Identification of keystone taxa in rhizosphere microbial communities using different methods and their effects on compounds of the host Cinnamomum migao

Exploring keystone taxa affecting microbial community stability and host function is crucial for understanding ecosystem functions. However, identifying keystone taxa from humongous microbial communities remains challenging. We collected 344 rhizosphere and bulk soil samples from the endangered plant C. migao for 2 years consecutively. Used high-throughput sequencing 16S rDNA and ITS to obtain the composition of bacterial and fungal communities. We explored keystone taxa and the applicability and limitations of five methods (SPEC-OCCU, Zi-Pi, Subnetwork, Betweenness, and Module), as well as the impact of microbial community domain, time series, and rhizosphere boundary on the identification of keystone taxa in the communities. Our results showed that the five methods, identified abundant keystone taxa in rhizosphere and bulk soil microbial communities. However, the keystone taxa shared by the rhizosphere and bulk soil microbial communities over time decreased rapidly decrease in the five methods. Among five methods on the identification of keystone taxa in the rhizosphere community, Module identified 113 taxa, SPEC-OCCU identified 17 taxa, Betweenness identified 3 taxa, Subnetwork identified 3 taxa, and Zi-Pi identified 4 taxa. The keystone taxa are mainly conditionally rare taxa, and their ecological functions include chemoheterotrophy, aerobic chemoheterotrophy, nitrate reduction, and anaerobic photoautotrophy. The results of the random forest model and structural equation model predict that keystone taxa Mortierella and Ellin6513 may have an effects on the accumulation of 1, 4, 7, - Cycloundecatriene, 1, 5, 9, 9-tetramethyl-, Z, Z, Z-, beta-copaene, bicyclogermacrene, 1,8-Cineole in C. migao fruits, but their effects still need further evidence. Our study evidence an unstable microbial community in the bulk soil, and the definition of microbial boundary and ecologically functional affected the identification of keystone taxa in the community. Subnetwork and Module are more in line with the definition of keystone taxa in microbial ecosystems in terms of maintaining community stability and hosting function.

Graph- and transformer-guided boundary aware network for medical image segmentation

BACKGROUND AND OBJECTIVE

Despite the considerable progress achieved by U-Net-based models, medical image segmentation remains a challenging task due to complex backgrounds, irrelevant noises, and ambiguous boundaries. In this study, we present a novel approach called U-shaped Graph- and Transformer-guided Boundary Aware Network (GTBA-Net) to tackle these challenges.

METHODS

GTBA-Net uses the pre-trained ResNet34 as its basic structure, and involves Global Feature Aggregation (GFA) modules for target localization, Graph-based Dynamic Feature Fusion (GDFF) modules for effective noise suppression, and Uncertainty-based Boundary Refinement (UBR) modules for accurate delineation of ambiguous boundaries. The GFA modules employ an efficient self-attention mechanism to facilitate coarse target localization amidst complex backgrounds, without introducing additional computational complexity. The GDFF modules leverage graph attention mechanism to aggregate information hidden among high- and low-level features, effectively suppressing target-irrelevant noises while preserving valuable spatial details. The UBR modules introduce an uncertainty quantification strategy and auxiliary loss to guide the model's focus towards target regions and uncertain "ridges", gradually mitigating boundary uncertainty and ultimately achieving accurate boundary delineation.

RESULTS

Comparative experiments on five datasets encompassing diverse modalities (including X-ray, CT, endoscopic procedures, and ultrasound) demonstrate that the proposed GTBA-Net outperforms existing methods in various challenging scenarios. Subsequent ablation studies further demonstrate the efficacy of the GFA, GDFF, and UBR modules in target localization, noise suppression, and ambiguous boundary delineation, respectively.

CONCLUSIONS

GTBA-Net exhibits substantial potential for extensive application in the field of medical image segmentation, particularly in scenarios involving complex backgrounds, target-irrelevant noises, or ambiguous boundaries.

Nanoprecipitation through solvent-shifting using rapid mixing: Dispelling the Ouzo boundary to reach large solute concentrations

HYPOTHESIS

The addition of a non-solvent to a solute in good solvent solution leads to nanoprecipitation, which is the spontaneous formation of nanodomains. Yet, increasing solute concentration usually leads to the formation of macrodomains that quickly separate into a bulk phase, which is a severe process limitation. The corresponding concentration threshold, often termed as the Ouzo boundary, remains a mystery that could find its origin in the complex interplay between nanoprecipitation and mixing.

EXPERIMENTS

We performed a systematic investigation of nanoprecipitation thermodynamics and kinetics as well as its interplay with mixing hydrodynamics for the hexadecane-acetone-water system, in the presence of the non-ionic C16EO8 surfactant. The binodal curve and its underlying tie-lines were obtained using Raman spectroscopy, allowing the computation of the spinodal curve. Kinetics were probed using a continuous flow setup that combines two sequential rapid mixers. The impact of mixing efficiency was probed systematically by varying the oil concentration for respectively slow and rapid mixing, while the uncoupling from mixing and nanoprecipitation was quantified by modifying systematically the flow rate in a continuous flow approach.

FINDINGS

We elucidate the nature of the Ouzo boundary that marks the maximal solute concentration leading to nanoobjects. Rather than a thermodynamic boundary, as evidenced by its uncorrelation to the spinodal curve, it results from the coupling of nanoprecipitation and mixing when both processes occur within the same time range, leading to heterogeneous conditions and the escape of some objects to the macroscale. Increasing the solute concentration speeds up nanoprecipitation and thus requires increasingly faster mixing times to uncouple both processes. Accordingly, if the mixing efficiency is large enough, it is possible to dispel the Ouzo boundary and reach very large solute concentrations. Implementing rapid mixing strategies in continuous flow approaches is thus the solution to overcome the most stringent condition of nanoprecipitation and open the way to scale-up, while also providing efficient means to probe its fast mechanism. Overall, the simultaneous control of hydrodynamics and physical chemistry is thus key to boost up the Ouzo effect.

The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth

The maize ligule is an epidermis-derived structure that arises from the preligule band (PLB) at a boundary between the blade and sheath. A hinge-like auricle also develops immediately distal to the ligule and contributes to blade angle. Here, we characterize the stages of PLB and early ligule development in terms of topography, cell area, division orientation, cell wall rigidity and auxin response dynamics. Differential thickening of epidermal cells and localized periclinal divisions contributed to the formation of a ridge within the PLB, which ultimately produces the ligule fringe. Patterns in cell wall rigidity were consistent with the subdivision of the PLB into two regions along a distinct line positioned at the nascent ridge. The proximal region produces the ligule, while the distal region contributes to one epidermal face of the auricles. Although the auxin transporter PIN1 accumulated in the PLB, observed differential auxin transcriptional response did not underlie the partitioning of the PLB. Our data demonstrate that two zones with contrasting cellular properties, the preligule and preauricle, are specified within the ligular region before ligule outgrowth.

Work-life boundary management of peer support workers when engaging in virtual mental health support during the COVID-19 pandemic: a qualitative case study

BACKGROUND

Mental health care needs have increased since the COVID-19 pandemic was declared. Peer support workers (PSWs) and the organizations that employ them have strived to provide services to meet increasing needs. During pandemic lockdowns in Ontario, Canada, these services moved online and were provided by PSWs from their homes. There is paucity of research that examines how providing mental health support by employees working from home influences their work-life boundaries. This research closes the gap by examining experiences of work-life boundary challenges and boundary management strategies of PSWs.

METHODS

A qualitative case study approach was adopted. Interviews with PSWs who held formal, paid positions in a peer support organization were conducted. Data was analyzed thematically using both inductive and deductive approaches. Descriptive coding that closely utilized participants' words was followed by inferential coding that grouped related themes into conceptual categories informed by boundary theory. Member checking was conducted.

RESULTS

PSWs provided accounts of work-life boundary challenges that we grouped into three categories: temporal (work schedule encroachments, continuous online presence), physical (minimal workspace segregation, co-presence of household members and pets) and task-related (intersecting work-home activities). Strategies used by PSWs to manage the boundaries consisted of segmenting the work-life domains by creating separate timescapes, spaces and tasks; and integrating domains by allowing some permeability between the areas of work and life.

CONCLUSION

The findings from this study can help inform management, practices, future research and policy on health care workforce. The study highlights the need to attend to the consequences of greater work-life integration for mental health workers since their successful practice is largely dependent on maintaining self-care. Training regarding work-life boundary management is highlighted as one of the ways to approach situations where work from home is required.

RBS-Net: Hippocampus segmentation using multi-layer feature learning with the region, boundary and structure loss

Hippocampus has great influence over the Alzheimer's disease (AD) research because of its essential role as a biomarker in the human brain. Thus the performance of hippocampus segmentation influences the development of clinical research for brain disorders. Deep learning using U-net-like networks becomes prevalent in hippocampus segmentation on Magnetic Resonance Imaging (MRI) due to its efficiency and accuracy. However, current methods lose sufficient detailed information during pooling, which hinders the segmentation results. And weak supervision on the details like edges or positions results in fuzzy and coarse boundary segmentation, causing great differences between the segmentation and ground-truth. In view of these drawbacks, we propose a Region-Boundary and Structure Net (RBS-Net), which consists of a primary net and an auxiliary net. (1) Our primary net focuses on the region distribution of hippocampus and introduces a distance map for boundary supervision. Furthermore the primary net adds a multi-layer feature learning module to compensate the information loss during pooling and strengthen the differences between the foreground and background, improving the region and boundary segmentation. (2) The auxiliary net concentrates on the structure similarity and also utilizes the multi-layer feature learning module, and this parallel task can refine encoders by similarizing the structure of the segmentation and ground-truth. We train and test our network using 5-fold cross-validation on HarP, a public available hippocampus dataset. Experimental results demonstrate that our proposed RBS-Net achieves a Dice of 89.76% in average, outperforming several state-of-the-art hippocampus segmentation methods. Furthermore, in few shot circumstances, our proposed RBS-Net achieves better results in terms of a comprehensive evaluation compared to several state-of-the-art deep learning-based methods. Finally we can observe that visual segmentation results for the boundary and detailed regions are improved by our proposed RBS-Net.

Cropland nitrous oxide emissions exceed the emissions of RCP 2.6: A global spatial analysis

Nitrous oxide (N₂O), as a potent greenhouse gas, must be limited to prevent the global temperature increasing by >2 °C. Cropland is the largest source of anthropogenic N₂O emissions; however, earlier estimates for emissions and their exceedances still remain uncertainties. Here, we used a spatially explicit model to estimate cropland N₂O emission in 2014 by refined grid-level crop-specific EFs and considered the background emission. We also sought to determine where N₂O emissions exceed the "boundary" through analysis of spatial data from representative concentration pathway (RCP) 2.6. The global cropland N₂O emission was 2.92 ± 0.59 Tg N yr^-1, which far exceeds the 0.82 Tg N yr^-1 boundary, over 90 % of cropland areas exceeded the boundary. Western Europe, Southeastern China, Pakistan, and the Ganges Plain exceeded the boundary by >2 kg N ha^-1 yr^-1. The boundary exceedances showed a positive linear response with respect to total cropland emission and a quadratic response to GDP per capita at the country level. Our study highlights the necessity of accurate estimations of spatial variations in cropland N₂O emissions and evaluation of exceedances, to facilitate the development of more effective mitigation measures in different regions.

Direction and distance information in memory for locations of objects relative to landmarks and boundaries

An observer often remembers an object's location on the basis of its direction and distance from reference objects. Two kinds of reference object are of particular interest: landmarks and boundaries. We compared how well observers remembered the direction and distance of target objects from a landmark and a boundary. Patterns of variable error implied that the landmark was more effective than the boundary in supporting memory for target object direction. When the predictions of the landmark and the boundary were placed in conflict, patterns of constant error implied that the boundary was more effective than the landmark in supporting memory for target object distance. These results suggest affinities between direction information and landmarks and between distance information and boundaries. They raise the possibility that, rather than collapsing across direction and distance error, theoretical analyses should distinguish the two kinds of error in assessing the reliability of landmarks and boundaries.

Navigational roots of spatial and temporal memory structure

Our minds are constantly in transit, from the present to the past to the future, across places we have and have not directly experienced. Nevertheless, memories of our mental time travel are not organized continuously and are adaptively chunked into contexts and episodes. In this paper, I will review evidence that suggests that spatial boundary representations play a critical role in providing structure to both our spatial and temporal memories. I will illustrate the intimate connection between hippocampal spatial mapping and temporal sequencing of episodic memory to propose that high-level cognitive processes like mental time travel and conceptual mapping are rooted in basic navigational mechanisms that we humans and nonhuman animals share. Our neuroscientific understanding of hippocampal function across species may provide new insight into the origins of even the most uniquely human cognitive abilities.

Developmental trajectories of health and long-term care systems: The transitions of solidarity in four Asian countries

PURPOSE

Different from the development of health sector, there are significant variations in the underpinnings and formation timings of solidarity-based long-term care (LTC) systems. This paper compares the historical developmental trajectories and identifies factors of the transitions of the actual practices of solidarity - the scope of community, the scope of interdependence, and the costs of joint action - in the health and LTC sectors in four East Asian countries: Japan, South Korea, Taiwan, and Singapore.

METHODS

Comparative policy analysis.

RESULTS

Healthcare tends to be considered a universal value such that its boundary should include all residents, while LTC is closer to an entitlement of citizens. The differing solidarity reflects path dependency as well as historical legacies and policy diffusion between the health and LTC sectors. In both health and LTC sectors, the costs involved in collective service provision are not distributed evenly between generations.

DISCUSSION

Centralized governance is a prevailing feature of health and LTC sectors in East Asia, allowing solidarity-based institutional arrangements to be established without an overall sense of solidarity. The relationship between solidarity and health and LTC systems is complex and dynamic.

Luminance texture boundaries and luminance step boundaries are segmented using different mechanisms

In natural scenes, two adjacent surfaces may differ in mean luminance without any sharp change in luminance at their boundary, but rather due to different relative proportions of light and dark regions within each surface. We refer to such boundaries as luminance texture boundaries (LTBs), and in this study we investigate whether LTBs are segmented using different mechanisms than luminance step boundaries (LSBs). We develop a novel method to generate luminance texture boundaries from natural uniform textures, and using these natural LTB stimuli in a boundary segmentation task, we find that observers are much more sensitive to identical luminance differences which are defined by textures (LTBs) than by uniform luminance steps (LSBs), consistent with the possibility of different mechanisms. In a second and third set of experiments, we characterize observer performance segmenting natural LTBs in the presence of masking LSBs which observers are instructed to ignore. We show that there is very little effect of masking LSBs on LTB segmentation performance. Furthermore, any masking effects we find are far less than those observed in a control experiment where both the masker and target are LSBs, and far less than those predicted by a model assuming identical mechanisms. Finally, we perform a fourth set of boundary segmentation experiments using artificial LTB stimuli comprised of differing proportions of white and black dots on opposite sides of the boundary. We find that these stimuli are also highly robust to masking by supra-threshold LSBs, consistent with our results using natural stimuli, and with our earlier studies using similar stimuli. Taken as a whole, these results suggest that the visual system contains mechanisms well suited to detecting surface boundaries that are robust to interference from luminance differences arising from luminance steps like those formed by cast shadows.

The impact of artificial intelligence on learner-instructor interaction in online learning

Artificial intelligence (AI) systems offer effective support for online learning and teaching, including personalizing learning for students, automating instructors' routine tasks, and powering adaptive assessments. However, while the opportunities for AI are promising, the impact of AI systems on the culture of, norms in, and expectations about interactions between students and instructors are still elusive. In online learning, learner-instructor interaction (inter alia, communication, support, and presence) has a profound impact on students' satisfaction and learning outcomes. Thus, identifying how students and instructors perceive the impact of AI systems on their interaction is important to identify any gaps, challenges, or barriers preventing AI systems from achieving their intended potential and risking the safety of these interactions. To address this need for forward-looking decisions, we used Speed Dating with storyboards to analyze the authentic voices of 12 students and 11 instructors on diverse use cases of possible AI systems in online learning. Findings show that participants envision adopting AI systems in online learning can enable personalized learner-instructor interaction at scale but at the risk of violating social boundaries. Although AI systems have been positively recognized for improving the quantity and quality of communication, for providing just-in-time, personalized support for large-scale settings, and for improving the feeling of connection, there were concerns about responsibility, agency, and surveillance issues. These findings have implications for the design of AI systems to ensure explainability, human-in-the-loop, and careful data collection and presentation. Overall, contributions of this study include the design of AI system storyboards which are technically feasible and positively support learner-instructor interaction, capturing students' and instructors' concerns of AI systems through Speed Dating, and suggesting practical implications for maximizing the positive impact of AI systems while minimizing the negative ones.

The dynamics of maize leaf development: Patterned to grow while growing a pattern

Leaves are a significant component of the shoot system in grasses, functioning in light capture and photosynthesis. Leaf width, length, and angle are expressions of development that collectively define canopy architecture. Thus, the distinctive morphology of grass leaves is an interdependent readout of developmental patterning and growth along the proximal-distal, medial-lateral, and adaxial-abaxial axes. Here, we review the chronology of patterning and growth, namely along the proximal-distal axis, during maize leaf development. We underscore that patterning and growth occur simultaneously, making use of shared developmental gradients and molecular pathways.

Structure bound guide to access cavity preparation for molar root canal treatment

A good access cavity preparation is the gateway to success in endodontic treatment. This article presents occlusal landmarks that can be used as the boundary for the endodontic access at the occlusal surfaces of maxillary and mandibular molars. Further this article gives a structure or landmark guided three simple stages of preparation to reach the pulp chamber. This assures an ideal access cavity reducing the risk of dentin gouging and eliminating iatrogenic deleterious events. All canal orifices will be within this boundary and can often be located easily.

The application of laparoscopy combined with indocyanine green fluorescence imaging technique for hepatic cystic echinococcosis

Background

With the mature application of laparoscopy in hepatobiliary surgery, laparoscopic treatment of hepatic cystic echinococcosis (CE) has made certain progress. But, due to the inherent limitations of laparoscopy and the growth characteristics of cystic echinococcosis, distinguishing the boundary between cystic lesion and normal hepatic parenchyma is pivotal importance for successful surgery. Indocyanine green (ICG) fluorescence imaging technology can view the boundary of lesion and normal tissue during the treatment of hepatic cystic echinococcosis. Applied laparoscopy combined with ICG fluorescence imaging technique for hepatic cystic echinococcosis may be an effective surgical strategy.

Methods

The clinical data contained nine patients with hepatic cystic echinococcosis who underwent laparoscopic surgery with indocyanine green fluorescence imaging technique in authors’ institution from December 2018 to December 2019 were retrospectively analyzed. Indocyanine green was administered intravenously three days prior to surgery. The fluorescence acquisition system for real-time imaging was used during the surgery and the patients were followed up after surgery.

Results

Of reported nine patients, six are male and the remaining three are female. The average age is (36.4 ± 7.6) years. For all subjects, surgical procedures were performed under laparoscopy with indocyanine green fluorescence system. This technique showed the clear boundary of the hepatic cyst with normal liver parenchyma. Total cystectomy in six patients, subtotal cystectomy in two patients and partial hepatectomy in one patient were performed respectively. The average operation time was 3.8 ± 0.9 h, blood loss 206.0 ± 120.7 ml. Neither blood transfusion nor post-operative complication was experienced. The average abdominal drainage time was 3.4 ± 0.9 days with hospital stay 5.7 ± 2.1 days. During the 6–12 months follow-up period, neither recurrence nor intraperitoneal implantation was found.

Conclusions

Applied laparoscopy combined with ICG fluorescence imaging technique for hepatic cystic echinococcosis is safe and feasible. Enhanced boundary image can assist surgeons to complete radical resection and reduce complications.

Mechanical adaptions of collective cells nearby free tissue boundaries

Mechanical adaptions of cells, including stiffness variation, cytoskeleton remodeling, motion coordination, and shape changing, are essential for tissue morphogenesis, wound healing, and malignant progression. In this paper, we take confluent monolayers of Madin-Darby canine kidney (MDCK) and mouse myoblast (C2C12) cells as model systems to probe how cells collectively adapt their mechanical features in response to a free tissue boundary. We show that the free boundary not only can trigger unjamming transition but also induces cell fluidization nearby the boundary. The Young's moduli of cells near the boundary are found to be much lower than those of interior cells. We demonstrate that the stiffness of cells in monolayers with a free tissue boundary exhibits negative dependence on the projected cell area, in contrast to previous studies where cells were found to stiffen as cellular area increases in a confluent MDCK monolayer without boundary. In addition, the free tissue boundary may activate cell remodeling, rendering volume enlargement and cell-specified cytoskeleton organization. Our study emphasizes the important role of geometrical boundary in regulating biomechanical properties of cell aggregates.

Kidney edge detection in laparoscopic image data for computer-assisted surgery : Kidney edge detection

PURPOSE

In robotic-assisted kidney surgery, computational methods make it possible to augment the surgical scene and potentially improve patient outcome. Most often, soft-tissue registration is a prerequisite for the visualization of tumors and vascular structures hidden beneath the surface. State-of-the-art volume-to-surface registration methods, however, are computationally demanding and require a sufficiently large target surface. To overcome this limitation, the first step toward registration is the extraction of the outer edge of the kidney.

METHODS

To tackle this task, we propose a deep learning-based solution. Rather than working only on the raw laparoscopic images, the network is given depth information and distance fields to predict whether a pixel of the image belongs to an edge. We evaluate our method on expert-labeled in vivo data from the EndoVis sub-challenge 2017 Kidney Boundary Detection and define the current state of the art.

RESULTS

By using a leave-one-out cross-validation, we report results for the most suitable network with a median precision-like, recall-like, and intersection over union (IOU) of 39.5 px, 143.3 px, and 0.3, respectively.

CONCLUSION

We conclude that our approach succeeds in predicting the edges of the kidney, except in instances where high occlusion occurs, which explains the average decrease in the IOU score. All source code, reference data, models, and evaluation results are openly available for download: https://github.com/ghattab/kidney-edge-detection/.

Boundary maintenance in the ancestral metazoan Hydra depends on histone acetylation

Much of boundary formation during development remains to be understood, despite being a defining feature of many animal taxa. Axial patterning of Hydra, a member of the ancient phylum Cnidaria which diverged prior to the bilaterian radiation, involves a steady-state of production and loss of tissue, and is dependent on an organizer located in the upper part of the head. We show that the sharp boundary separating tissue in the body column from head and foot tissue depends on histone acetylation. Histone deacetylation disrupts the boundary by affecting numerous developmental genes including Wnt components and prevents stem cells from entering the position dependent differentiation program. Overall, our results suggest that reversible histone acetylation is an ancient regulatory mechanism for partitioning the body axis into domains with specific identity, which was present in the common ancestor of cnidarians and bilaterians, at least 600 million years ago.

Relating categorization to set summary statistics perception

Two cognitive processes have been explored that compensate for the limited information that can be perceived and remembered at any given moment. The first parsimonious cognitive process is object categorization. We naturally relate objects to their category, assume they share relevant category properties, often disregarding irrelevant characteristics. Another scene organizing mechanism is representing aspects of the visual world in terms of summary statistics. Spreading attention over a group of objects with some similarity, one perceives an ensemble representation of the group. Without encoding detailed information of individuals, observers process summary data concerning the group, including set mean for various features (from circle size to face expression). Just as categorization may include/depend on prototype and intercategory boundaries, so set perception includes property mean and range. We now explore common features of these processes. We previously investigated summary perception of low-level features with a rapid serial visual presentation (RSVP) paradigm and found that participants perceive both the mean and range extremes of stimulus sets, automatically, implicitly, and on-the-fly, for each RSVP sequence, independently. We now use the same experimental paradigm to test category representation of high-level objects. We find participants perceive categorical characteristics better than they code individual elements. We relate category prototype to set mean and same/different category to in/out-of-range elements, defining a direct parallel between low-level set perception and high-level categorization. The implicit effects of mean or prototype and set or category boundaries are very similar. We suggest that object categorization may share perceptual-computational mechanisms with set summary statistics perception.

Coarticulatory vowel nasalization in American English: Data of individual differences in acoustic realization of vowel nasalization as a function of prosodic prominence and boundary

This article provides acoustic measurements data for vowel nasalization which are based on speech recorded from fifteen (8 female and 7 male) native speakers of American English in a laboratory setting. Each individual speaker's production patterns for the vowel nasalization in tautosyllabic CVN and NVC words are documented in terms of three acoustic parameters: the duration of nasal consonant (N-Duration), the duration of vowel (V-Duration) and the difference between the amplitude of the first formant (A1) and the first nasal peak (P0) obtained from the vowel (A1-P0) as an indication of the degree of vowel nasalization. The A1-P0 is measured at three different time points within the vowel –i.e., the near point (25%), midpoint (50%), and distant point (75%), either from the onset (CVN) or the offset (NVC) of the nasal consonant. These measures are taken from the target words in various prosodic prominence and boundary contexts: phonologically focused (PhonFOC) vs. lexically focused (LexFOC) vs. unfocused (NoFOC) conditions; phrase-edge (i.e., phrase-final for CVN and phrase-initial for NVC) vs. phrase-medial conditions. The data also contain a CSV file with each speaker's mean values of the N-Duration, V-Duration, and A1-P0 (z-scored) for each prosodic context along with the information about the speakers' gender. For further discussion of the data, please refer to the full-length article entitled “Prosodically-conditioned fine-tuning of coarticulatory vowel nasalization in English”(Cho et al., 2017).

Boundary shapes guide selection of reference points in goal localization

In this study, we contrasted two hypotheses theorizing the role of the global shape of a boundary in object location memory: People might differentiate reference points based on the global shape extracted from the environment configuration and choose appropriate parts for encoding a specific location, or, alternatively, only the number of reference points provided by a shape might be important for accurate encoding. We designed a location memory task in an immersive virtual environment in order to examine these two hypotheses. Participants first learned four target locations with a circular wall and a landmark array. During testing, participants recalled the locations with either one entire cue or part of one cue removed. Location memory was impaired when the testing cues did not form a circle, but it was not impaired when the testing configuration retained the circular shape. In Experiment 2, the circle formed by a landmark array and the circular wall did not share the same center during learning. Memory performance decreased when either the wall or the landmark array was removed during testing. These results indicated that participants might segment the shape of the circular wall into parts (similar to segmenting a clock face into 12 hours) and encode target locations relative to the differentiated parts. When such segmentation could be recovered from the testing configuration, object location memory was retained. Otherwise, impairment occurred during testing. These findings suggest that although the individual reference points on a boundary are important for encoding specific target locations, the global shape of the boundary nonetheless affects segmentation and the selection of individual reference points.

Thinking outside of the box II: Disrupting the cognitive map

A number of influential spatial learning theories posit that organisms encode a viewpoint independent (i.e. allocentric) representation of the global boundary shape of their environment in order to support spatial reorientation and place learning. In contrast to the trial and error learning mechanisms that support domain-general processes, a representation of the global-shape of the environment is thought to be encoded automatically as part of a cognitive map, and without interference from other spatial cues. To date, however, this core theoretical assumption has not been appropriately examined. This is because previous attempts to address this question have failed to employ tasks that fully dissociate reorientation based on an allocentric representation of global-shape from egocentric reorientation strategies. Here, we address this issue in two experiments. Participants were trained to navigate to a hidden goal on one side of a virtual arena (e.g. the inside) before being required to find the same point on the alternative side (e.g. the outside). At test, performing the correct search behaviour requires an allocentric representation of the global boundary-shape. Using established associative learning procedures of overshadowing and blocking, we find that search behaviour at test is disrupted when participants were able to form landmark-goal associations during training. These results demonstrate that encoding of an allocentric representation of boundary information is susceptible to interference from landmark cues, and is not acquired through special means. Instead, the results suggest that allocentric representations of environmental boundaries are acquired through the same kind of error-correction mechanisms that support domain-general non-spatial learning.

Expected Number and Height Distribution of Critical Points of Smooth Isotropic Gaussian Random Fields

We obtain formulae for the expected number and height distribution of critical points of smooth isotropic Gaussian random fields parameterized on Euclidean space or spheres of arbitrary dimension. The results hold in general in the sense that there are no restrictions on the covariance function of the field except for smoothness and isotropy. The results are based on a characterization of the distribution of the Hessian of the Gaussian field by means of the family of Gaussian orthogonally invariant (GOI) matrices, of which the Gaussian orthogonal ensemble (GOE) is a special case. The obtained formulae depend on the covariance function only through a single parameter (Euclidean space) or two parameters (spheres), and include the special boundary case of random Laplacian eigenfunctions.

Control of directionality of chromatin folding for the inter- and intra-domain contacts at the Tfap2c-Bmp7 locus

BACKGROUND

Contact domains of chromatin serve as a fundamental unit to regulate action of enhancers for target genes. Looping between a pair of CCCTC-binding factor (CTCF)-binding sites in convergent orientations underlies the formation of contact domains, while those in divergent orientations establish domain boundaries. However, every CTCF site is not necessarily engaged in loop or boundary structures, leaving functions of CTCF in varied genomic contexts still elusive. The locus containing Tfap2c and Bmp7 encompasses two contact domains separated by a region between the two genes, termed transition zone (TZ), characterized by two arrays of CTCF sites in divergent configuration. In this study, we created deletion and inversion alleles of these and other regions across the locus and investigated how they impinge on the conformation.

RESULTS

Deletion of the whole two CTCF arrays with the CRISPR/Cas9 system resulted in impairment of blocking of chromatin contacts by the TZ, as assessed by the circular chromatin conformation capture assay (4C-seq). Deletion and inversion of either of the two arrays similarly, but less pronouncedly, led to reduction in the blocking activity. Thus, the divergent configuration provides the TZ with the strong boundary activity. Uniquely, we show the TZ harbors a 50-kb region within one of the two arrays that contacts broadly with the both flanking intervals, regardless of the presence or orientation of the other CTCF array. Further, we show the boundary CTCF array has little impact on intra-domain folding; instead, locally associating CTCF sites greatly affect it.

CONCLUSIONS

Our results show that the TZ not only separates the two domains, but also bears a wide interval that shows isotropic behavior of chromatin folding, indicating a potentially complex nature of actual boundaries in the genome. We also show that CTCF-binding sites inside a domain greatly contribute to the intra-domain folding of chromatin. Thus, the study reveals diverse and context-dependent roles of CTCF in organizing chromatin conformation at different levels.

Philosophy of nature and organism's autonomy: on Hegel, Plessner and Jonas' theories of living beings

Following the revival in the last decades of the concept of "organism", scholarly literature in philosophy of science has shown growing historical interest in the theory of Immanuel Kant, one of the "fathers" of the concept of self-organisation. Yet some recent theoretical developments suggest that self-organisation alone cannot fully account for the all-important dimension of autonomy of the living. Autonomy appears to also have a genuine "interactive" dimension, which concerns the organism's functional interactions with the environment and does not simply derive from its internal organisation. Against this background, we focus on a family of natural philosophical approaches that historically have already strongly taken in account this aspect of autonomy, notably going beyond Kant's perspective on self-organisation. We thus review Hegel, Plessner, and Jonas' different perspectives on living beings, focussing in particular on four points: the distinction between organic and inorganic, the theory of biological organisation, the processuality of the living, and the "boundary" between inside and outside, through which the organism establishes its relationship to the environment. We, then, compare the three perspectives on these four points, and finally address the question of what advantages their contribution present-especially compared to Kant's theory-with respect to the topic of organism's autonomy. This could help-we hope-to better understand what is at the stake still today.

Diagnosing pituitary adenoma in unstained sections based on multiphoton microscopy

PURPOSE

If we can find a new method that can achieve rapid diagnosis of adenoma during operation, it will help surgeon shorten the operation time and enhance the treatment efficacy. This study discusses the feasibility of multiphoton microscopy (MPM) in diagnosing pituitary adenoma.

METHOD

MPM, based on two-photon excited fluorescence (TPEF) and second harmonic generation (SHG) is performed for the diagnosis of pituitary adenoma in unstained sections.

RESULTS

Our results show that MPM can reveal the variation of reticulin fiber by SHG signals of collagen, combined with the measurement of area of acinus, thickness of collagen fiber and collagen percentage. MPM can further reflect the change of meshwork in normal pituitary and hyperplasia quantitatively. And the characteristics of typical growth patterns of pituitary adenoma are demonstrated by the overlay of SHG and TPEF images. What's more, we can identify the boundary of normal pituitary, hyperplasia and adenoma from MPM images. And the experiment also results verify the feasibility of this method in frozen sections.

CONCLUSION

These results indicated that MPM can make a diagnosis of pituitary adenoma by the morphological changes without routine pathological processing including hematoxylin-eosin (H&E) staining and other special staining. Therefore, this technique is expected to help diagnosis of pituitary adenoma during operation.

Asymmetry at cell-cell interfaces direct cell sorting, boundary formation, and tissue morphogenesis

During development, cells of seemingly homogenous character sort themselves out into distinct compartments in order to generate cell types with specialized features that support tissue morphogenesis and function. This process is often driven by receptors at the cell membrane that probe the extracellular microenvironment for specific ligands and alter downstream signaling pathways impacting transcription, cytoskeletal organization, and cell adhesion to regulate cell sorting and subsequent boundary formation. This review will focus on two of these receptor families, Eph and Notch, both of which are intrinsically non-adhesive and are activated by a unique set of ligands that are asymmetrically distributed from their receptor on neighboring cells. Understanding the requirement of asymmetric ligand-receptor signaling at the membrane under homeostatic conditions gives insight into how misregulation of these pathways contributes to boundary disruption in diseases like cancer.

A novel floor plate boundary defined by adjacent En1 and Dbx1 microdomains distinguishes midbrain dopamine and hypothalamic neurons

The mesodiencephalic floor plate (mdFP) is the source of diverse neuron types. Yet, how this structure is compartmentalized has not been clearly elucidated. Here, we identify a novel boundary subdividing the mdFP into two microdomains, defined by engrailed 1 (En1) and developing brain homeobox 1 (Dbx1). Utilizing simultaneous dual and intersectional fate mapping, we demonstrate that this boundary is precisely formed with minimal overlap between En1 and Dbx1 microdomains, unlike many other boundaries. We show that the En1 microdomain gives rise to dopaminergic (DA) neurons, whereas the Dbx1 microdomain gives rise to subthalamic (STN), premammillary (PM) and posterior hypothalamic (PH) populations. To determine whether En1 is sufficient to induce DA neuron production beyond its normal limit, we generated a mouse strain that expresses En1 in the Dbx1 microdomain. In mutants, we observed ectopic production of DA neurons derived from the Dbx1 microdomain, at the expense of STN and PM populations. Our findings provide new insights into subdivisions in the mdFP, and will impact current strategies for the conversion of stem cells into DA neurons.

Exact p-values for Simon's two-stage designs in clinical trials

In a one-sided hypothesis testing problem in clinical trials, the monotonic condition of a tail probability function is fundamentally important to guarantee that the actual type I and II error rates occur at the boundary of their associated parameter spaces. Otherwise, one has to search for the actual rates over the complete parameter space, which could be very computationally intensive. This important property has been extensively studied in traditional one-stage study settings (e.g., non-inferiority or superiority between two binomial proportions), but there is very limited research for this property in a two-stage design setting, e.g., Simon's two-stage design. In this note, we theoretically prove that the tail probability is an increasing function of the parameter in Simon's two-stage design. This proof not only provides theoretical justification that p-value occurs at the boundary of the parameter space, but also helps to reduce the computational intensity for study design search.

Boundary and analytic attitude: reflections on a summer holiday break

The effect of a boundary in analytic work at the summer holiday break is discussed in relation to archetypal experiences of exclusion, loss and limitation. Some attempts by patients to mitigate an analyst's act of separation are reviewed as enactments, and in particular the meanings of a gift made by one patient. Analytic attitude towards enactment from within different schools of practice is sketched, with reference to the effect on the analyst of departing from the received practice of their own allegiance. A theory is adumbrated that the discomfort of 'contravening the rules' has a useful effect in sparking the analyst into consciousness, with greater attention to salient features in an individual case. Interpretation as an enactment is briefly considered, along with the possible effects of containing the discomfort of a patient's enactment in contrast to confronting it with interpretation.

A systematic comparison between visual cues for boundary detection

The detection of object boundaries is a critical first step for many visual processing tasks. Multiple cues (we consider luminance, color, motion and binocular disparity) available in the early visual system may signal object boundaries but little is known about their relative diagnosticity and how to optimally combine them for boundary detection. This study thus aims at understanding how early visual processes inform boundary detection in natural scenes. We collected color binocular video sequences of natural scenes to construct a video database. Each scene was annotated with two full sets of ground-truth contours (one set limited to object boundaries and another set which included all edges). We implemented an integrated computational model of early vision that spans all considered cues, and then assessed their diagnosticity by training machine learning classifiers on individual channels. Color and luminance were found to be most diagnostic while stereo and motion were least. Combining all cues yielded a significant improvement in accuracy beyond that of any cue in isolation. Furthermore, the accuracy of individual cues was found to be a poor predictor of their unique contribution for the combination. This result suggested a complex interaction between cues, which we further quantified using regularization techniques. Our systematic assessment of the accuracy of early vision models for boundary detection together with the resulting annotated video dataset should provide a useful benchmark towards the development of higher-level models of visual processing.

Widespread colocalization of the Drosophila histone acetyltransferase homolog MYST5 with DREF and insulator proteins at active genes

MYST family histone acetyltransferases play important roles in gene regulation. Here, we have characterized the Drosophila MYST histone acetyltransferase (HAT) encoded by cg1894, whose closest homolog is Drosophila MOF, and which we have termed MYST5. We found it localized to a large number of interbands as well as to the telomeres of polytene chromosomes, and it showed strong colocalization with the interband protein Z4/Putzig and RNA polymerase II. Accordingly, genome-wide location analysis by ChIP-seq showed co-occurrence of MYST5 with the Z4-interacting partner Chriz/Chromator. Interestingly, MYST5 bound to the promoter of actively transcribed genes, and about half of MYST5 sites colocalized with the transcription factor DNA replication-related element-binding factor (DREF), indicating a role for MYST5 in gene expression. Moreover, we observed substantial overlap of MYST5 binding with that of the insulator proteins CP190, dCTCF, and BEAF-32, which mediate the organization of the genome into functionally distinct topological domains. Altogether, our data suggest a broad role for MYST5 both in gene-specific transcriptional regulation and in the organization of the genome into chromatin domains, with the two roles possibly being functionally interconnected.

Boundary problem in Simon's two-stage clinical trial designs

The activity of a new treatment in clinical trials with binary endpoints can be assessed by comparing the observed response rate to the target response rate. Traditionally, a one-sided hypothesis is used to make statistical inference, and the actual Type I error rate has to be computed over the parameter space of the null hypothesis. The monotonicity property is a fundamental property that guarantees the actual Type I error rate occurring at the boundary. One-arm two-stage designs are considered in this article. We theoretically proved this important property when the final threshold value of a design is less than the first-stage sample size together with another weak condition being satisfied. The method used in this article may finally lead to the final complete proof of this property in the future. We also numerically proved that the monotonicity property is satisfied for designs with the first-stage and the second-stage sample sizes from 10 to 100.

Something Blossoms in Between: Silence-Phenomena as a Bordering Notions in Psychology

Mysterious yet unavoidable, silence-phenomena appear to us in inherent ambiguity. In its plurality of meanings, phenomena related to silence are often perceived as overwhelming because they transcend the communicative capacity of language making it a challenge for cultural psychology to understand its involvement in our processes of making sense of experience and existence. Human growth and development involve processes where presence, void and content, voice, sound and noise, motion, transition and stillness, have dialectic interactions. In this article I discuss silence-phenomena as a bordering notion in terms of its discursive quality, the silent quality of speech, and the awareness of the ineffable. In addition, I highlight the possible implications of such notion in the understanding of affect from the perspective of Semiotic Cultural Psychology. I also emphasize the importance of considering psychological borders as multi-dimensional, taking the phenomenological experience of temporality as an illustration, which is also related to high emotional involvement of attention.

Strong sum distance in fuzzy graphs

In this paper the idea of strong sum distance which is a metric, in a fuzzy graph is introduced. Based on this metric the concepts of eccentricity, radius, diameter, center and self centered fuzzy graphs are studied. Some properties of eccentric nodes, peripheral nodes and central nodes are obtained. A characterisation of self centered complete fuzzy graph is obtained and conditions under which a fuzzy cycle is self centered are established. We have proved that based on this metric, an eccentric node of a fuzzy tree G is a fuzzy end node of G and a node is an eccentric node of a fuzzy tree if and only if it is a peripheral node of G and the center of a fuzzy tree consists of either one or two neighboring nodes. The concepts of boundary nodes and interior nodes in a fuzzy graph based on strong sum distance are introduced. Some properties of boundary nodes, interior nodes and complete nodes are studied.

CoinFLP: a system for efficient mosaic screening and for visualizing clonal boundaries in Drosophila

Screens in mosaic Drosophila tissues that use chemical mutagenesis have identified many regulators of growth and patterning. Many of the mutant phenotypes observed were contingent upon the presence of both wild-type and mutant cells in the same tissue. More recently, large collections of RNAi lines or cDNAs expressed under Gal4/UAS control have been used to alter gene expression uniformly in specific tissues. However, these newer approaches are not easily combined with the efficient generation of genetic mosaics. The CoinFLP system described here enables mosaic screens in the context of gene knockdown or overexpression by automatically generating a reliable ratio of mutant to wild-type tissue in a developmentally controlled manner. CoinFLP-Gal4 generates mosaic tissues composed of clones of which only a subset expresses Gal4. CoinFLP-LexGAD/Gal4 generates tissues composed of clones that express either Gal4 or LexGAD, thus allowing the study of interactions between different types of genetically manipulated cells. By combining CoinFLP-LexGAD/Gal4 with the split-GFP system GRASP, boundaries between genetically distinct cell populations can be visualized at high resolution.

The tomato NAC transcription factor SlNAM2 is involved in flower-boundary morphogenesis

Being composed of several whorls of distinct floral organs, the flower is one of the most complex organs in the plant. As such, the formation and maintenance of boundaries that separate the meristem from the floral organ primordium and adjacent organs are critical for its normal development. In Arabidopsis, the miR164-regulated NAM genes play key roles in floral-boundary specification. By contrast, much less is known about floral-boundary establishment in the model crop tomato. It was found that the miR164-regulated NAM gene GOBLET is expressed in the floral meristem-organ boundaries and its loss-of-function mutant produces flowers with fused organs, indicating its requirement for tomato floral-boundary formation. It was found here that sly-miR164 targets the transcripts of three additional uncharacterized NAM genes in developing flowers. It is shown that, after floral-boundary initiation, the NAM gene Solyc03g115850 (SlNAM2) is expressed as stripes that mark the boundaries between sepals and between different floral whorls. Furthermore, ectopic accumulation of SlNAM2-encoding transcripts caused various growth-suppression and extraorgan phenotypes typically observed in plants over-expressing known boundary genes. Flower-specific silencing of sly-miR164-targeted NAM genes (AP1>>MIR164) caused defects in the separation of sepals and floral whorls indicating abnormal boundary specification. However, supplementing these NAM-deficient flowers with miR164-resistant SlNAM2 suppressed their fusion phenotypes and completely restored floral boundaries. Together, our results strongly suggest that SlNAM2 participates in the establishment of tomato flower whorl and sepal boundaries.

The art of trans-boundary governance: the case of synthetic biology

Synthetic biology raises few, if any, social concerns that are distinctively new. Similar to many other convergent technologies, synthetic biology's interface across various scientific communities and interests groups presents an incessant challenge to political and conceptual boundaries. However, the scale and intensity of these interfaces seem to necessitate a reflection over how corresponding governance capacities can be developed. This paper argues that, in addition to existing regulatory approaches, such capacities may be gained through the art of trans-boundary governance, which is not only attentive to the crossing and erosion of particular boundaries but also adept in keeping up with the dynamics among evolving networks of actors.