Surrogate Models for Stress-Strain Mapping of Microscale Physics

•Learn the difference between different neural networks within machine learning (ML) •Develop a working understanding of the ML tool Pytorch and machine learning operator: Recurrent Neural Operator •Use MATLAB to create and process time dependent stress/strain matrices to display the hyper-parameters for different RNOs •Apply RNO to train the strain-stress mapping of tri-laminate and granular case

Multisensory causal inference in the brain

At any given moment, our brain processes multiple inputs from its different sensory modalities (vision, hearing, touch, etc.). In deciphering this array of sensory information, the brain has to solve two problems: (1) which of the inputs originate from the same object and should be integrated and (2) for the sensations originating from the same object, how best to integrate them. Recent behavioural studies suggest that the human brain solves these problems using optimal probabilistic inference, known as Bayesian causal inference. However, how and where the underlying computations are carried out in the brain have remained unknown. By combining neuroimaging-based decoding techniques and computational modelling of behavioural data, a new study now sheds light on how multisensory causal inference maps onto specific brain areas. The results suggest that the complexity of neural computations increases along the visual hierarchy and link specific components of the causal inference process with specific visual and parietal regions

Grouping by feature of cross-modal flankers in temporal ventriloquism

Signals in one sensory modality can influence perception of another, for example the bias of visual timing by audition: temporal ventriloquism. Strong accounts of temporal ventriloquism hold that the sensory representation of visual signal timing changes to that of the nearby sound. Alternatively, underlying sensory representations do not change. Rather, perceptual grouping processes based on spatial, temporal, and featural information produce best-estimates of global event properties. In support of this interpretation, when feature-based perceptual grouping conflicts with temporal information-based in scenarios that reveal temporal ventriloquism, the effect is abolished. However, previous demonstrations of this disruption used long-range visual apparent-motion stimuli. We investigated whether similar manipulations of feature grouping could also disrupt the classical temporal ventriloquism demonstration, which occurs over a short temporal range. We estimated the precision of participants’ reports of which of two visual bars occurred first. The bars were accompanied by different cross-modal signals that onset synchronously or asynchronously with each bar. Participants’ performance improved with asynchronous presentation relative to synchronous - temporal ventriloquism - however, unlike the long-range apparent motion paradigm, this was unaffected by different combinations of cross-modal feature, suggesting that featural similarity of cross-modal signals may not modulate cross-modal temporal influences in short time scales

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as ‘accidental cell death’ (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. ‘Regulated cell death’ (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death

Sex-specific local life-history adaptation in surface- and cave-dwelling Atlantic mollies (Poecilia mexicana)

Cavefishes have long been used as model organisms showcasing adaptive diversification, but does adaptation to caves also facilitate the evolution of reproductive isolation from surface ancestors? We raised offspring of wild-caught surface- and cave-dwelling ecotypes of the neotropical fish Poecilia mexicana to sexual maturity in a 12-month common garden experiment. Fish were raised under one of two food regimes (high vs. low), and this was crossed with differences in lighting conditions (permanent darkness vs. 12:12 h light:dark cycle) in a 2 × 2 factorial design, allowing us to elucidate potential patterns of local adaptation in life histories. Our results reveal a pattern of sex-specific local life-history adaptation: Surface molly females had the highest fitness in the treatment best resembling their habitat of origin (high food and a light:dark cycle), and suffered from almost complete reproductive failure in darkness, while cave molly females were not similarly affected in any treatment. Males of both ecotypes, on the other hand, showed only weak evidence for local adaptation. Nonetheless, local life-history adaptation in females likely contributes to ecological diversification in this system and other cave animals, further supporting the role of local adaptation due to strong divergent selection as a major force in ecological speciation

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Summary Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (TP53, ATRX, RB1) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ∼280 bp or ∼3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed

The flipped classroom: for active, effective and increased learning – especially for low achievers

Higher education has been pressured to shift towards more flexible, effective, active, and student-centered teaching strategies that mitigate the limitations of traditional transmittal models of education. Lately, the flipped classroom model has been suggested to support this transition. However, research on the use of flipped classroom in higher education is in its infancy and little is known about student's perceptions of learning through flipped classroom. This study examined students' perceptions of flipped classroom education in a last year university course in research methods. A questionnaire was administered measuring students' (n = 240) perceptions of flipped classroom in general, video as a learning tool, and Moodle (Learning Management System) as a supporting tool within the frame of a flipped classroom model. The results revealed that a large majority of the students had a positive attitude towards flipped classroom, the use of video and Moodle, and that a positive attitude towards flipped classroom was strongly correlated to perceptions of increased motivation, engagement, increased learning, and effective learning. Low achievers significantly reported more positively as compared to high achievers with regards to attitudes towards the use of video as a learning tool, perceived increased learning, and perceived more effective learning.</p

Population level determinants of acute mountain sickness among young men: a retrospective study

<p>Abstract</p> <p>Background</p> <p>Many visitors, including military troops, who enter highland regions from low altitude areas may suffer from acute mountain sickness (AMS), which negatively impacts workable man-hours and increases healthcare costs. The aim of this study was to evaluate the population level risk factors and build a multivariate model, which might be applicable to reduce the effects of AMS on Chinese young men traveling to this region.</p> <p>Methods</p> <p>Chinese highland military medical records were used to obtain data of young men (n = 3727) who entered the Tibet plateau between the years of 2006-2009. The relationship between AMS and travel profile, demographic characteristics, and health behaviors were evaluated by logistic regression. Univariate logistic models estimated the crude odds ratio. The variables that showed significance in the univariate model were included in a multivariate model to derive adjusted odds ratios and build the final model. Data corresponding to odd and even years (2 subsets) were analyzed separately and used in a simple cross-validation.</p> <p>Results</p> <p>Univariate analysis indicated that travel profile, prophylactic use, ethnicity, and province of birth were all associated with AMS in both subsets. In multivariate analysis, young men who traveled from lower altitude (600-800 m <it>vs</it>. 1300-1500 m, adjusted odds ratio (AOR) = 1.32-1.44) to higher altitudes (4100-4300 m <it>vs</it>. 2900-3100 m, AOR = 3.94-4.12; 3600-3700 m <it>vs</it>. 2900-3100 m, AOR = 2.71-2.74) by air or rapid land transport for emergency mission deployment (emergency land deployment <it>vs</it>. normal land deployment, AOR = 2.08-2.11; normal air deployment <it>vs</it>. normal land deployment, AOR = 2.00-2.20; emergency air deployment <it>vs</it>. normal land deployment, AOR = 2.40-3.34) during the cold season (cold <it>vs</it>. warm, AOR = 1.25-1.28) are at great risk for developing AMS. Non-Tibetan male soldiers (Tibetan <it>vs</it>. Han, AOR = 0.03-0.08), born and raised in lower provinces (eastern <it>vs</it>. northwestern, AOR = 1.32-1.39), and deployed without prophylaxis (prophylactic drug <it>vs</it>. none, AOR = 0.75-0.76), also represented a population at significantly increased risk for AMS. The predicted model was built; the area under receiver operating characteristic curve was 0.703.</p> <p>Conclusion</p> <p>Before a group of young men first enter a high altitude area, it is important that a health service plan should be made referring to the group's travel profile and with respect to young men's ethnicity and province of birth. Low-cost Chinese traditional prophylactic drugs might have some effect on decreasing the risk of AMS, although this needs further verification.</p