Variability in the analysis of a single neuroimaging dataset by many teams

Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses1. The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset2-5. Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed.

Ontological Dimensions of Cognitive-Neural Mappings

The growing literature reporting results of cognitive-neural mappings has increased calls for an adequate organizing ontology, or taxonomy, of these mappings. This enterprise is non-trivial, as relevant dimensions that might contribute to such an ontology are not yet agreed upon. We propose that any candidate dimensions should be evaluated on their ability to explain observed differences in functional neuroimaging activation patterns. In this study, we use a large sample of task-based functional magnetic resonance imaging (task-fMRI) results and a data-driven strategy to identify these dimensions. First, using a data-driven dimension reduction approach and multivariate distance matrix regression (MDMR), we quantify the variance among activation maps that is explained by existing ontological dimensions. We find that 'task paradigm' categories explain more variance among task-activation maps than other dimensions, including latent cognitive categories. Surprisingly, 'study ID', or the study from which each activation map was reported, explained close to 50% of the variance in activation patterns. Using a clustering approach that allows for overlapping clusters, we derived data-driven latent activation states, associated with re-occurring configurations of the canonical frontoparietal, salience, sensory-motor, and default mode network activation patterns. Importantly, with only four data-driven latent dimensions, one can explain greater variance among activation maps than all conventional ontological dimensions combined. These latent dimensions may inform a data-driven cognitive ontology, and suggest that current descriptions of cognitive processes and the tasks used to elicit them do not accurately reflect activation patterns commonly observed in the human brain.

Brain activity links performance in science reasoning with conceptual approach

Understanding how students learn is crucial for helping them succeed. We examined brain function in 107 undergraduate students during a task known to be challenging for many students-physics problem solving-to characterize the underlying neural mechanisms and determine how these support comprehension and proficiency. Further, we applied module analysis to response distributions, defining groups of students who answered by using similar physics conceptions, and probed for brain differences linked with different conceptual approaches. We found that integrated executive, attentional, visual motion, and default mode brain systems cooperate to achieve sequential and sustained physics-related cognition. While accuracy alone did not predict brain function, dissociable brain patterns were observed when students solved problems by using different physics conceptions, and increased success was linked to conceptual coherence. Our analyses demonstrate that episodic associations and control processes operate in tandem to support physics reasoning, offering potential insight to support student learning.

Sex differences in brain correlates of STEM anxiety

Anxiety is known to dysregulate the salience, default mode, and central executive networks of the human brain, yet this phenomenon has not been fully explored across the STEM learning experience, where anxiety can impact negatively academic performance. Here, we evaluated anxiety and large-scale brain connectivity in 101 undergraduate physics students. We found sex differences in STEM-related and clinical anxiety, with longitudinal increases in science anxiety observed for both female and male students. Sex-specific relationships between STEM anxiety and brain connectivity emerged, with male students exhibiting distinct inter-network connectivity for STEM and clinical anxiety, and female students demonstrating no significant within-sex correlations. Anxiety was negatively correlated with academic performance in sex-specific ways at both pre- and post-instruction. Moreover, math anxiety in male students mediated the relation between default mode-salience connectivity and course grade. Together, these results reveal complex sex differences in the neural mechanisms driving how anxiety is related to STEM learning.

Automated, Efficient, and Accelerated Knowledge Modeling of the Cognitive Neuroimaging Literature Using the ATHENA Toolkit

Neuroimaging research is growing rapidly, providing expansive resources for synthesizing data. However, navigating these dense resources is complicated by the volume of research articles and variety of experimental designs implemented across studies. The advent of machine learning algorithms and text-mining techniques has advanced automated labeling of published articles in biomedical research to alleviate such obstacles. As of yet, a comprehensive examination of document features and classifier techniques for annotating neuroimaging articles has yet to be undertaken. Here, we evaluated which combination of corpus (abstract-only or full-article text), features (bag-of-words or Cognitive Atlas terms), and classifier (Bernoulli naïve Bayes, k-nearest neighbors, logistic regression, or support vector classifier) resulted in the highest predictive performance in annotating a selection of 2,633 manually annotated neuroimaging articles. We found that, when utilizing full article text, data-driven features derived from the text performed the best, whereas if article abstracts were used for annotation, features derived from the Cognitive Atlas performed better. Additionally, we observed that when features were derived from article text, anatomical terms appeared to be the most frequently utilized for classification purposes and that cognitive concepts can be identified based on similar representations of these anatomical terms. Optimizing parameters for the automated classification of neuroimaging articles may result in a larger proportion of the neuroimaging literature being annotated with labels supporting the meta-analysis of psychological constructs.

Non-curative treatment of patients with oral tongue squamous-cell carcinoma

Purpose

Late-stage OTSCC is associated with poor overall survival (OS). Non-curative treatment approach aims to improve quality of life and prolong survival of patients deemed incurable. The purpose of this study was to investigate the used non-curative treatment modalities for OTSSC and patient survival.

Methods

All patients diagnosed with OTSCC and treated with non-curative intent at the HUS Helsinki University Hospital (Helsinki, Finland) during the 12-year period of 2005–2016 were included. Survival analysis after the non-curative treatment decision was conducted using the Kaplan–Meier method in this population-based study.

Results

Eighty-two patients were identified. A non-curative treatment decision was made at presentation without any previous treatment in 26 patients (7% of all patients diagnosed with OTSCC during the study period). Palliative radiotherapy was administered to 24% of all patients. The average survival time after the non-curative treatment decision was 3.7 months (median 2 and range 0–26).

Conclusions

Due to the short mean survival time after decision for treatment with non-curative intent, and the notable symptom burden in this patient population, a prompt initiation of all non-curative measures is warranted.

Myofibroblasts in oral potentially malignant disorders: Is it related to malignant transformation?

In oral cancer, acquisition of α-smooth muscle actin (α-SMA)-positive fibroblasts, known as myofibroblasts or carcinoma-associated fibroblasts (CAF), is an important event for progression and metastasis. However, the contribution of myofibroblasts in oral potentially malignant disorders (OPMD) remains controversial. This systematic review provides evidence that immunodetection of myofibroblasts may identify oral submucous fibrosis (OSMF) with high risk of malignant transformation, but does not represent an auxiliary tool to predict the malignant potential of leukoplakia and erythroplakia, the most common OPMD.

Meta-analytic evidence for a core problem solving network across multiple representational domains

Problem solving is a complex skill engaging multi-stepped reasoning processes to find unknown solutions. The breadth of real-world contexts requiring problem solving is mirrored by a similarly broad, yet unfocused neuroimaging literature, and the domain-general or context-specific brain networks associated with problem solving are not well understood. To more fully characterize those brain networks, we performed activation likelihood estimation meta-analysis on 280 neuroimaging problem solving experiments reporting 3166 foci from 1919 individuals across 131 papers. The general map of problem solving revealed broad fronto-cingulo-parietal convergence, regions similarly identified when considering separate mathematical, verbal, and visuospatial problem solving domain-specific analyses. Conjunction analysis revealed a common network supporting problem solving across diverse contexts, and difference maps distinguished functionally-selective sub-networks specific to task type. Our results suggest cooperation between representationally specialized sub-network and whole-brain systems provide a neural basis for problem solving, with the core network contributing general purpose resources to perform cognitive operations and manage problem demand. Further characterization of cross-network dynamics could inform neuroeducational studies on problem solving skill development.

Toward a Neurobiological Basis for Understanding Learning in University Modeling Instruction Physics Courses

Modeling Instruction (MI) for University Physics is a curricular and pedagogical approach to active learning in introductory physics. A basic tenet of science is that it is a model-driven endeavor that involves building models, then validating, deploying, and ultimately revising them in an iterative fashion. MI was developed to provide students a facsimile in the university classroom of this foundational scientific practice. As a curriculum, MI employs conceptual scientific models as the basis for the course content, and thus learning in a MI classroom involves students appropriating scientific models for their own use. Over the last 10 years, substantial evidence has accumulated supporting MI's efficacy, including gains in conceptual understanding, odds of success, attitudes toward learning, self-efficacy, and social networks centered around physics learning. However, we still do not fully understand the mechanisms of how students learn physics and develop mental models of physical phenomena. Herein, we explore the hypothesis that the MI curriculum and pedagogy promotes student engagement via conceptual model building. This emphasis on conceptual model building, in turn, leads to improved knowledge organization and problem solving abilities that manifest as quantifiable functional brain changes that can be assessed with functional magnetic resonance imaging (fMRI). We conducted a neuroeducation study wherein students completed a physics reasoning task while undergoing fMRI scanning before (pre) and after (post) completing a MI introductory physics course. Preliminary results indicated that performance of the physics reasoning task was linked with increased brain activity notably in lateral prefrontal and parietal cortices that previously have been associated with attention, working memory, and problem solving, and are collectively referred to as the central executive network. Critically, assessment of changes in brain activity during the physics reasoning task from pre- vs. post-instruction identified increased activity after the course notably in the posterior cingulate cortex (a brain region previously linked with episodic memory and self-referential thought) and in the frontal poles (regions linked with learning). These preliminary outcomes highlight brain regions linked with physics reasoning and, critically, suggest that brain activity during physics reasoning is modifiable by thoughtfully designed curriculum and pedagogy.

Extracellular vesicles from oral squamous carcinoma cells display pro- and anti-angiogenic properties

BACKGROUND

A new intercellular communication mode established by neoplastic cells and tumor microenvironment components is based on extracellular vesicles (EVs). However, the biological effects of the EVs released by tumor cells on angiogenesis are not completely understood. Here, we aimed to understand the biological effects of EVs isolated from two cell lines of oral squamous cell carcinoma (OSCC) (SCC15 and HSC3) on endothelial cell tubulogenesis.

METHODS

OSCC-derived EVs were isolated with a polymer-based precipitation method, quantified using nanoparticle tracking analysis and verified for EV markers by dot blot. Functional assays were performed to assess the angiogenic potential of the OSCC-derived EVs.

RESULTS

The results showed that EVs derived from both cell lines displayed typical spherical-shaped morphology and expressed the EV markers CD63 and Annexin II. Although the average particle concentration and size were quite similar, SCC15-derived EVs promoted a pronounced tubular formation associated with significant migration and apoptosis rates of the endothelial cells, whereas EVs derived from HSC3 cells inhibited significantly endothelial cell tubulogenesis and proliferation.

CONCLUSION

The findings of this study reveal that EVs derived from different OSCC cell lines by a polymer-based precipitation method promote pro- or anti-angiogenic effects.

Topical tacrolimus, triamcinolone acetonide, and placebo in oral lichen planus: a pilot randomized controlled trial

OBJECTIVE

To carry out a double-blind randomized controlled trial (RCT) to compare the effectiveness of topical tacrolimus (TAC), triamcinolone acetonide (TRI), and placebo (PLA) in symptomatic oral lichen planus (OLP).

SUBJECTS AND METHODS

A clinical score (CS, range 0-130) was developed to measure the clinical signs and symptoms of OLP. Twenty-seven OLP patients with a CS of ≥20 were randomly allocated to receive 0.1% TAC ointment (n = 11), 0.1% TRI paste (n = 7), or Orabase^® paste as PLA (n = 9) for 3 weeks. If the CS dropped ≥20% (interpreted as response), the patients continued the same medication for another 3 weeks. If the CS dropped <20% or increased (non-response), the patients were switched to TAC for 6 weeks. A 6-month follow-up period ensued. The primary outcome variable was the change in CS from baseline to week 3. In primary outcome analysis, CS values between the treatment arms were compared.

RESULTS

Tacrolimus and TRI were more effective (P = 0.012 and 0.031, respectively) than PLA in reducing the CS at week 3. No difference in the efficacy was noted between TAC and TRI (P = 0.997).

CONCLUSIONS

This pilot RCT provides evidence for the effectiveness of TAC and TRI over PLA in the management of OLP.

Distinct neural correlates for attention lapses in patients with schizophrenia and healthy participants

Momentary lapses in attention are common in healthy populations. This phenomenon has recently received increased investigation, particularly in relationship to the default mode network (DMN). Previous research has suggested that these lapses may be due to intrusive task-irrelevant thoughts. The study of this phenomenon in schizophrenia, which is characterized by a wide variety of cognitive deficits including deficits in attention, has not previously been explored. We used the AX Continuous Performance Task to investigate attention lapses in healthy participants as well as patients with schizophrenia. We found distinct patterns of network activation between these two groups. Lapses in healthy participants were associated with DMN activation, while in patients, the same behavioral phenomenon was associated with deactivations in frontal-parietal control network (FPCN) regions. When considered in contrast to the results observed in healthy participants, these results suggest an additional origin of attention lapses in patients derived from a loss of task-related context, rather than intrusive task-irrelevant thoughts.

The prognostic value of histopathological grading systems in oral squamous cell carcinomas

OBJECTIVE

This study evaluated the association of four histopathological grading systems (WHO grading system, malignancy grading of the deep invasive margins (MG), histological risk (HR) model, and tumor budding and depth of invasion (BD) model) with clinicopathological parameters and outcome of 113 oral squamous cell carcinomas to identify their roles in prognosis.

METHODS

Demographic and clinical features were obtained from patients' records. Sections from all paraffin-embedded blocks were evaluated according to the four grading systems. Demographic and clinical associations were analyzed using chi-square test, and correlations between the grading systems were established with the Spearman's rank correlation test. Survival curves were performed with Kaplan-Meier method, and multivariate analysis based on Cox proportional hazard model was calculated.

RESULTS

Significant associations with survival were observed for WHO grading system and BD model in the univariate analysis, but only the BD model was significantly associated with disease outcome as an independent prognostic marker. Age, tumor size, and presence of regional metastasis were also independent markers of reduced survival.

CONCLUSION

A significant association between the BD model and outcome of OSCC patients was observed, indicating this new histopathological grading system as a possible prognostic tool.

Phosphorus in manure and sewage sludge more recyclable than in soluble inorganic fertilizer

Phosphorus (P) flow from deposits through agriculture to waterways leads to eutrophication and depletion of P reserves. Therefore, P must be recycled. Low and unpredictable plant availability of P in residues is considered to be a limiting factor for recycling. We identified the determinants for the plant-availability of P in agrifood residues. We quantified P in Italian ryegrass (Lolium multiflorum) and in field soil fractions with different plant availabilities of P as a response to manure and sewage sludge with a range of P capture and hygienization treatments. P was more available in manure and in sludge, when it was captured biologically or with a moderate iron (Fe)/P (1.6), than in NPK. Increasing rate of sludge impaired P recovery and high Fe/P (9.8) prevented it. Anaerobic digestion (AD) reduced plant-availability at relevant rates. The recovery of P was increased in AD manure via composting and in AD sludge via combined acid and oxidizer. P was not available to plants in the sludge hygienized with a high calcium/P. Contrary to assumed knowledge, the recyclability of P in appropriately treated residues can be better than in NPK. The prevention of P sorption in soil by organic substances in fertilizers critically enhances the recyclability of P.

Role of dentin MMPs in caries progression and bond stability

Dentin can be described as a biological composite with collagen matrix embedded with nanosized hydroxyapatite mineral crystallites. Matrix metalloproteinases (MMPs) and cysteine cathepsins are families of endopeptidases. Enzymes of both families are present in dentin and collectively capable of degrading virtually all extracellular matrix components. This review describes these enzymes and their presence in dentin, mainly focusing on their role in dentin caries pathogenesis and loss of collagen in the adhesive hybrid layer under composite restorations. MMPs and cysteine cathepsins present in saliva, mineralized dentin, and/or dentinal fluid may affect the dentin caries process at the early phases of demineralization. Changes in collagen and noncollagenous protein structure may participate in observed decreases in mechanical properties of caries-affected dentin and reduce the ability of caries-affected dentin to remineralize. These endogenous enzymes also remain entrapped within the hybrid layer during the resin infiltration process, and the acidic bonding agents themselves (irrespective of whether they are etch-and-rinse or self-etch) can activate these endogenous protease proforms. Since resin impregnation is frequently incomplete, denuded collagen matrices associated with free water (which serves as a collagen cleavage reagent for these endogenous hydrolase enzymes) can be enzymatically disrupted, finally contributing to the degradation of the hybrid layer. There are multiple in vitro and in vivo reports showing that the longevity of the adhesive interface is increased when nonspecific enzyme-inhibiting strategies are used. Different chemicals (i.e., chlorhexidine, galardin, and benzalkonium chloride) or collagen cross-linker agents have been successfully employed as therapeutic primers in the bonding procedure. In addition, the incorporation of enzyme inhibitors (i.e., quaternary ammonium methacrylates) into the resin blends has been recently promoted. This review will describe MMP functions in caries and hybrid layer degradation and explore the potential therapeutic role of MMP inhibitors for the development of improved intervention strategies for MMP-related oral diseases.

[Nutraceuticals in the combat against oral cancer]

Head and neck squamous cell carcinoma (HNSCC), the eighth most common cancer worldwide, accounts for approximately 600,000 new cases per year. The mobile tongue is the most common site for oral cancer and is associated with a poorer survival than other HNSCC sites. Standard therapeutic strategies have failed to significantly improve survival rates that have remained around 50% over the past four decades. In the last decade intense investigations on oral cancer highlighted the mandatory role of the tumor microenvironment (TME), in addition to the genetic aberrations and molecular biology changes within the cancer cells. Furthermore, the molecular crosstalk between cancer cells and TME components (i.e., cancer-associated fibroblasts, inflammatory pro-tumorigenic cells, etc.) has a crucial role in growth, invasion, spread and metastases of the cancer cells and consequently leads to poor prognosis. Recent studies suggest that plant-derived dietary agents nutraceuticals, especially curcumin and green tea, have the advantage to combat both malignant cells and TME components, unlike standard anti-cancer protocols that target only cancer cells. However, due to a very low bioavailability, nutraceuticals do not currently constitute an integral part of these protocols. Ongoing developments in nanotechnology for improved delivery are expected to overcome their challenging pharmacokinetics.

Clinicopathological prognostic factors of oral tongue squamous cell carcinoma: a retrospective study of 202 cases

Although several histopathological parameters and grading systems have been described as predictive of the treatment response and outcome of oral squamous cell carcinoma (OSCC), none is universally accepted. A new scoring system, the histological risk model, was recently described to be a powerful predictive tool for recurrence and overall survival in OSCC. The aim of this study was to verify the predictive role of the histological risk model in a cohort of 202 patients at all stages of oral/mobile tongue squamous cell carcinoma (OTSCC). Demographic and clinical data were collected from the medical records and the tumours were evaluated using the histological risk model. Statistical analyses were performed using the χ(2) test, the Kaplan-Meier method, and the Cox regression model. The histological risk model showed no statistical correlation with demographic or clinical parameters and did not Predict the outcome of the OTSCC patients. However, multivariate regression analysis revealed a significant correlation of the clinical disease stage with the disease outcome. Despite major efforts to identify new predictive parameters and histological systems, clinical features are still the most reliable prognostic factors for patients with OTSCC.

Sodium fluoride inhibits MMP-2 and MMP-9

The importance of fluoride (F) in preventing dental caries by favorably interfering in the demineralization-remineralization processes is well-established, but its ability to inhibit matrix metalloproteinases (MMPs), which could also help to prevent dentin caries, has not been investigated. This study assessed the ability of F to inhibit salivary and purified human gelatinases MMPs-2 and -9. Saliva was collected from 10 healthy individuals. Pooled saliva was centrifuged, and supernatants were incubated for 1 hr at 37°C and subjected to zymography. Sodium fluoride (50-275 ppm F) was added to the incubation buffer. The reversibility of the inhibition of MMPs-2 and -9 by NaF was tested by the addition of NaF (250-5,000 ppm F) to the incubation buffer, after which an additional incubation was performed in the absence of F. F decreased the activities of pro- and active forms of salivary and purified human MMPs in a dose-response manner. Purified gelatinases were completely inhibited by 200 ppm F (IC50 = 100 and 75 ppm F for MMPs-2 and -9, respectively), and salivary MMP-9 by 275 ppm F (IC50 = 200 ppm F). Inhibition was partially reversible at 250-1,500 ppm F, but was irreversible at 5,000 ppm F. This is the first study to describe the ability of NaF to inhibit MMPs completely.