Department of Public HealthAmsterdam Public Health Research Institute, Amsterdam UMCUniversity of AmsterdamAmsterdamthe Netherlands
- Department of Obstetrics & GynaecologyAmsterdam UMCUniversity of AmsterdamAmsterdamthe Netherlands
- Department of Clinical EpidemiologyBiostatistics and BioinformaticsAmsterdam Public Health Research InstituteAmsterdam UMCUniversity of Amsterdamthe Netherlands
| | - RC Wilson
- Institute of Health and SocietyNewcastle UniversityNewcastleUK
| | - C Agyemang
- Department of Public HealthAmsterdam Public Health Research Institute, Amsterdam UMCUniversity of AmsterdamAmsterdamthe Netherlands
| | - PR Burton
- Institute of Health and SocietyNewcastle UniversityNewcastleUK
| | - C Cooper
- MRC Lifecourse Epidemiology Unit (University of Southampton)Southampton General HospitalSouthamptonUK
- NIHR Southampton Biomedical Research CentreUniversity Hospital Southampton NHS Foundation Trust and University of SouthamptonSouthamptonUK
| | - E Corpeleijn
- Department of EpidemiologyUniversity Medical Center GroningenUniversity of GroningenGroningenthe Netherlands
| | - D Dabelea
- Department of EpidemiologyColorado School of Public HealthUniversity of Colorado Anschutz Medical CampusDenverCOUSA
| | - W Hanke
- Department of Environmental EpidemiologyNofer Institute of Occupational MedicineLodzPoland
| | - HM Inskip
- MRC Lifecourse Epidemiology Unit (University of Southampton)Southampton General HospitalSouthamptonUK
- NIHR Southampton Biomedical Research CentreUniversity Hospital Southampton NHS Foundation Trust and University of SouthamptonSouthamptonUK
| | - FM McAuliffe
- Obstetrics & GynaecologyUCD Perinatal Research CentreSchool of MedicineUniversity College DublinNational Maternity HospitalDublinIreland
| | - SF Olsen
- Department of Epidemiology ResearchCentre for Fetal ProgrammingState Serum InstituteCopenhagenDenmark
| | - TG Vrijkotte
- Department of Public HealthAmsterdam Public Health Research Institute, Amsterdam UMCUniversity of AmsterdamAmsterdamthe Netherlands
| | - S Brage
- MRC Epidemiology UnitUniversity of CambridgeCambridgeUK
| | - A Kennedy
- 3U Diabetes Consortium and School of Health and Human PerformanceDublin City UniversityDublinIreland
- School of Biological SciencesDublin Institute of TechnologyDublinIreland
| | - D O'Gorman
- NIHR Southampton Biomedical Research CentreUniversity Hospital Southampton NHS Foundation Trust and University of SouthamptonSouthamptonUK
| | - P Scherer
- MRC Epidemiology UnitUniversity of CambridgeCambridgeUK
| | - K Wijndaele
- MRC Epidemiology UnitUniversity of CambridgeCambridgeUK
| | - NJ Wareham
- MRC Epidemiology UnitUniversity of CambridgeCambridgeUK
| | - G Desoye
- Department of Obstetrics & GynaecologyMedical University of GrazGrazAustria
| | - KK Ong
- MRC Epidemiology UnitUniversity of CambridgeCambridgeUK
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Affiliation(s)
- Robert C. Wilson
- Department of Psychology and Cognitive Science Program, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
| | - Matthew R. Nassar
- Department of Psychology, Brown University, Providence, Rhode Island, United States of America
| | - Gaia Tavoni
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joshua I. Gold
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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