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Journal of Experimental Psychology.... Sep 2019At the scale in which we live, space is continuous. Nevertheless, our perception and cognition parse the world into categories, whether physical, like or or abstract,...
At the scale in which we live, space is continuous. Nevertheless, our perception and cognition parse the world into categories, whether physical, like or or abstract, like or 7. The present study focuses on 2 categories of special angles in planar geometry, and and we evaluate how these categories might be reflected in adults' basic angle discrimination. In the first experiment, participants were most precise when detecting 2 parallel or perpendicular lines among other pairs of lines at different relative orientations. Detection was also enhanced for 2 connected lines whose angle approached 90°, with precision peaking at 90°. These patterns emerged despite large variations in the scales and orientations of the angle exemplars. In the second experiment, the enhanced detection of perpendiculars persisted when stimuli were rotated in depth, indicating a capacity to discriminate shapes based on perpendicularity in 3 dimensions despite large variation in angles' 2-dimensional projections. The results suggest that 2 categorical concepts which lie at the foundation of Euclidean geometry, parallelism and perpendicularity, are reflected in our discrimination of simple visual forms, and they pave the way for future studies exploring the developmental and evolutionary origins of these cognitive categories. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Topics: Adult; Concept Formation; Discrimination, Psychological; Female; Humans; Male; Mathematical Concepts; Pattern Recognition, Visual; Space Perception; Young Adult
PubMed: 31219284
DOI: 10.1037/xhp0000663 -
Journal of Ayurveda and Integrative... 2022Kerala's contribution to Ayurveda practice and literature is held with high esteem by scholars all over the country. Literary works of Kerala comprises of both works... (Review)
Review
Kerala's contribution to Ayurveda practice and literature is held with high esteem by scholars all over the country. Literary works of Kerala comprises of both works which are unique in nature and works which have parallels in other regions of India. Despite these facts, most of these works, except a few like Sahasrayoga have not yet been studied well. The scholarliness of the authors of such works also remains unknown to the current generation. Unless a serious effort is made to study these, the concern is that the wisdom in the regional literature of Ayurveda will be lost as most of these works will become unavailable in near future. This article focuses on the life, works and achievements of Pandit C K Vasudeva Sarma, an eminent scholar physician from Kerala. The review is prepared as a life profile based on published documents, oral reports etc. Major works were identified and the parallel to Jejjata was drawn following that. Vachaspathya commentary on Carakasamhita, Hridayollasa commentary on Sushrutasamhita, Vasudeviya commentary on Ashtangahridaya, Vaidyapriya commentary on Sarngadharasamhita, commentary on Yogaratnakara called Vaidyaratnam are some of his prominent works on Sanskrit texts. Apart from authoring some unique Ayurvedic texts in Malayalam he also authored several non-Ayurveda textbooks. These rich regional diversity in the Ayurveda literature and practice worth detailed study by future generations. Value of the works of Pandit C K Vasudeva Sarma underlines the concern on regional literature and stresses the need for further studies in similar areas.
PubMed: 36495714
DOI: 10.1016/j.jaim.2022.100659 -
Journal of Computational and Graphical... 2024Large-scale observational health databases are increasingly popular for conducting comparative effectiveness and safety studies of medical products. However, increasing...
Large-scale observational health databases are increasingly popular for conducting comparative effectiveness and safety studies of medical products. However, increasing number of patients poses computational challenges when fitting survival regression models in such studies. In this paper, we use graphics processing units (GPUs) to parallelize the computational bottlenecks of massive sample-size survival analyses. Specifically, we develop and apply time- and memory-efficient single-pass parallel scan algorithms for Cox proportional hazards models and forward-backward parallel scan algorithms for Fine-Gray models for analysis with and without a competing risk using a cyclic coordinate descent optimization approach. We demonstrate that GPUs accelerate the computation of fitting these complex models in large databases by orders of magnitude as compared to traditional multi-core CPU parallelism. Our implementation enables efficient large-scale observational studies involving millions of patients and thousands of patient characteristics. The above implementation is available in the open-source R package Cyclops (Suchard et al., 2013).
PubMed: 38716090
DOI: 10.1080/10618600.2023.2213279 -
Communicative & Integrative Biology 2021The linguistic behavior of humans is usually considered the point of reference for studying the origin and evolution of language. As commonly defined, language is a form... (Review)
Review
The linguistic behavior of humans is usually considered the point of reference for studying the origin and evolution of language. As commonly defined, language is a form of communication between human beings; many have argued that it is unique to humans as there is no apparent equivalent for it in non-human organisms. How language is used as a means of communication is examined in this essay from a biological perspective positing that it is effectively and meaningfully used by non-human organisms and, more specifically, by plants. We set out to draw parallels between some aspects characterizing human language and the chemical communication that occurs between plants. The essay examines the similarities in ways of communicating linked to three properties of language: its combinatorial structure, meaning-making activities and the existence of dialects. In accordance with the findings of researchers who have demonstrated that plants do indeed communicate with one another and with organisms in their environment, the essay concludes with the appeal for an interdisciplinary approach conceptualizing a broader ecological definition of language and a constructive dialogue between the biological sciences and the humanities.
PubMed: 34434483
DOI: 10.1080/19420889.2021.1956719 -
GigaScience May 2020Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned,...
BACKGROUND
Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: thus, the prediction of deleterious variants is a challenging, highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data.
RESULTS
To overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and substantially speed up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in genomic medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a high-performance computing cluster. Results with synthetic data and with single-nucleotide variants associated with Mendelian diseases and with genome-wide association study hits in the non-coding regions of the human genome, involhing millions of examples, show that parSMURF achieves state-of-the-art results and an 80-fold speed-up with respect to the sequential version.
CONCLUSIONS
parSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and high scalability allow us to efficiently fit problems characterized by big and imbalanced genomic data. The C++ OpenMP multi-core version tailored to a single workstation and the C++ MPI/OpenMP hybrid multi-core and multi-node parSMURF version tailored to a High Performance Computing cluster are both available at https://github.com/AnacletoLAB/parSMURF.
Topics: Algorithms; Computational Biology; Databases, Genetic; Genetic Predisposition to Disease; Genetic Variation; Genome-Wide Association Study; Genomics; Humans; Machine Learning; Reproducibility of Results; Software
PubMed: 32444882
DOI: 10.1093/gigascience/giaa052 -
The Journal of Cell Biology Jun 2021Immune synapses are formed between immune cells to facilitate communication and coordinate the immune response. The reorganization of receptors involved in recognition... (Review)
Review
Immune synapses are formed between immune cells to facilitate communication and coordinate the immune response. The reorganization of receptors involved in recognition and signaling creates a transient area of plasma membrane specialized in signaling and polarized secretion. Studies on the formation of the immune synapse between cytotoxic T lymphocytes (CTLs) and their targets uncovered a critical role for centrosome polarization in CTL function and suggested a striking parallel between the synapse and primary cilium. Since these initial observations, a plethora of further morphological, functional, and molecular similarities have been identified between these two fascinating structures. In this review, we describe how advances in imaging and molecular techniques have revealed additional parallels as well as functionally significant differences and discuss how comparative studies continue to shed light on the molecular mechanisms underlying the functions of both the immune synapse and primary cilium.
Topics: Animals; Cilia; Humans; Immunological Synapses; Signal Transduction; T-Lymphocytes, Cytotoxic
PubMed: 33956049
DOI: 10.1083/jcb.202102089 -
Antioxidants (Basel, Switzerland) May 2023Cardiometabolic conditions are closely associated with inflammation and oxidative stress. Dietary berries may serve as a beneficial nutrition intervention to address the... (Review)
Review
Cardiometabolic conditions are closely associated with inflammation and oxidative stress. Dietary berries may serve as a beneficial nutrition intervention to address the features of cardiometabolic dysfunction and associated oxidative stress. The high antioxidant status of dietary berries may increase antioxidant capacity and reduce biomarkers of oxidative stress. This systematic review was conducted to investigate these effects of dietary berries. The search was conducted using PubMed, Cochrane Library, Web of Science, and citation searching. Through this search we identified 6309 articles and 54 were included in the review. Each study's risk of bias was assessed using the 2019 Cochrane Methods' Risk of Bias 2 tool. Antioxidant and oxidative stress outcomes were evaluated, and the magnitude of effect was calculated using Cohen's . A range of effectiveness was reported in the included studies and the quality of the studies differed between the parallel and crossover trials. Considering the inconsistency in reported effectiveness, future investigations are warranted to determine the acute and sustained reductions of oxidative stress biomarkers from dietary berry intake (PROSPERO registration# CRD42022374654).
PubMed: 37371912
DOI: 10.3390/antiox12061182 -
Journal of Medical Education and... 2024We created a serious game to teach first year anesthesiology (CA-1) residents to perform general anesthesia for cesarean delivery. We aimed to investigate resident...
We created a serious game to teach first year anesthesiology (CA-1) residents to perform general anesthesia for cesarean delivery. We aimed to investigate resident knowledge gains after playing the game and having received one of 2 modalities of debriefing. We report on the development and validation of scores from parallel test forms for criterion-referenced interpretations of resident knowledge. The test forms were intended for use as pre- and posttests for the experiment. Validation of instruments measuring the study's primary outcome was considered essential for adding rigor to the planned experiment, to be able to trust the study's results. Parallel, multiple-choice test forms development steps included: (1) assessment purpose and population specification; (2) content domain specification and writing/selection of items; (3) content validation by experts of paired items by topic and cognitive level; and (4) empirical validation of scores from the parallel test forms using Classical Test Theory (CTT) techniques. Field testing involved online administration of 52 shuffled items from both test forms to 24 CA-1's, 21 second-year anesthesiology (CA-2) residents, 2 fellows, 1 attending anesthesiologist, and 1 of unknown rank at 3 US institutions. Items from each form yielded near-normal score distributions, with similar medians, ranges, and standard deviations. Evaluations of CTT item difficulty (item p values) and discrimination (D) indices indicated that most items met assumptions of criterion-referenced test design, separating experienced from novice residents. Experienced residents performed better on overall domain scores than novices ( < .05). Kuder-Richardson Formula 20 (KR-20) reliability estimates of both test forms were above the acceptability cut of .70, and parallel forms reliability estimate was high at .86, indicating results were consistent with theoretical expectations. Total scores of parallel test forms demonstrated item-level validity, strong internal consistency and parallel forms reliability, suggesting sufficient robustness for knowledge outcomes assessments of CA-1 residents.
PubMed: 38357687
DOI: 10.1177/23821205241229778 -
Advances in Experimental Medicine and... May 2024Transcriptional control of lipid metabolism uses a framework that parallels the control of lipid metabolism at the protein or enzyme level, via feedback and feed-forward...
Transcriptional control of lipid metabolism uses a framework that parallels the control of lipid metabolism at the protein or enzyme level, via feedback and feed-forward mechanisms. Increasing the substrates for an enzyme often increases enzyme gene expression, for example. A paucity of product can likewise potentiate transcription or stability of the mRNA encoding the enzyme or enzymes needed to produce it. In addition, changes in second messengers or cellular energy charge can act as on/off switches for transcriptional regulators to control transcript (and protein) abundance. Insects use a wide range of DNA-binding transcription factors (TFs) that sense changes in the cell and its environment to produce the appropriate change in transcription at gene promoters. These TFs work together with histones, spliceosomes, and additional RNA processing factors to ultimately regulate lipid metabolism. In this chapter, we will first focus on the important TFs that control lipid metabolism in insects. Next, we will describe non-TF regulators of insect lipid metabolism such as enzymes that modify acetylation and methylation status, transcriptional coactivators, splicing factors, and microRNAs. To conclude, we consider future goals for studying the mechanisms underlying the control of lipid metabolism in insects.
PubMed: 38782870
DOI: 10.1007/5584_2024_808 -
Genetics Jul 2021Changes in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have...
Changes in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find evidence for parallel expression evolution between them, with stronger parallelism at larval and adult stages than for pupae. We also implement a flexible method to estimate cis- vs trans-encoded contributions to expression or splicing differences at the adult stage. The apparent contributions of cis- vs trans-regulation to adaptive evolution vary substantially among population pairs. While two of three population pairs show a greater enrichment of cis-regulatory differences among adaptation candidates, trans-regulatory differences are more likely to be implicated in parallel expression changes between population pairs. Genes with significant cis-effects are enriched for signals of elevated genetic differentiation between cold- and warm-adapted populations, suggesting that they are potential targets of local adaptation. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.
Topics: Acclimatization; Animals; Cold Temperature; Drosophila Proteins; Drosophila melanogaster; Evolution, Molecular; Models, Genetic
PubMed: 33989401
DOI: 10.1093/genetics/iyab077