Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating Factors Affecting Students’ Loyalty to Continue Higher Education in the Same Institute

The current challenge among institutes nowadays is to keep their old students for continuance in higher education. Different literatures have considered individual factors of behavioral and cognitive aspects to assess student loyalty. However, limited studies have tried to holistically cover student's loyalty for retention in the same institute throughout the years. Therefore, the main goal of this study was to investigate factors affecting students’ loyalty to continue higher education in the same university. Specifically, factors under the self-determination theory and theory of planned behavior was applied in this study, extended with other factors such as student satisfaction and university image to completely assess the intention towards loyalty among high school students. This study utilized a machine learning algorithm, random forest classifier due to its capability to have high accuracy rate in predicting factors affecting human behavior. It was deduced that highly significant factors such as autonomy and affective behavior would lead to very high loyalty among students. On the other hand, perceived behavioral control and university image are significant which would lead to a high loyalty behavior among students. With 92% accuracy rate, it could be suggested that the integration and extension of SDT and TPB provided holistic measurement of the behavioral and cognitive aspects of students for institute retention and option. Moreover, it is suggested that tools such as structural equation modeling and machine learning algorithm be integrated to have highly holistic measurement of significant factors affecting human behavior in different field.
Implicature of complex sentences in error models

Due to their intensive discussion, implicatures of complex sentences became a kind of benchmark for testing different frameworks of Gricean pragmatics. We propose a novel approach which is based on a communication model with feedback and speaker errors in signal selection. The communication model is introduced as an extension of standard signalling games. In this model, implicatures are explained by the speaker’s tendency to omit parts of their utterances. In this explanation, the error coping strategy of the hearer plays an essential role. In order to account for implicature cancellation, clausal implicatures, and implicatures of complex sentences with disjunction, an additional nonmonotonic component is needed which represents normality assumptions about the level of speaker expertise. Keywords:﻿﻿ complex sentences; error models; game theory; preferential models; scalar implicatures
VitTCR: A deep learning method for peptide recognition prediction

The identification of the interaction between T-cell receptors (TCRs) and immunogenic peptides is important for the development of novel cancer immunotherapies and vaccines. However, experimentally determining whether a TCR recognizes a peptide is still time– and labour-consuming. In this study, we introduced VitTCR, a predictive model based on the architecture of the vision transformer (ViT), designed to forecast TCR-peptide interactions. Prior to prediction, VitTCR converts the TCR-peptide interactions into a numerical tensor named AtchleyMaps using Atchley factors. Subsequently, VitTCR takes AtchleyMaps as inputs and predicts whether an interaction between a TCR and a peptide exists. Through comprehensive evaluations, we demonstrate that VitTCR surpasses other published methods in classifying TCR-peptide pairs, exhibiting superior performance in terms of the area under the receiver operating characteristic (AUROC) and the area under the precision-recall curve (AUPR). To determine the focal contact point between TCRs and peptides, we obtained a positional bias weight matrix (PBWM) from the empirical amino acid (AA) contact probabilities derived from 83 structurally resolved pMHC-TCR complexes. The comparison of VitTCR with and without the integration of the PBWM revealed significant enhancements in the performance of the model. Moreover, the predicted probabilities generated by VitTCR exhibit significant correlations with immunological factors such as the clonal expansion and activation percentages of T cells. This further supports the efficacy of VitTCR in capturing biologically meaningful TCR-peptide interactions. In conclusion, VitTCR provides a useful computational tool for the prediction of TCR-peptide interactions, thereby contributing to our understanding in this field.
Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect akuBGL activity

The defensive-offensive associations between algae and herbivores determine marine ecology. Brown algae utilize phlorotannin as their chemical defense against the predator Aplysia kurodai, which uses β-glucosidase (akuBGL) to digest the laminarin in algae to glucose. Moreover, A. kurodai employs Eisenia hydrolysis-enhancing protein (EHEP) as an offense to protect akuBGL activity from phlorotannin inhibition by precipitating phlorotannin. To underpin the molecular mechanism of this digestive-defensive-offensive system, we determined the structures of apo and tannic-acid (TNA, a phlorotannin-analog) bound form of EHEP, as well as apo akuBGL. EHEP consisted of three peritrophin-A domains formed in a triangle and bound TNA in the center without significant conformational changes. Structural comparison between EHEP and EHEP–TNA led us to find that EHEP can be resolubilized from phlorotannin-precipitation at an alkaline pH, which reflects a requirement in the digestive tract. akuBGL contained two GH1 domains, only one of which conserved the active site. Combining docking analysis, we propose the mechanisms by which phlorotannin inhibits akuBGL by occupying the substrate-binding pocket, and EHEP protects akuBGL against the inhibition by binding with phlorotannin to free the akuBGL pocket.
Mutator transposon insertions within maize genes often provide a novel outward reading promoter

The highly active family of Mutator (Mu) DNA transposons has been widely used for forward and reverse genetics in maize. There are examples of Mu-suppressible alleles which result in conditional phenotypic effects based on the activity of Mu. Phenotypes from these Mu- suppressible mutations are observed in Mu-active genetic backgrounds, but absent when Mu activity is lost. For some Mu-suppressible alleles, phenotypic suppression likely results from an outward-reading promoter within Mu that is only active when the autonomous Mu element is silenced or lost. We isolated 35 Mu alleles from the UniformMu population that represent insertions in 24 different genes. Most of these mutant alleles are due to insertions within gene coding sequences, but several 5’ UTR and intron insertions were included. RNA-seq and de novo transcript assembly were utilized to document the transcripts produced from 33 of these Mu insertion alleles. For 20 of the 33 alleles, there was evidence of transcripts initiating within the Mu sequence reading through the gene. This outward-reading promoter activity was detected in multiple types of Mu elements and doesn’t depend on the orientation of Mu. Expression analyses of Mu-initiated transcripts revealed the Mu promoter often provides gene expression levels and patterns that are similar to the wild-type gene. These results suggest the Mu promoter may represent a minimal promoter that can respond to gene cis-regulatory elements. Findings from this study have implications for maize researchers using the UniformMu population, and more broadly highlights a strategy for transposons to co-exist with their host. Article Summary Mutator (Mu) transposable elements are a widely used tool for insertional mutagenesis in maize and often insert in the 5’ regions of genes. The characterization of transcripts for Mu insertion alleles reveals complex transcripts. These often result in one transcript that covers the first portion of the gene terminating in Mu and a second transcript initiating within Mu covering the latter portion of the gene. This may reflect a strategy for Mu to minimize the consequences of insertions within genes.
Alpha-band frequency and temporal windows in perception: A review and meta-analysis of 25 experiments

Temporal windows in perception refer to windows of time within which distinct stimuli interact to influence perception. A simple example is two brief stimuli fusing into a single percept when they occur within a certain time range. It has long been hypothesized that the human alpha rhythm (an 8-13 Hz neural oscillation maximal over posterior cortex) is linked to temporal windows, with higher frequencies corresponding to shorter windows and finer-grained temporal resolution. Recently, this hypothesis has garnered support from studies demonstrating a correlation between individual differences in alpha frequency (IAF) and behavioral measures of temporal processing. However, non-significant effects have also been reported. Here, we review and meta-analyze 25 experiments correlating IAF with measures of temporal processing in visual and audio-visual perception. Our results estimate the true correlation in the population to be between 0.39 to 0.52, a medium-to-large effect. The effect held when considering visual or audio-visual experiments separately and when examining different IAF estimation protocols (i.e., eyes-open and eyes-closed). Moreover, using analysis choices that favor a null result, we still find a significant population effect. Our review shows that 1) effects have been internally and independently replicated 2) several positive effects are based on larger sample sizes than the null effects and 3) many reported null effects are actually in the direction predicted by the hypothesis. We discuss possible factors underlying the reported null effects as well as design recommendations and open questions for future researchers investigating the link between alpha frequency and temporal windows in perception.
Early acquisition of S-specific Tfh clonotypes after SARS-CoV-2 vaccination is associated with the longevity of anti-S antibodies

SARS-CoV-2 vaccines have been used worldwide to combat COVID-19 pandemic. To elucidate the factors that determine the longevity of spike (S)-specific antibodies, we traced the characteristics of S-specific T cell clonotypes together with their epitopes and anti-S antibody titers before and after BNT162b2 vaccination over time. T cell receptor (TCR) αβ sequences and mRNA expression of the S-responded T cells were investigated using single-cell TCR- and RNA-sequencing. Highly expanded 199 TCR clonotypes upon stimulation with S peptide pools were reconstituted into a reporter T cell line for the determination of epitopes and restricting HLAs. Among them, we could determine 78 S epitopes, most of which were conserved in variants of concern (VOCs). After the 2nd vaccination, T cell clonotypes highly responsive to recall S stimulation were polarized to follicular helper T (Tfh)-like cells in donors exhibiting sustained anti-S antibody titers (designated as “sustainers”), but not in “decliners”. Even before vaccination, S-reactive CD4+ T cell clonotypes did exist, most of which cross-reacted with environmental or symbiotic bacteria. However, these clonotypes contracted after vaccination. Conversely, S-reactive clonotypes dominated after vaccination were undetectable in pre-vaccinated T cell pool, suggesting that highly-responding S-reactive T cells were established by vaccination from rare clonotypes. These results suggest that de novo acquisition of memory Tfh-like cells upon vaccination may contribute to the longevity of anti-S antibody titers.
Investigating pedigree- and SNP-associated components of heritability in a wild population of Soay sheep

Estimates of narrow sense heritability derived from genomic data that contain related individuals may be biased due to the within-family effects such as dominance, epistasis and common environmental factors. However, for many wild populations, removal of related individuals from the data would result in small sample sizes. In 2013, Zaitlen et al. proposed a method to estimate heritability in populations that include close relatives by simultaneously fitting an identity-by-state genomic relatedness matrix (GRM) and an identity-by-descent GRM. The IBD GRM is identical to the IBS GRM, except relatedness estimates below a specified threshold are set to 0. We applied this method to a sample of 8557 wild Soay sheep from St. Kilda, with genotypic information for 419,281 single nucleotide polymorphisms to investigate polygenic and monogenic traits. We also implemented a variant of the model in which the IBD GRM was replaced by a GRM constructed from SNPs with low minor allele frequency to examine whether any additive genetic variance is captured by rare alleles. Each model was compared to an animal model with a single GRM based on all genotyped markers (the IBS GRM) using a log likelihood ratio test. Whilst the inclusion of the IBD GRM did not significantly improve the fit of the model for the monogenic traits, it improved the fit for some of the polygenic traits, suggesting that dominance, epistasis and/or common environment not already captured by the non-genetic random effects fitted in our models may influence these traits.
Phosphoprotein dynamics of interacting tumor and T cells by HySic

Functional interactions between cytotoxic T cells and tumor cells are central to anti-cancer immunity. Some of the proteins involved, particularly immune checkpoints expressed by T cells, serve as promising clinical targets in immunotherapy. However, our understanding of the complexity and dynamics of the interactions between tumor cells and T cells is only rudimentary. Here we present HySic (for Hybrid quantification of SILAC (Stable Isotope Labelling by Amino acids in Cell culture)-labeled interacting cells) as an innovative method to quantify protein and phosphorylation dynamics between and within physically interacting (heterotypic) cells. We show that co-cultured HLA/antigen-matched tumor and T cells engage in physical and stable interactions, allowing for in-depth HySic analysis. This method does not require physical separation of the two cell types for subsequent MS proteome and phosphoproteome measurement using label free quantification (LFQ). We demonstrate that HySic can be used to unravel proteins contributing to functional T cell:tumor cell interactions. We validated HySic with established interactions, including those mediating IFNγ signaling. Using HySic we identified the RHO/RAC/PAK1 signaling pathway to be activated upon interaction of T cells and tumor cells. Pharmacologic inhibition of PAK1 sensitized tumor cells to T cell killing. Thus, HySic is an innovative and simple method to study short-term protein signaling dynamics in physically interacting cells, which can be easily extended to other biological systems.
Melatonin suppression by light involves different retinal photoreceptors in young and older adults

Introduction Age-related sleep and circadian rhythm disturbances may be due to altered non-visual photoreception. Here, we investigated the temporal dynamics of light-induced melatonin suppression in young and older individuals. Methods In a within-subject design study, young and older participants were exposed for 60 minutes (0030-0130 at night) to 9 narrow-band lights (range: 420 to 620 nm). Plasma melatonin suppression was calculated at 15, 30, 45, and 60 min time intervals. Individual spectral sensitivity of melatonin suppression and photoreceptor contribution were predicted for each interval and age group. Results In young participants, melanopsin solely drove melatonin suppression at all time intervals, with an invariant peak sensitivity at ∼485 nm established only after 15 minutes of light exposure. Conversely, in older participants, spectral light-driven melatonin suppression was best explained by a model combining melanopsin + L-cones with a stable peak sensitivity (∼499 nm) at 30, 45, and 60 minutes of light exposure. Conclusion Aging is associated with a distinct photoreceptor contribution to melatonin suppression by light. While in young adults melanopsin-only photoreception is a reliable predictor of melatonin suppression, in older individuals this process is jointly driven by melanopsin and L-cones. These findings offer new prospects for customizing light therapy for older individuals.
Discovering the mechanics of artificial and real meat

Artificial meat is an eco-friendly alternative to real meat that is marketed to have a similar taste and feel. The mechanical properties of artificial meat significantly influence our perception of taste, but how precisely the mechanics of artificial meat compare to real meat remains insufficiently understood. Here we perform mechanical tension, compression, and shear tests on isotropic artificial meat (Tofurky® Plant-Based Deli Slices), anisotropic artificial meat (Daring™ Chick’n Pieces) and anisotropic real meat (chicken) and analyze the data using constitutive neural networks and automated model discovery. Our study shows that, when deformed by 10%, artificial and real chicken display similar maximum stresses of 21.0 kPa and 21.8 kPa in tension, -7.2 kPa and -16.4 kPa in compression, and 2.4 kPa and 0.9 kPa in shear, while the maximum stresses for tofurky were 28.5 kPa, -38.3 kP, and 5.5 kPa. To discover the mechanics that best explain these data, we consulted two constitutive neural networks of Ogden and Valanis-Landel type. Both networks robustly discover models and parameters to explain the complex nonlinear behavior of artificial and real meat for individual tension, compression, and shear tests, and for all three tests combined. When constrained to the classical neo Hooke, Blatz Ko, and Mooney Rivlin models, both networks discover shear moduli of 94.4 kPa for tofurky, 35.7 kPa for artificial chick’n, and 21.4 kPa for real chicken. Our results suggests that artificial chicken succeeds in re-producing the mechanical properties of real chicken across all loading modes, while tofurky does not, and is about three times stiffer. Strikingly, all three meat products display shear softening and their resistance to shear is about an order of magnitude lower than their resistance to tension and compression. We anticipate our study to inspire more quantitative, mechanistic comparisons of artificial and real meat. Our automated-model-discovery based approach has the potential to inform the design of more authentic meat substitutes with an improved perception of taste, with the ultimate goal to reduce environmental impact, improve animal welfare, and mitigate climate change, while still offering the familiar taste and texture of traditional meat. Our source code, data, and examples will be available at https://github.com/LivingMatterLab/CANNs.
Conjunctive vector coding and place coding in hippocampus share a common directional signal

Vector coding is becoming increasingly understood as a major mechanism by which neural systems represent an animal’s location in both a global reference frame and a local, item-based reference frame. Landmark vector cells (LVCs) in the hippocampus complement classic place cells by encoding the vector relationship (angle and distance) between the individual and specific landmarks in the environment. How these properties of hippocampal principal cells interact is not known. We simultaneously recorded the activities of place cells and LVCs via in vivo calcium imaging of the CA1 region of freely moving rats during classic, cue-card rotation studies. The firing fields of place cells rotated relative to the center of the platform to follow the cue card rotation, whereas the firing fields of simultaneously recorded LVCs rotated by the same amount as the place cells, but the axis of rotation was the nearby local landmarks, not the environmental center. We identified a novel type of place cell that exhibited conjunctive coding of the classic place field properties and LVC properties. These results demonstrate the capacity of CA1 neurons to encode both world-centered spatial information and animals’ location relative to the local landmarks, with a common directional input presumably provided by the head direction cell system.
Monocyte Adhesion and Transmigration Through Endothelium Following Cardiopulmonary Bypass Shearing is Mediated by IL-8 Signaling

Background The use of cardiopulmonary bypass (CPB) can induce sterile systemic inflammation that contributes to morbidity and mortality, especially in children. Patients have been found to have increased expression of cytokines and transmigration of leukocytes during and after CPB. Previous work has demonstrated that the supraphysiologic shear stresses present during CPB are sufficient to induce proinflammatory behavior in non-adherent monocytes. The interactions between shear stimulated monocytes and vascular endothelial cells have not been well studied and have important translational implications. Methods To test the hypothesis that non-physiological shear stress experienced by monocytes during CPB affects the integrity and function of the endothelial monolayer via IL-8 signaling pathway, we have used an in vitro CPB model to study the interaction between THP-1 monocyte-like cells and human neonatal dermal microvascular endothelial cells (HNDMVECs). THP-1 cells were sheared in polyvinyl chloride (PVC) tubing at 2.1 Pa, twice of physiological shear stress, for 2 hours. Interactions between THP-1 cells and HNDMVECs were characterized after coculture. Results We found that sheared THP-1 cells adhered to and transmigrated through the HNDMVEC monolayer more readily than static controls. When co-culturing, sheared THP-1 cells also disrupted in the VE-cadherin and led to reorganization of cytoskeletal F-actin of HNDMVECs. Treating HNDMVECs with IL-8 resulted in upregulation of vascular cell adhesion molecule 1 (VCAM-1) and intercellular adhesion molecule 1 (ICAM-1) while also increasing the adherence of non-sheared THP-1 cells. Preincubating HNDMVECs with Reparixin, an inhibitor of CXCR2/IL-8 receptor inhibited sheared THP-1 cell adhesion to the HNDMVECs. Conclusions These results suggested that IL-8 not only increases the endothelium permeability during monocyte migration, but also affects the initial adhesion of monocytes in a CPB setup. This study revealed a novel mechanism of post-CPB inflammation and will contribute to the development of targeted therapeutics to prevent and repair the damage to neonatal patients. Highlights Shear stress in a CPB-like environment promoted the adhesion and transmigration of monocytes to and through endothelial monolayer. Treating endothelial monolayer with sheared monocytes led to disruption of VE-cadherin and reorganization of F-actin. Interaction between sheared monocytes resulted in a significant increase of IL-8 release. Inhibiting IL-8 receptor prevented sheared monocyte adhesion, while IL-8 promoted naive monocyte adhesion.