Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping UPR elements in male reproductive system: a bioinformatics approach

The unfolded protein response (UPR) is an essential cell defense response against defects in protein folding and it is mainly triggered by the activation of ATF6, PERK and IRE1. Each sensor leads to different signal transduction mechanisms through the production of transcription factors that, in turn, regulate genes that increase the cell's ability to correct conformation of poorly folded proteins, ultimately hindering their aggregation. The past years shed light on the role of the UPR in several diseases. Regarding male infertility, few studies have focused on the implications of UPR components, hence the need to a prior approach concerning the presence of these components on the male reproductive system. Through a database search and using bioinformatics approaches, with the aim of identifying potential candidates associated with infertility phenotypes, a collection of UPR proteins in the testis, spermatozoa and seminal plasma was performed. To determine potential targets to scrutinize possible involvement in male infertility, a protein-protein interaction network analysis was performed, depicting 6 key proteins highly interconnected: HSP90AA1, HSPA5, SEC61A1, VCP, PERK and ATF4. Considering their functional value, the effector proteins of the PERK pathway, GADD34 and eIF2 were highlighted for experimental studies. Thus, the presence of the PERK and GADD34 were confirmed for the first time in human spermatozoa. These results constitute the first fundamental step towards further studies on the expression and activity levels of these candidates and understand their contribution to the UPR signaling pathway and their possible deregulation in male infertility. Mapping UPR elements in male reproductive system: A bioinformatics approach University of Aveiro, Department of Medical Sciences i CONTENTS
Global Dissipation Models for Simulating Tsunamis at Far-Field Coasts up to 60 hours Post-Earthquake: Multi-Site Tests in Australia

At far-field coasts the largest tsunami waves may occur many hours post-arrival, and hazardous waves may persist for more than 1 day. Such tsunamis are often simulated by nesting high-resolution nonlinear shallow water models (covering sites of interest) within low-resolution reduced-physics global-scale models (to efficiently simulate propagation). These global models often ignore friction and are mathematically energy conservative, so in theory the modeled tsunami will persist indefinitely. In contrast, real tsunamis exhibit slow dissipation at the global-scale with an energy e-folding time of approximately 1 day. How strongly do these global-scale approximations affect nearshore tsunamis simulated at far-field coasts? To investigate this we compare modeled and observed tsunamis at sixteen nearshore tide-gauges in Australia, generated by the following earthquakes: M w 9.5 Chile 1960; M w 9.2 Sumatra 2004; M w 8.8 Chile 2010; M w 9.1 Tohoku 2011; and M w 8.3 Chile 2015. Each tsunami is represented using multiple published source models, to prevent bias in any single source from dominating the results. Each tsunami is simulated for 60 h with a nested global-to-local model. On nearshore grids we solve the nonlinear shallow water equations with Manning-friction, while on the global grid we test three reduced-physics propagation models which combine the linear shallow water equations with alternative treatments of friction: 1) frictionless; 2) nonlinear Manning-friction; and 3) constant linear-friction. Compared with data, the frictionless global model well simulates nearshore tsunami maxima for ≃ 8 h after tsunami arrival, and Manning-friction gives similar predictions in this period. Constant linear-friction underestimates the size of early arriving waves. As the simulation duration is increased from 36 to 60 h, the frictionless model increasingly overestimates observed wave heights, whereas models with global-scale friction work relatively well. The constant linear-friction model can be improved using delayed-linear-friction, where propagation is simulated with an initial frictionless period (12 h herein). This prevents systematic underestimation of early wave heights. While nonlinear Manning-friction offers comparably good performance, a practical advantage of the linear-friction models herein is that solutions can be computed, to high accuracy, via a simple transformation of frictionless solutions. This offers a pragmatic approach to improving unit-source based global tsunami simulations at late times.
Process noise distinguishes between indistinguishable population dynamics

Model selection is becoming increasingly important in mathematical biology. Model selection often involves comparing a set of observations with predictions from a suite of continuum mathematical models and selecting the model that provides the best explanation of the data. In this work we consider the more challenging problem of model selection in a stochastic setting. We consider five different stochastic models describing population growth. Through simulation we show that all five stochastic models gives rise to classical logistic growth in the limit where we consider a large number of identically prepared realisations. Therefore, comparing mean data from each of the models gives indistinguishable predictions and model selection based on population-level information is impossible. To overcome this challenge we extract process noise from individual realisations of each model and identify properties in the process noise that differ between the various stochastic models. Using a Bayesian framework, we show how process noise can be used successfully to make a probabilistic distinction between the various stochastic models. The relative success of this approach depends upon the identification of appropriate summary statistics and we illustrate how increasingly sophisticated summary statistics can lead to improved model selection, but this improvement comes at the cost of requiring more detailed summary statistics.
Hyperanalyticity of space-time

New mathematical object - hyperanalytic function is introduced. The convergence of hyperanalytic functions is substantially above than the convergence of analytic functions. A specific sample of hyperanalytic function is the reticulum function (RF). This function describes the reticulum space-time. RF can't be decomposed into the Fourier series and, therefore, RF does not provide the conservation of parity as the analytic functions do. Thanks to this, the RF can be decomposed in an endless series of two primitive hyperanalytic functions by sequential attempts of decomposition in the even and odd functions. The unique parameter of such series is the fine structure constant $\alpha$. It allows combine all fundamental interactions into the Naturally-Unified Quantum Theory of Interactions. The price of such quantum unification is the reticulum space-time.
Screening of Mungbean Genotypes for Drought Tolerance Using Different Water Potential Levels

Drought is one of the limiting factors for better plant performance and higher yield. New variety selection is difficult due to the wide range of plant stress responses with overlapping functions between their components creating complex mechanisms of resistance. One of the prerequisites for successful breeding for drought tolerance is availability of reliable methods for screening of desirable genotypes. Classical breeding may be complemented with laboratory methods creating models for simulation of water deficiency and drought conditions. Studies were conducted to find out the effect of reduced water potential treatments on germination and five seedling growth related characters viz., plumule length, radicle length, fresh and dry weight of plumule and radicle and vigour index in mungbean genotypes. In laboratory experiments, water deficiency was simulated by polyethylene glycol (PEG) of MW 6000 in the following concentrations viz., -0.4, -0.6 and -0.8 MPa for seed germination. A linear reduction in germination, shoot and root length, and their corresponding fresh and dry weight was observed for the genotypes as the concentration of PEG increased. The level of the negative effect of the osmoticum on developmental processes was genotype and the reduced water potential dependent. Amongst screened mungbean genotypes, genotype SML-837 recorded no germination at -0.8MPa and this would be critical level of water stress for mungbean whereas genotypes with higher germination index SML-1411 and SML-1136 were found to possess higher level of tolerance to drought.
Glass sponge grounds on the Scotian Shelf and their associated biodiversity

Emerald Basin on the Scotian Shelf off Nova Scotia, Canada, is home to a globally unique population of the glass sponge Vazella pourtalesi. Through the analysis of both in situ photo graphs and trawl catch data from annual multispecies bottom-trawl surveys, we examined community composition, species density, and abundance of epibenthos and fish associated with V. pourtalesi compared to locations without this sponge. Using generalized linear models and analysis of similarities, the importance of V. pourtalesi in enhancing species density and abundance of the associated epibenthic community was assessed against that of the hard substrate on which it settles. Our results indicated that the megafaunal assemblage associated with V. pourtalesi was significantly different in composition and higher in species density and abundance compared to locations without V. pourtalesi. Analysis of similarity of trawl catch data indicated that fish communities associated with the sponge grounds are significantly different from those without V. pourtalesi, although no species were found exclusively on the sponge grounds. Our study provides further evidence of the role played by sponge grounds in shaping community structure and biodiversity of associated deep-sea epibenthic and fish communities. The mechanism for biodiversity enhancement within the sponge grounds formed by V. pourtalesi is likely the combined effect of both the sponge itself and its attachment substrate, which together comprise the habitat of the sponge grounds. We also discuss the role of habitat provision between the mixed-species tetractinellid sponges of the Flemish Cap and the monospecific glass sponge grounds of Emerald Basin.
Single cell ATAC-seq identifies broad changes in neuronal abundance and chromatin accessibility in Down Syndrome

Down Syndrome (DS) is caused by triplication of chr21 and is associated with cognitive impairment, Alzheimer’s Disease, and other developmental alterations. The Ts65Dn mouse model for DS has triplication of sequences syntenic with human chr21, and traits resembling those seen in humans with DS. We performed single-cell combinatorial indexing assay for transposase accessible chromatin using sequencing (sci-ATAC-seq) on cortices of adult Ts65Dn mice and control littermates. Analyses of 13,766 cells revealed 26 classes of cells. The most abundant class of excitatory neurons was reduced by 17% in Ts65Dn mice, and three of the four most common classes of interneurons were increased by 50%. Ts65Dn mice display changes in accessibility at binding motifs for transcription factors that are determinants of neuronal lineage, and others encoded within triplicated regions. These studies define previously uncharacterized cellular and molecular features of DS, and potential mechanisms underlying the condition.
Effects of dietary yeast beta-1,3-1,6-glucan on growth performance, intestinal morphology and chosen immunity parameters changes in Haidong chicks

Objective This study investigated the effects of 1,3-1,6 beta-glucan added to the diet of Haidong chicks reared under hypoxic conditions, to ascertain the growth performances, immunity and intestinal morphology changes. Methods A total of 750 chicks were divided into five groups and fed diets containing 0.5 g/kg, 1.0 g/kg, and 2.0 g/kg 1,3-1,6 beta-glucan from yeast (G1, G2, G3, respectively), 0.2 g/kg Taylor rhizomorph and a control feed. Results The body weight and body weight gain were higher in chicks fed 1,3-1,6 beta-glucan and Taylor rhizomorph than in control group. Feed conversion ratio significantly differed for G2 and G3 groups in comparison to control group. The relative weight of bursa was higher in G1, G2, and G3 groups. The white blood cells and lymphocytes were significantly increased in groups fed 1,3-1,6 beta-glucan. The immunoglobulin G of serum peak appeared in the G3 group. The villous height of the duodenum was higher in 1,3-1,6 beta-glucan feed groups. In the jejunum, the villous height was higher in G2 and G3 groups and crypt depth for all the groups fed β-glucan. At ileum level the villous height and crypt depth was higher for groups G1, G2, and G3. Conclusion The growth performance of Haidong chicks is improved when 10 and 20 g/kg 1,3-1,6 beta-glucan is included in the diet; hence, it is suggested that 1,3-1,6 beta-glucan be included in poultry diet to reduce and replace the use of antibiotics.
Age- and Sex-Specific Prevalence and Modifiable Risk Factors of Mild Cognitive Impairment Among Older Adults in China: A Population-Based Observational Study

Background Minimal data are available on the prevalence of mild cognitive impairment (MCI) in older Chinese adults. Moreover, the current information on MCI shows important geographical variations. Objective We aimed to assess the prevalence and risk factors for MCI by age and sex among older adults in a North Chinese population. Methods In this population-based cross-sectional study, we enrolled a random sample of 4,943 adults aged ≥ 60 years between March 2018 and June 2019 in Tianjin, China. Of these, 312 individuals were excluded due to a lack of data (e.g., fasting blood test). As a result, 4,631 subjects were assessed. Individuals with MCI were identified using neuropsychological assessments, including the Mini-Mental State Examination and Activities of Daily Living scale, based on a modified version of the Petersen’s criteria. Results The mean (SD) age of the 4,631 participants was 67.6 (4.89) years, and 2,579 (55.7%) were female. The overall age- and sex-standardized prevalence of MCI in our study population was 10.7%. There were significant associations of MCI with age [65–69 vs. 60–64 years, OR = 0.74; 95% confidence interval (CI): 0.58, 0.96], physical activity (≥23.0 vs. <23.0 MET-hours/week, OR = 0.79; 95% CI: 0.64, 0.96), body mass index (BMI) (OR = 0.92; 95% CI: 0.89, 0.95), grip strength (OR = 0.50; 95% CI: 0.38, 0.67), hypertension (yes vs. no, OR = 1.44; 95% CI: 1.18, 1.77), higher levels of sleepiness (OR = 1.80; 95% CI: 1.36, 2.37), and longer sleep duration (OR = 1.40; 95% CI: 1.14, 1.72). The inverse association between BMI and MCI was stronger in older age groups (P for heterogeneity = 0.003). Moreover, the magnitude of association between triglycerides and MCI was different between the sexes (P for heterogeneity = 0.029). Conclusion The age- and sex-standardized prevalence of MCI was 10.7% in the study sample. Physical activity, BMI, grip strength, sleepiness, sleep duration, and hypertension were associated with the prevalence of MCI. Additionally, triglycerides and BMI might be differently associated with the presence of MCI for different sexes and age stages, respectively.
Polarity Establishment and Maintenance in Ascidian Notochord

Cell and tissue polarity due to the extracellular signaling and intracellular gene cascades, in turn, signals the directed cell behaviors and asymmetric tissue architectures that play a crucial role in organogenesis and embryogenesis. The notochord is a characteristic midline organ in chordate embryos that supports the body structure and produces positioning signaling. This review summarizes cellular and tissue-level polarities during notochord development in ascidians. At the early stage, planar cell polarity (PCP) is initialized, which drives cell convergence extension and migration to form a rod-like structure. Subsequently, the notochord undergoes a mesenchymal-epithelial transition, becoming an unusual epithelium in which cells have two opposing apical domains facing the extracellular lumen deposited between adjacent notochord cells controlled by apical-basal (AB) polarity. Cytoskeleton distribution is one of the main downstream events of cell polarity. Some cytoskeleton polarity patterns are a consequence of PCP: however, an additional polarized cytoskeleton, together with Rho signaling, might serve as a guide for correct AB polarity initiation in the notochord. In addition, the notochord’s mechanical properties are associated with polarity establishment and transformation, which bridge signaling regulation and tissue mechanical properties that enable the coordinated organogenesis during embryo development.
Patterning a Leaf by Establishing Polarities

Leaves are the major organ for photosynthesis in most land plants, and leaf structure is optimized for the maximum capture of sunlight and gas exchange. Three polarity axes, the adaxial–abaxial axis, the proximal-distal axis, and the medial-lateral axis are established during leaf development to give rise to a flattened lamina with a large area for photosynthesis and blades that are extended on petioles for maximum sunlight. Adaxial cells are elongated, tightly packed cells with many chloroplasts, and their fate is specified by HD-ZIP III and related factors. Abaxial cells are rounder and loosely packed cells and their fate is established and maintained by YABBY family and KANADI family proteins. The activities of adaxial and abaxial regulators are coordinated by ASYMMETRIC LEAVES2 and auxin. Establishment of the proximodistal axis involves the BTB/POZ domain proteins BLADE-ON-PETIOLE1 and 2, whereas homeobox genes PRESSED FLOWER and WUSCHEL-RELATED HOMEOBOX1 mediate leaf development along the mediolateral axis. This review summarizes recent advances in leaf polarity establishment with a focus on the regulatory networks involved.
TruSight Oncology 500: Enabling Comprehensive Genomic Profiling and Biomarker Reporting with Targeted Sequencing

Background As knowledge of mechanisms that drive the development of cancer grows, there has been corresponding growth in therapies specific to a mechanism. While these therapies show improvements in patient outcomes, they can be expensive and are effective only for a subset of patients. These treatments drive interest in research focused on the assignment of cancer therapies based on aberrations in individual genes or biomarkers that assess the broader mutational landscape, including microsatellite instability (MSI) and tumor mutational burden (TMB). Methods Here we describe the TruSight™ Oncology 500 (TSO500; Research Use Only) bioinformatics workflow. This tumor-only approach leverages the next-generation sequencing-based assay TSO500 to enable high fidelity determination of DNA variants across 523 cancer-relevant genes, as well as MSI status and TMB in formalin-fixed paraffin-embedded (FFPE) samples. Results The TSO500 bioinformatic workflow integrates unique molecular identifier (UMI)-based error correction and a dual approach variant filtering strategy that combines statistical modeling of error rates and database annotations to achieve detection of variants with allele frequency approaching 5% with 99.9998% per base specificity and 99% sensitivity in FFPE samples representing a variety of tumor types. TMB determined using the tumor-only workflow of TSO500 correlated well with tumor-normal (N =170, adjusted R2=0.9945) and whole-exome sequencing (N=108, adjusted R2=0.933). Similarly, MSI status determined by TSO500 showed agreement (N=106, 98% agreement) with a MSI-PCR assay. Conclusion TSO500 is an accurate tumor-only workflow that enables researchers to systematically characterize tumors and identify the next generation of clinical biomarkers.
Resonance Raman Spectra for the In Situ Identification of Bacteria Strains and Their Inactivation Mechanism

The resonance Raman spectra of bacterial carotenoids have been employed to identify bacterial strains and their intensity changes as a function of ultraviolet (UV) radiation dose have been used to differentiate between live and dead bacteria. In addition, the resonance-enhanced Raman spectra enabled us to detect bacteria in water at much lower concentrations (∼108 cells/mL) than normally detected spectroscopically. A handheld spectrometer capable of recording resonance Raman spectra in situ was designed, constructed, and was used to record the spectra. In addition to bacteria, the method presented in this paper may also be used to identify fungi, viruses, and plants, in situ, and detect infections within a very short period of time. Graphical Abstract
The effect of six weeks’ massage in water on walking speed, postural control, pain intensity, fatigue and quality of life in women with multiple sclerosis

Aims and background: Nowadays, multiple sclerosis disorder has been increased. The aim of this study was to investigate the effect of six weeks of massage in water on walking speed, postural control, pain intensity, fatigue and quality of life in women with multiple sclerosis in Khomeini city. Materials and methods: In this study, a trial was performed in which 30 patients with multiple sclerosis (EDSS 2-5) were randomly selected and randomly assigned to two blind groups of 15 patients. The massage group was in water (mean age 39.60 ± 8.33, 160 ± 6.04 cm and body weight 26.59 ± 3.74 cm2 and control group 36 ± 6.56 years, Height 158.86±2.92 cm, and body mass 26.95 ± 2.33 kg/m2). The experimental group performed a massage therapy program in water for six weeks, three sessions per week and the duration of 20 minutes for lower extremities (thighs, knees, legs, wrists and feet), the control group performed the natural activities of daily living, before and after the training, speed of walking with rocket test, static and dynamic equilibrium Arranged by a modified stamina and Y test, pain intensity by visual acuity scale, Fatigue was assessed by MFIS questionnaire and quality of life by SF scale of 36 The data were refined using descriptive statistics. Measurement of the nature of the data was performed by Shapiro-Wilk test and data analysis was used to compare the independent t-test. Also, SPSS version 25 was used. The significance level was considered as (p<0.05). Finding: The results of the study showed that six weeks of massage in water had a significant effect on walking speed, postural control (static and dynamic balance), pain intensity, fatigue and quality of life in women with multiple sclerosis (p<0.05). Conclusion: Based on this study, it can be concluded that water massage could be effective for people with multiple sclerosis. Therefore, massage therapists are to be advised to use these rehab techniques to improve walking speed, postural control (static and dynamic balance), pain intensity, fatigue, and quality of life in people with multiple sclerosis.