Miracle-dz/UniFAR-FTUs huggingface dataset:
GMEmbeddings: An R Package to Apply Embedding Techniques to Microbiome Data

Large-scale microbiome studies investigating disease-inducing microbial roles base their findings on differences between microbial count data in contrasting environments (e.g., stool samples between cases and controls). These microbiome survey studies are often impeded by small sample sizes and database bias. Combining data from multiple survey studies often results in obvious batch effects, even when DNA preparation and sequencing methods are identical. Relatedly, predictive models trained on one microbial DNA dataset often do not generalize to outside datasets. In this study, we address these limitations by applying word embedding algorithms (GloVe) and PCA transformation to ASV data from the American Gut Project and generating translation matrices that can be applied to any 16S rRNA V4 region gut microbiome sequencing study. Because these approaches contextualize microbial occurrences in a larger dataset while reducing dimensionality of the feature space, they can improve generalization of predictive models that predict host phenotype from stool associated gut microbiota. The GMEmbeddings R package contains GloVe and PCA embedding transformation matrices at 50, 100 and 250 dimensions, each learned using ∼15,000 samples from the American Gut Project. It currently supports the alignment, matching, and matrix multiplication to allow users to transform their V4 16S rRNA data into these embedding spaces. We show how to correlate the properties in the new embedding space to KEGG functional pathways for biological interpretation of results. Lastly, we provide benchmarking on six gut microbiome datasets describing three phenotypes to demonstrate the ability of embedding-based microbiome classifiers to generalize to independent datasets. Future iterations of GMEmbeddings will include embedding transformation matrices for other biological systems. Available at: https://github.com/MaudeDavidLab/GMEmbeddings.
Case Report: Right Heart Failure Mistaken for Obesity—A Fault of Telemedicine

As a result of the COVID-19 pandemic, telemedicine has become an important branch of healthcare worldwide. Apart from their undeniable advantages, the virtual visits lack physical examination, which can lead to important diagnostic mistakes. We hereby present a case of a pediatric patient whose weight gain, initially attributed to a sedentary lifestyle was, in fact, due to sub-acute right heart failure in the context of a ruptured sinus of Valsalva aneurysm. The condition was not diagnosed until the patient presented at the emergency. The boy was successfully treated with two percutaneous interventions and returned to his previous stature.
Facial Palsy as Initial Symptom in Glycine Receptor Antibody Positive Progressive Encephalomyelitis With Rigidity and Myoclonus: A Case Report

Progressive encephalomyelitis with rigidity and myoclonus (PERM) is a rare and disabling syndrome characterized by painful spasms, myoclonic jerks, hyperekplexia, brainstem signs, and dysautonomia, which is considered to be a severe form of stiff person spectrum disorder (SPSD) and is mostly associated with glycine receptor antibodies. The PERM has an acute or subacute course, with complex and varied initial symptoms mainly manifest as stiffness and pain. The authors present the case of a male patient admitted for intractable stiffness and paroxysmal myoclonus of the lower extremities preceded by a 5-day history of facial weakness. After admission, his symptoms deteriorated rapidly. He developed progressive generalized hypertonia and painful spasms, which quickly spread to the upper extremities, and he suffered frequent paroxysmal myoclonus. Serum and cerebrospinal fluid (CSF) were tested by a cell-based assay, and both were positive for glycine receptor antibodies (GlyR-Abs). The patient developed complications, such as crushed teeth, lumbar vertebral compression fractures, and psoas major muscle abscess, during rapid disease progression, although he responded well after being treated with intravenous methylprednisolone and immunoglobulin. This report of PERM, initiated as facial palsy followed by acute progression, helps to expand the clinical spectrum of this rare autoimmune disorder and raise awareness of the prevention of complications.
The Feasibility of a Web-Based Educational Lifestyle Program for People With Multiple Sclerosis: A Randomized Controlled Trial

Background Modifiable lifestyle factors are important to aid people with multiple sclerosis in the self-management of their disease. Current self-management programs are limited by their face-to-face mode of delivery but there is immense potential with the internet to deliver these programs effectively. Objective The aims of this study are to assess the feasibility of a digitalized educational lifestyle self-management program for people with MS. Methods In this randomized controlled trial, people with MS were randomly allocated to participate in a 6-week tailored web-based educational lifestyle program or 6-week generic standard-care educational course, and were blinded to their allocation. Participants were recruited through multiple sclerosis (MS) Societies in four countries: Australia, New Zealand, Canada, and the United States. The primary outcome was to assess acceptability of the program defined as percentage completion of all modules at 6-weeks post-course commencement. Secondary outcomes included evaluating participant responses to the follow-up survey across three domains: accessibility, learnability, and desirability. Results Thirty-five participants from Australia, Canada, New Zealand, and the US completed the baseline survey and were randomized. Four participants were deemed ineligible due to incomplete baseline data; therefore, nine out of 15 and eight out of 16 participants completed 100% of the course in the intervention and standard-care arm courses, respectively. Conclusions This study found that this web-based educational lifestyle program is a feasible means of delivering educational content to people with MS via the internet according to our a priori targets of >40% of participants in the intervention arm, and >25% in the control arm to completing 100% of the course. It is therefore appropriate to evaluate this intervention further in a large, randomized controlled trial. Trial registration This study was prospectively registered with the Australian New Zealand Clinical Trials Registry (ID: ACTRN12621000245897).
Combination of Genome-Scale Models and Bioreactor Dynamics to Optimize the Production of Commodity Chemicals

The current production of a number of commodity chemicals relies on the exploitation of fossil fuels and hence has an irreversible impact on the environment. Biotechnological processes offer an attractive alternative by enabling the manufacturing of chemicals by genetically modified microorganisms. However, this alternative approach poses some important technical challenges that must be tackled to make it competitive. On the one hand, the design of biotechnological processes is based on trial-and-error approaches, which are not only costly in terms of time and money, but also result in suboptimal designs. On the other hand, the manufacturing of chemicals by biological processes is almost exclusively carried out by batch or fed-batch cultures. Given that batch cultures are expensive and not easy to scale, technical means must be developed to make continuous cultures feasible and efficient. In order to address these challenges, we have developed a mathematical model able to integrate in a single model both the genome-scale metabolic model for the organism synthesizing the chemical of interest and the dynamics of the bioreactor in which the organism is cultured. Such a model is based on the use of Flexible Nets, a modeling formalism for dynamical systems. The integration of a microscopic (organism) and a macroscopic (bioreactor) model in a single net provides an overall view of the whole system and opens the door to global optimizations. As a case study, the production of citramalate with respect to the substrate consumed by E. coli is modeled, simulated and optimized in order to find the maximum productivity in a steady-state continuous culture. The predicted computational results were consistent with the wet lab experiments.
Dietary Flavonoids as Modulators of Lipid Metabolism in Poultry

Flavonoids, naturally-occurring compounds with multiple phenolic structures, are the most widely distributed phytochemicals in the plant kingdom, and are mainly found in vegetables, fruits, grains, roots, herbs, and tea and red wine products. Flavonoids have health-promoting effects and are indispensable compounds in nutritional and pharmaceutical (i.e., nutraceutical) applications. Among the demonstrated bioactive effects of flavonoids are anti-oxidant, anti-inflammatory, and anti-microbial in a range of research models. Through dietary formulation strategies, numerous flavonoids provide the ability to support bird health while improving the nutritional quality of poultry meat and eggs by changing the profile of fatty acids and reducing cholesterol content. A number of such compounds have been shown to inhibit adipogenesis, and promote lipolysis and apoptosis in adipose tissue cells, and thereby have the potential to affect fat accretion in poultry at various ages and stages of production. Antioxidant and anti-inflammatory properties contribute to animal health by preventing free radical damage in tissues and ameliorating inflammation in adipose tissue, which are concerns in broiler breeders and laying hens. In this review, we summarize the progress in understanding the effects of dietary flavonoids on lipid metabolism and fat deposition in poultry, and discuss the associated physiological mechanisms.
Synapse Formation and Function Across Species: Ancient Roles for CCP, CUB, and TSP-1 Structural Domains

The appearance of synapses was a crucial step in the creation of the variety of nervous systems that are found in the animal kingdom. With increased complexity of the organisms came a greater number of synaptic proteins. In this review we describe synaptic proteins that contain the structural domains CUB, CCP, or TSP-1. These domains are found in invertebrates and vertebrates, and CUB and CCP domains were initially described in proteins belonging to the complement system of innate immunity. Interestingly, they are found in synapses of the nematode C. elegans, which does not have a complement system, suggesting an ancient function. Comparison of the roles of CUB-, CCP-, and TSP-1 containing synaptic proteins in various species shows that in more complex nervous systems, these structural domains are combined with other domains and that there is partial conservation of their function. These three domains are thus basic building blocks of the synaptic architecture. Further studies of structural domains characteristic of synaptic proteins in invertebrates such as C. elegans and comparison of their role in mammals will help identify other conserved synaptic molecular building blocks. Furthermore, this type of functional comparison across species will also identify structural domains added during evolution in correlation with increased complexity, shedding light on mechanisms underlying cognition and brain diseases.
Effect of Digital Financial Inclusion on Dredging the Path of Green Growth—New Evidence From Front-End and Back-End Perspectives

To dredge China’s green growth path, this paper analyzes the front-end and back-end factors affecting green growth and also investigates the mediation role of digital financial inclusion from different dimensions. This study employs China’s provincial panel data in 2011–2018 and uses the dynamic threshold model to study the threshold effect of technological progress (TP) on green growth (GG) and the threshold effect of green growth (GG) on floating population (FP). The empirical results show that: first, with the digital financial inclusion as the threshold variable, there is a nonlinear relationship between technological progress (TP) and green growth (GG); second, with digital financial inclusion as the threshold variable, there is a nonlinear relationship between green growth (GG) and floating population (FP); third, output biased technological progress needs more support from digital financial inclusion than input biased technological progress than can significantly promote green growth. From the dimension of “digitization+financial scale+inclusion” digital financial inclusion not only improves the positive effect of technological progress on green growth but also alleviates the negative effect of green growth on the floating population. This study makes up for the research gap in the back-end impact of green growth based on new ideas of digital financial inclusion and floating population and has important theoretical reference significance for removing the obstacles in the green development path and realizing sustainable green growth.
Trends in HIV Prevalence and HIV-Related Risk Behaviors Among Male Students Who Have Sex With Men From 2016 to 2020 in Nanjing, China: Consecutive Cross-Sectional Surveys

Background The growing HIV epidemic among student men who have sex with men (MSM) necessitates immediate attention from public health. In China, male students who have sex with men (SMSM) were also at an increasing risk of HIV transmission. The aim of this study was to investigate the trends in HIV prevalence, HIV-related risk behaviors, and HIV testing, as well as analyze the factors associated with HIV infection among SMSM in Nanjing. Methods Data were collected through face-to-face questionnaire interviews and laboratory testing in Nanjing. The participants were recruited among SMSM by snowball sampling and internet-recruited convenience sampling annually from 2016 to 2020. The self-report data primarily included demographics, HIV knowledge, HIV-related behaviors, and HIV testing, while the laboratory test results of HIV and syphilis were collected. Linear-by-linear chi-square test was used to analyze the trends of HIV/syphilis prevalence and its risk behaviors. The binary logistic regression model was used to explore the factors associated with HIV infection. Results During the 5 years from 2016 to 2020, a total of 775 SMSM were recruited in our survey (220, 112, 171, 142, and 120, respectively). The HIV prevalence was 5.2, 6.3, 5.3, 7.0, and 8.3%, without a significant increasing trend (P = 0.277). Syphilis prevalence fluctuated from 5.7% in 2016 to 4.2% in 2020, without a significant decreasing trend (P = 0.318). The proportion of consistent condom use in anal intercourse (48.5 to 56.2%, P < 0.05), and HIV testing in the past 12 months (51.0 to 59.2%, P < 0.05) were increasing. A remarkable growing trend has been reported in the percentage of MSM with more than one male sex partner (46.2 to 59.2%, P < 0.05). Multivariate analysis showed that HIV testing in the past 12 months was a protective factor against HIV infection. MSM who had unprotected anal intercourse (UAI) in the past 6 months, recreational drug use, and currently syphilis infection were risk factors for HIV infection. Conclusions We observed stable HIV/ syphilis prevalence, increasing consistent condom use, increasing HIV testing rate, and increasing multiple male sex partners dramatically among SMSM in China. The original comprehensive intervention measures should be continuously strengthened for the subgroup. To satisfy the current HIV prevention requirements, new biological interventions should be introduced and carried out as major components of combination prevention programs.
Barriers Impeding Active Mixing of Swimming Microbes in a Hyperbolic Flow

We present experiments on the motion of swimming microbes in a laminar, hyperbolic flow. We test a theory that predicts the existence of swimming invariant manifolds (SwIMs) that act as invisible, one-way barriers that block the motion of the microbes. The flow is generated in a cross-channel in a PDMS cell, driven by syringe pumps. The swimming microbes are euglena and tetraselmis, both single-celled, eukaryotic algae. The algae are not ideal smooth-swimmers: there is significant rocking in their motion with occasional tumbles and a swimming speed that can vary. The experiments show that the swimming algae are bound very effectively by the predicted SwIMs. The different shapes and swimming behavior of the euglena and tetraselmis affect the distribution of swimming angles, with the elongated euglena having a larger probability of swimming in a direction parallel to the outflow directions. The differences in swimming orientation affect the ability of the microbes to penetrate the manifolds that act as barriers to passive tracers. The differing shapes of the euglena and tetraselmis also affect probabilities for the microbes to escape in one direction or the other along the outflow.
Mechanisms of Salt Tolerance and Molecular Breeding of Salt-Tolerant Ornamental Plants

As the area of salinized soils increases, and freshwater becomes more scarcer worldwide, an urgent measure for agricultural production is to use salinized land and conserve freshwater resources. Ornamental flowering plants, such as carnations, roses, chrysanthemums, and gerberas, are found around the world and have high economic, ornamental, ecological, and edible value. It is therefore prudent to improve the salt tolerance of these important horticultural crops. Here, we summarize the salt-adaptive mechanisms, genes, and molecular breeding of ornamental flowering crops. We also review the genome editing technologies that provide us with the means to obtain novel varieties with high salinity tolerance and improved utility value, and discuss future directions of research into ornamental plants like salt exclusion mechanism. We considered that the salt exclusion mechanism in ornamental flowering plants, the acquisition of flowers with high quality and novel color under salinity condition through gene editing techniques should be focused on for the future research.
Calcium Mediated Cold Acclimation in Plants: Underlying Signaling and Molecular Mechanisms

Exposure of plants to low temperatures adversely affects plant growth, development, and productivity. Plant response to cold stress is an intricate process that involves the orchestration of various physiological, signaling, biochemical, and molecular pathways. Calcium (Ca2+) signaling plays a crucial role in the acquisition of several stress responses, including cold. Upon perception of cold stress, Ca2+ channels and/or Ca2+ pumps are activated, which induces the Ca2+ signatures in plant cells. The Ca2+ signatures spatially and temporally act inside a plant cell and are eventually decoded by specific Ca2+ sensors. This series of events results in the molecular regulation of several transcription factors (TFs), leading to downstream gene expression and withdrawal of an appropriate response by the plant. In this context, calmodulin binding transcription activators (CAMTAs) constitute a group of TFs that regulate plant cold stress responses in a Ca2+ dependent manner. The present review provides a catalog of the recent progress made in comprehending the Ca2+ mediated cold acclimation in plants.
Computation of Optical Properties of Core-Shell Super-Spheroids Using a GPU Implementation of the Invariant Imbedding T-Matrix Method

Particles with internal inclusions or cores are ubiquitous in the atmosphere. One example is dust particles coated with water-soluble aerosols such as sulfate or nitrate. For these particles, the dust non-sphericity and the core-shell structure of the particle both fundamentally impact the optical properties. However, it is challenging to obtain an accurate and comprehensive parameterization of the optical properties of coated atmospheric particles. Recent studies have found that super-spheroids could provide a robust model for representing the non-sphericity of irregular particles, such as dust, sea salt, and ice particles. This important finding warrants further investigations on coated super-spheroids for the development of mixed-aerosol models. In this study, we developed a GPU version of the invariant imbedding T-matrix program (GPU-IITM) to improve the computational efficiency. This version allows for efficient computation of the optical properties of coated super-spheroids with extensive shape parameters and refractive indices. The GPU-IITM is 8–25 times more efficient than the conventional CPU-IITM, depending on the size parameter of the coated super-spheroids. The single-scattering properties of coated super-spheroids computed from the GPU-IITM allows for close examination of the optical differences between homogeneous and inhomogeneous particles. As an example, we present the linear depolarization ratios (LDRs) of coated super-spheroids, which have implications in active lidar remote-sensing research. We found that the LDR decreases obviously as the real part of the shell’s refractive index increases from 1.3 to 1.6. Greater LDRs occur for particles with a thin coating, while a rounder shape of the particle decreases the LDRs. However, special attention should be given to nearly spherical particles, for which the LDRs could be enhanced. In comparison to homogeneous particles, the degree of enhancement decreases or increases depending on whether the shell’s refractive index is smaller or larger than the core refractive index.
Prevalence of Bullying Behaviors Among Students From a National University in the United Arab Emirates: A Cross-Sectional Study

Background This study aims to investigate bullying behaviors among college students at one of the national universities in UAE, and also to examine the psychological characteristics of those who were exposed to, or have experienced bullying. Methods A cross-sectional study was conducted on 839 undergraduate students at one of the national universities in the UAE. Students from all colleges participated in this study and were selected by using stratified random sampling. Participants completed a bullying survey designed for the study, in addition to three psychological measures [i.e., Aggression Questionnaire, Buss and Perry, 1992; The Primary Care Anxiety and Depression, El-Rufaie et al., 1997; and the Post Traumatic Stress Disorder (PTSD) for Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition (PCL-5), Weathers et al., 2013]. Results The prevalence rate of students being exposed to or engaged in bullying was 26.3% (221 out of 839). Of those, 72 students (8.7%) reported being bullied, 29 (3.6%) reported bullying others, and 185 (22.8%) reported witnessing friends being bullied. The most common types of bullying reported were traditional bullying (e.g., face-to-face bullying, verbal, and physical). Cyberbullying was not very common. More females reported being bullied in comparison to males and most of the aggressors were peer students. Overall, moderate level of aggressive personality traits and low levels of symptoms of depression, anxiety, and PTSD were reported for the total sample. T-tests revealed significant differences in the three psychological measures between those who did not experience bullying and those who did. The mean scores on the Aggression Questionnaire for those who bullied others were significantly higher than those who did not experience bullying. Conclusion Experiences of bullying seem to impact college students’ mental health in the UAE. Therefore, efforts need to focus on developing preventive programs to increase students’ awareness of bullying and its negative impact on campus environment. Offering psychological help for those who were exposed to bullying would help them to deal effectively with this trauma.