Miracle-dz/UniFAR-FTUs huggingface dataset:
How Does the University Food Environment Impact Student Dietary Behaviors? A Systematic Review

The food environment has been implicated in creating an obesogenic generation; and while previous research has focused on population-wide initiatives, the university population resides in a research gap. To explore detailed components of the university food environment and what shaped dietary behaviors, we retrieved literature from the following databases: ScienceDirect, Scopus, PubMed, Medline, and EMBASE. Eleven studies were identified for qualitative content analysis and study quality assessment identified most of the studies as of good quality (n 8) and some as of fair quality (n 3). The certainty of evidence remained at a low level for all (n 11) studies due to the cross-sectional, observational nature of studies. Three major themes emerged: (1) food environment, (2) student perceptions (SPs), and (3) dietary outcome (DO). In a university food environment, the taste of food was paramount for the food choices of students, followed by the availability of food and the price of food. When university students perceive and choose foods and beverages, they sometimes regard unhealthy foods and beverages as healthy options. The diet quality of university students is more susceptible to living arrangements and socioeconomic status, but higher salt, fat, and added sugar consumption generally resulted in poorer quality of diet on campus. Future research could use novel methods to explore a wider range and deeper level of students' dietary behavior determinants in university food environments. Systematic Review Registration https://www.crd. york.ac. uk/prospero/, identifier: CRD42021283562.
Neurobiology of Loneliness, Isolation, and Loss: Integrating Human and Animal Perspectives

In social species such as humans, non-human primates, and even many rodent species, social interaction and the maintenance of social bonds are necessary for mental and physical health and wellbeing. In humans, perceived isolation, or loneliness, is not only characterized by physical isolation from peers or loved ones, but also involves negative perceptions about social interactions and connectedness that reinforce the feelings of isolation and anxiety. As a complex behavioral state, it is no surprise that loneliness and isolation are associated with dysfunction within the ventral striatum and the limbic system – brain regions that regulate motivation and stress responsiveness, respectively. Accompanying these neural changes are physiological symptoms such as increased plasma and urinary cortisol levels and an increase in stress responsivity. Although studies using animal models are not perfectly analogous to the uniquely human state of loneliness, studies on the effects of social isolation in animals have observed similar physiological symptoms such as increased corticosterone, the rodent analog to human cortisol, and also display altered motivation, increased stress responsiveness, and dysregulation of the mesocortical dopamine and limbic systems. This review will discuss behavioral and neuropsychological components of loneliness in humans, social isolation in rodent models, and the neurochemical regulators of these behavioral phenotypes with a neuroanatomical focus on the corticostriatal and limbic systems. We will also discuss social loss as a unique form of social isolation, and the consequences of bond disruption on stress-related behavior and neurophysiology.
COVID-19 Quarantine Impact on Wellbeing and Cognitive Functioning During a 10-Week High-Intensity Functional Training Program in Young University Students

Physical exercise can improve cognitive functioning and wellbeing; however, the degree of change in either of these two variables seems to be related to the exercise intensity or type. Therefore, new physical training (PT) programs have been developed to increase exercise efficiency. One such example is high-intensity functional training (HIFT), which has proven to be a time-efficient and highly effective strategy to improve physical fitness. This study analyzed whether HIFT can affect reaction time (RT) and vitality, as well as positive and negative affect. Forty-two college students participated in the study, 21 in the experimental group and 21 in the control group. The experimental group completed 10 weeks of training, five of which were supervised, and the remainder consisted of online training during the COVID-19 quarantine. Participants were evaluated at the beginning, at the end of the 5 weeks of supervised training, and after the 5 weeks of online training. HIFT improved RT without changes in psychological wellbeing during the entire period of training supervised and online. Therefore, during the HIFT program, the quarantine situation did not adversely affect this population’s wellbeing, but it did negatively affect adherence to the training program.
Epigenetic Regulation in Kidney Transplantation

Kidney transplantation is a standard care for end stage renal disease, but it is also associated with a complex pathogenesis including ischemia-reperfusion injury, inflammation, and development of fibrosis. Over the past decade, accumulating evidence has suggested a role of epigenetic regulation in kidney transplantation, involving DNA methylation, histone modification, and various kinds of non-coding RNAs. Here, we analyze these recent studies supporting the role of epigenetic regulation in different pathological processes of kidney transplantation, i.e., ischemia-reperfusion injury, acute rejection, and chronic graft pathologies including renal interstitial fibrosis. Further investigation of epigenetic alterations, their pathological roles and underlying mechanisms in kidney transplantation may lead to new strategies for the discovery of novel diagnostic biomarkers and therapeutic interventions.
Feasibility of a Machine Learning-Based Smartphone Application in Detecting Depression and Anxiety in a Generally Senior Population

Background Depression and anxiety create a large health burden and increase the risk of premature mortality. Mental health screening is vital, but more sophisticated screening and monitoring methods are needed. The Ellipsis Health App addresses this need by using semantic information from recorded speech to screen for depression and anxiety. Objectives The primary aim of this study is to determine the feasibility of collecting weekly voice samples for mental health screening. Additionally, we aim to demonstrate portability and improved performance of Ellipsis’ machine learning models for patients of various ages. Methods Study participants were current patients at Desert Oasis Healthcare, mean age 63 years (SD = 10.3). Two non-randomized cohorts participated: one with a documented history of depression within 24 months prior to the study (Group Positive), and the other without depression (Group Negative). Participants recorded 5-min voice samples weekly for 6 weeks via the Ellipsis Health App. They also completed PHQ-8 and GAD-7 questionnaires to assess for depression and anxiety, respectively. Results Protocol completion rate was 61% for both groups. Use beyond protocol was 27% for Group Positive and 9% for Group Negative. The Ellipsis Health App showed an AUC of 0.82 for the combined groups when compared to the PHQ-8 and GAD-7 with a threshold score of 10. Performance was high for senior participants as well as younger age ranges. Additionally, many participants spoke longer than the required 5 min. Conclusion The Ellipsis Health App demonstrated feasibility in using voice recordings to screen for depression and anxiety among various age groups and the machine learning models using Transformer methodology maintain performance and improve over LSTM methodology when applied to the study population.
Coagulation Profile in COVID-19 Patients and its Relation to Disease Severity and Overall Survival: A Single-Center Study

Objectives: This study aims to investigate hemostatic changes in patients with coronavirus disease (COVID-19) and their relationship to disease severity and survival. Methods: This study included 284 patients with COVID-19 who attended the Security Forces Hospital, Makkah, Saudi Arabia between October 2020 and March 2021, and retrospectively reviewed their demographic, radiological, and laboratory findings. The coagulation profile was assayed at the time of diagnosis for platelet counts using an automated hematology analyzer; Sysmex XN2000 while international normalized ratio (INR), activated partial thromboplastin time (aPTT), fibrinogen, D-dimer, factor VIII, ristocetin cofactor (RiCoF), and von Willebrand factor antigen (VWF-Ag) were measured by Stago kits on a Stago automated coagulation analyzer (STA Compact Max®). Results: In this study, 32.3% of the cases had severe disease, while 8.8% of the cases died. D-dimer, factor VIII, and RiCoF were the only independent predictors of disease severity, with factor VIII and RiCoF having significantly higher areas under the curve (AUCs) than D-dimer (all p < 0.001). Furthermore, age, aPTT, and factor VIII were associated with an increased risk of mortality in multivariate Cox regression analysis, with factor VIII having a higher AUC of 0.98 than aPTT with an optimal cut-off value of >314 IU/dl in predicting mortality. Cases with factor VIII levels >314 IU/dl, compared to those with factor VIII levels <314 IU/dl, were associated with a significantly shorter mean overall survival time (20.08 vs. 31.35 days, p < 0.001), a lower survival rate (30.3% vs. 99.2%, p < 0.001), and a 16.62-fold increased mortality risk. Conclusion: RiCoF is a novel predictor of disease severity in COVID-19, while factor VIII is confirmed as a predictor of severity and mortality in COVID-19 patients and is associated with lower overall survival and increased mortality risk.
New Insight Into Visual Adaptation in the Mudskipper Cornea: From Morphology to the Cornea-Related COL8A2 Gene

Much research has focused on visual system evolution in bony fishes. The capacity of visual systems to perceive and respond to external signals is integral to evolutionary success. However, integrated research on the mechanisms of adaptive evolution based on corneal structure and related genes remains limited. In this study, scanning electron microscopy (SEM) was used to assess the microstructure and adaptation of corneal epithelial cells. Then, the evolution of the cornea-related COL8A2 gene was investigated. We found various projections (microridges, microplicae, microholes, and microvilli) on the corneal epithelial cells of amphibious mudskippers. Compared with those of fully aquatic fishes, these microstructures were considered adaptations to the variable environments experienced by amphibious mudskippers, as they can resist dryness in terrestrial environments and infection in aquatic environments. Moreover, strong purifying selection was detected for COL8A2. In addition, some specific amino acid substitution sites were also identified in the COL8A2 sequence in mudskippers. Interestingly, the evolutionary rate of the COL8A2 gene was significantly and positively correlated with maximum diving depth in our dataset. Specifically, with increasing diving depth, the evolutionary rate of the COL8A2 gene seemed to gradually accelerate. The results indicated that the cornea of bony fishes has evolved through adaptation to cope with the different diving depths encountered during the evolutionary process, with the corneal evolution of the amphibious mudskipper group showing a unique pattern.
Multiple congenital malformations arise from somatic mosaicism for constitutively active Pik3ca signaling

Recurrent missense mutations of the PIK3CA oncogene are among the most frequent drivers of human cancers. These often lead to constitutive activation of its product p110α, a phosphatidylinositol 3-kinase (PI3K) catalytic subunit. In addition to causing a range of rare and common cancers, the H1047R mutation is also found in affected tissues of a distinct set of congenital tumours and malformations. Collectively termed PIK3CA-related disorders (PRDs), these lead to overgrowth of skin, brain, adipose, connective, musculoskeletal tissues and/or blood and lymphatic vessel components. Vascular malformations are frequently observed in PRD due to cell-autonomous activation of the PI3K signaling pathway within endothelial cells. These, like most muscle, connective tissue and bone, are derived from the embryonic mesoderm. However, important organ systems affected in PRDs are neuroectodermal derivatives. To further examine their development, we drove the most common post-zygotic activating mutation of Pik3ca in neural crest and related embryonic lineages. Effects in cells having once expressed Wnt1, including the brain roofplate and most neural crest, were most dramatic in the head. Outcomes included macrocephaly, cleft secondary palate and more subtle skull anomalies. Surprisingly, Pik3ca-mutant subpopulations of neural crest origin were also associated with widespread cephalic vascular anomalies. Mesectodermal neural crest is a major source of vascular mural cells in the head but not the body. To examine the potential of non-mesectodermal neural crest, we turned to other Cre drivers, leading us to incidentally discover previously undescribed lineages that had expressed the transcription factor Egr2 (Krox20) and that may be co-opted in pathogenesis. In particular, Schwann cell precursors having transcribed either Krox20 or Sox10 and expressing constitutively active PI3K also gave rise to adult-onset vascular tumors and cancers, including melanoma. These murine phenotypes may aid discovery of new candidate human PRDs affecting craniofacial and vascular smooth muscle development as well as the reciprocal paracrine signaling mechanisms leading to tissue overgrowth.
Listeria monocytogenes Co-opts Caveolin-Mediated E-cadherin Trafficking and Macropinocytosis for Epithelial Cell-to-Cell Spread

Listeria monocytogenes is an intracellular bacterial pathogen that spreads directly between adjacent host cells without exposure to the extracellular space. Recent studies have identified several host cell factors that promote L. monocytogenes cell-to-cell spread in epithelial monolayers, but details of the mechanism remain unclear. We find that the adherens junction protein, E-cadherin, promotes L. monocytogenes cell-to-cell spread at the recipient side of cell contacts. In particular, two point mutations in E-cadherin’s cytoplasmic domain that prevent its ubiquitination hinder bacterial cell-to-cell spread efficiency without reducing the extent of contact between neighboring cells. As ubiquitination induces E-cadherin endocytosis, we hypothesize that E-cadherin promotes protrusion engulfment, where donor cell protrusions containing L. monocytogenes are taken up by the recipient cell concurrently with E-cadherin internalization. In support of this hypothesis, we show that inhibiting caveolin-mediated membrane trafficking reduces L. monocytogenes cell-to-cell spread only under conditions where E-cadherin can be ubiquitinated. Additionally, we demonstrate that macropinocytosis also contributes to dissemination of L. monocytogenes through an epithelial monolayer.
Modeling naturalistic face processing in humans with deep convolutional neural networks

Deep convolutional neural networks (DCNNs) trained for face identification can rival and even exceed human-level performance. The ways in which the internal face representations in DCNNs relate to human cognitive representations and brain activity are not well understood. Nearly all previous studies focused on static face image processing with rapid display times and ignored the processing of naturalistic, dynamic information. To address this gap, we developed the largest naturalistic dynamic face stimulus set in human neuroimaging research (700+ naturalistic video clips of unfamiliar faces). We used this novel naturalistic dataset to compare representational geometries estimated from DCNNs, behavioral responses, and brain responses. We found that DCNN representational geometries were consistent across architectures, cognitive representational geometries were consistent across raters in a behavioral arrangement task, and neural representational geometries in face areas were consistent across brains. Representational geometries in late, fully-connected DCNN layers, which are optimized for individuation, were much more weakly correlated with cognitive and neural geometries than were geometries in late-intermediate layers. The late-intermediate face-DCNN layers successfully matched cognitive representational geometries, as measured with a behavioral arrangement task that primarily reflected categorical attributes, and correlated with neural representational geometries in known face-selective topographies. Our study suggests that current DCNNs successfully capture neural cognitive processes for categorical attributes of faces, but less accurately capture individuation and dynamic features.
Differential Auditory and Visual Phase-Locking Are Observed during Audio-Visual Benefit and Silent Lip-Reading for Speech Perception

Speech perception in noisy environments is enhanced by seeing facial movements of communication partners. However, the neural mechanisms by which audio and visual speech are combined are not fully understood. We explore MEG phase-locking to auditory and visual signals in MEG recordings from 14 human participants (6 females, 8 males) that reported words from single spoken sentences. We manipulated the acoustic clarity and visual speech signals such that critical speech information is present in auditory, visual, or both modalities. MEG coherence analysis revealed that both auditory and visual speech envelopes (auditory amplitude modulations and lip aperture changes) were phase-locked to 2-6 Hz brain responses in auditory and visual cortex, consistent with entrainment to syllable-rate components. Partial coherence analysis was used to separate neural responses to correlated audio-visual signals and showed non-zero phase-locking to auditory envelope in occipital cortex during audio-visual (AV) speech. Furthermore, phase-locking to auditory signals in visual cortex was enhanced for AV speech compared with audio-only speech that was matched for intelligibility. Conversely, auditory regions of the superior temporal gyrus did not show above-chance partial coherence with visual speech signals during AV conditions but did show partial coherence in visual-only conditions. Hence, visual speech enabled stronger phase-locking to auditory signals in visual areas, whereas phase-locking of visual speech in auditory regions only occurred during silent lip-reading. Differences in these cross-modal interactions between auditory and visual speech signals are interpreted in line with cross-modal predictive mechanisms during speech perception. SIGNIFICANCE STATEMENT Verbal communication in noisy environments is challenging, especially for hearing-impaired individuals. Seeing facial movements of communication partners improves speech perception when auditory signals are degraded or absent. The neural mechanisms supporting lip-reading or audio-visual benefit are not fully understood. Using MEG recordings and partial coherence analysis, we show that speech information is used differently in brain regions that respond to auditory and visual speech. While visual areas use visual speech to improve phase-locking to auditory speech signals, auditory areas do not show phase-locking to visual speech unless auditory speech is absent and visual speech is used to substitute for missing auditory signals. These findings highlight brain processes that combine visual and auditory signals to support speech understanding.
Large protein complex interfaces have evolved to promote cotranslational assembly

Assembly pathways of protein complexes should be precise and efficient to minimise misfolding and unwanted interactions with other proteins in the cell. One way to achieve this efficiency is by seeding assembly pathways during translation via the cotranslational assembly of subunits. While recent evidence suggests that such cotranslational assembly is widespread, little is known about the properties of protein complexes associated with the phenomenon. Here, using a combination of proteome-specific protein complex structures and publicly available ribosome profiling data, we show that cotranslational assembly is particularly common between subunits that form large intermolecular interfaces. To test whether large interfaces have evolved to promote cotranslational assembly, as opposed to cotranslational assembly being a non-adaptive consequence of large interfaces, we compared the sizes of first and last translated interfaces of heteromers in bacterial, yeast, and human complexes. We detect a clear preference in N-terminal interfaces, which will be translated first and thus more likely to form cotranslationally, to be larger than C-terminal interfaces, suggesting that large interfaces have evolved as a means to maximise the chance of successful cotranslational subunit binding.
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen and major cause of hospital acquired infections. The pathogenicity and virulence of P. aeruginosa is largely determined by its transcriptional regulatory network (TRN). We used 411 transcription profiles of P. aeruginosa from diverse growth conditions to construct a quantitative TRN by identifying independently modulated sets of genes (called iModulons) and their condition-specific activity levels. The current study focused on the use of iModulons to analyze pathogenicity and antibiotic resistance of P. aeruginosa. Our analysis revealed: 1) 116 iModulons, 81 of which show strong association with known regulators; 2) novel roles of two-component systems in regulating antibiotics efflux pumps; 3) substrate-efflux pump associations; 4) differential iModulon activity in response to beta-lactam antibiotics in bacteriological and physiological media; 5) differential activation of ‘Cell Division’ iModulon resulting from exposure to different beta-lactam antibiotics; and 6) a role of the PprB iModulon in the stress-induced transition from planktonic to biofilm lifestyle. In light of these results, the construction of an iModulon-based TRN provides a transcriptional regulatory basis for key aspects of P. aeruginosa infection, such as antibiotic stress responses and biofilm formation. Taken together, our results offer a novel mechanistic understanding of P. aeruginosa pathogenicity. Significance Large data sets and machine learning are impacting a growing number of areas of research in the life sciences. Once the compendia of bacterial transcriptomes reached a critical size, we could use source signal extraction algorithms to find lists of co-regulated genes (called iModulons) associated with a transcription factor (TF) to them. The gene composition of iModulons and their condition-dependent activity levels constitute a quantitative description of the composition of bacterial transcriptomes. This study shows how this approach can be used to reveal the responses of P. aeruginosa to antibiotics and thus yield a deep regulatory understanding of pathogenicity properties. This study motivates the execution of similar studies for the other ESKAPEEs to yield a broad understanding of the role of TRNs in antibiotic responses to these urgent threat bacterial pathogens.