Miracle-dz/UniFAR-FTUs huggingface dataset:
Using the Bayesian Normal Gamma prior to identify associated sequence variants

The Normal Gamma prior, a Bayesian adaptive shrinkage method which is implemented using MCMC, is compared to other statistical methods as an eQTL approach to identifying causal or associated genetic mutations. The methods are compared on simulated data, where the results show the Normal Gamma prior to be a far superior method. On human data it is more difficult to assess the results for accuracy, but we can conclude that the Normal Gamma prior highlights SNPs in concordance with other methods. We also note that the Normal Gamma prior, although enforcing very harsh shrinkage, reports many less false positive SNPs than other methods. We develop the Normal Gamma prior to include functional information which we use to differentially penalise synonymous and nonsynonymous SNPs, as well as intronic, intergenic, splicing, UTR3 and other SNPs where necessary. In initial simulation studies, the prior distribution penalises synonymous SNPs on average more than non-synonymous SNPs. Further developments increase the penalisation on intronic, intergenic, UTR3, synonymous and other SNPs more than splicing and non-synonymous SNPs due to larger functional significance scores for the latter. The effect of this on the differential shrinkage between the two sets of SNPs can be seen in the posterior rankings and effect size estimates. We believe that this differential shrinkage form of the Normal Gamma prior is a powerful tool for detecting causal or associated SNPs, and has been shown to increase the posterior mean effect size estimates for causal SNPs with respect to the standard Normal Gamma, as well as increasing the ranking of validated causal SNPs (with respect to the standard Normal Gamma).
Information Technology for Chest XRay Images Analysis

This paper presents the research and development of information technology for analysis and classification of chest X-ray images in order to automatically detect the signs of the disease, specifically pneumonia, what is the most relevant in the conditions of COVID-19 pandemic. Information technology is based on the developed mathematical model through complex training of neural networks. The dataset used for the experimental studies and neural networks training consisted of 35,000 images ranging in size from 200×200 px to 2500×2500 px. Convolutional neural networks were used to fulfill the goal of software creation based on developed information technology. As a result of experiments, the weighted average value of F1 metric of 97.05% was obtained, that is close to the recognition rate of a physician. During the research the decision support software based on developed information technology was created with an aim to assist the physician in making a decision, help in the analysis of lungs X-rays for pneumonia, and also allow to store all the necessary information about the patients in one repository. The program was developed using Microsoft technologies, including the C# programming language and a technology environment designed to develop a user interface - WPF. Also, software was implemented using the MVVM architecture and ML.NET as a tool for implementation of a neural network. The Nvidia RTX 2070 Super graphics processor (GPU) and CUDA technology were used to train the neural network. Created software based on developed information technology for chest X-ray images analysis allows to record patients, classify and process images, add confirmations of physicians, and can be used as an accessory instrument to diagnose pneumonia, which will reduce the strain on the radiologist and allow to process larger number of X-rays images more effective.
Distribution of Action Potential Duration and T-wave Morphology: a Simulation Study

The results of a simulation study of the action potential duration (APD) distribution and T-wave morphology taking into account the midmyocardial cells (M-cells) concept are described. To investigate the effect of M-cells we present a computer model in which ion channel action potential formulations are incorporated into three-dimensional whole heart model. We implemented inhomogeneous continuous action potential duration distribution based on different distributions of maximal slow delayed rectifier current conductance. Using the proposed action potential distribution procedure midmural zeniths with longest action potential length were created as islands of model cells in the depth of thickest areas of ventricular tissue. Different spatial functions on layer indexes were simulated and their influences on electrocardiogram waveforms were analyzed. Changing parameters of ion channel model we varied duration of minimal and maximal action potential and investigated T-wave amplitude, Q-Tpeak and QT intervals variations. The study demonstrated that the proposed original APD distribution is reasonable and produces realistic electrocardiographic waveforms.
S1759078721001094jra 879..891

The paper proposes a system consisting of novel programmable system on chip (PSoC)controlled phase shifters which in turn guides the beam of an antenna array attached to it. Four antennae forming an array receive individual inputs from the programmable phase shifters (IC 2484). The input to the PSoC-based phase shifter is provided from an optimized 1:4 Wilkinson power divider. The antenna consists of an inverted L-shaped dipole on the front and two mirrored inverted L-shaped dipoles mounted on a rectangular conductive structure on the back which resonates in the ISM/Wi-Fi band (2.40–2.48 GHz). The power divider is designed to provide the feed to the phase shifter using a beamforming network while ensuring good isolation among the ports. The power divider has measured S11, S21, S31, S41, and S51 to be −14, −6.25, −6.31, −6.28, and −6.31 dB, respectively at a frequency of 2.45 GHz. The ingenious controller is designed in-house using a PSoC microcontroller to regulate the control voltage of individual phase shifter IC and generate progressive phase shifts. To validate the calibration of the in-house designed control circuit, the phased array is simulated using sp touchstone file of IC 2484. This designed control circuit exhibits low insertion loss close to −8.5 dB, voltage standing wave ratio of 1.58:1, and reflection coefficient (S11) is −14.36 dB at 2.45 GHz. Low insertion loss variations confirm that the phased-array antenna gives equal amplitude and phase. The beamforming radiation patterns for different scan angles (30, 60, and 90°) for experimental and simulated phased-array antenna are matched accurately showing the accuracy of the control circuit designed. The average experimental and simulated gain is 13.03 and 13.48 dBi respectively. The in-house designed controller overcomes the primary limitations associated with the present electromechanical phased array such as cost weight, size, power consumption, and complexity in design which limits the use of a phased array to military applications only. The current study with novel design and enhanced performance makes the system worthy of the practical use of phased-array antennas for common society at large.
A Novel Approach to Managing Lower Face Complexity in Signing Avatars

An avatar that produces legible, easy-to-understand signing is one of the essential components to an effective automatic signed/spoken translation system. Facial nonmanual signals are essential to natural signing, but unfortunately signing avatars still do not produce acceptable facial expressions, particularly on the lower face. This paper reports on an innovative method to create more realistic lip postures. The approach manages the complexity of creating lip postures, thus making fewer demands on the artists making them. The method will be integral to our efforts to develop libraries containing lip postures to support the generation of facial expressions for several sign languages.
The mechanism of maintaining intracellular homeostasis in the red alga Pyropia haitanensis under hyposaline stress

The cultivation of hyposaline-tolerant varieties of the red alga Pyropia haitanensis is not only conducive to expanding the area of intertidal seaweed cultivation, but also contributes to preventing eutrophication of coastal waters. Research on the mechanism of hyposaline tolerance of P. haitanensis is an important prerequisite for breeding hyposaline-tolerant varieties. Here, we used proteomics and targeted metabolomics technologies to identify the key proteins and metabolites in thalli of P. haitanensis that changed under two hyposaline stress treatments: 0‰, LSS 0; 5‰, LSS 5. Responses of thalli of P. haitanensis to hyposaline stress included to inhibit protein synthesis, recruit molecular chaperones, and enhance the removal of misfolded proteins to maintain the dynamic balance of protein folding and removal; the response was similar under hypersaline stress. Glycolysis was the main energy supply pathway, and thalli actively maintained the stability of the cell membrane under hyposaline stress, which was distinct from the response to hypersaline stress. Compared with the LSS 0 treatment, P. haitanensis exhibited a more adequate energy supply, more stable endoplasmic reticulum environment and more intact membrane system under the LSS 5 treatment. The results improve understanding of the hyposaline tolerance mechanism of intertidal seaweed and provide a theoretical basis for the development of hyposaline-tolerant varieties.
Activation of TRPC6 by AngⅡ Induces Podocyte Injury and Participates in Proteinuria of Nephrotic Syndrome

Background: Nephrotic syndrome (NS) is a common glomerular disease, and podocyte injury is the character of primary NS, usually caused by minimal change disease and membranous nephropathy. Podocytopathy is primarily associated with glomerular proteinuria. Losartan, an angiotensin receptor blocker (ARB), is commonly used in the treatment of NS, and the AngiotensinⅡ (AngⅡ)–transient receptor potential ion channel 6 (TRPC6) axis has been reported to act on podocytes to regulate proteinuria in NS. Therefore, the purpose of this study was to explore the relationship in between AngⅡ–TRPC6, podocyte injury, and proteinuria based on the adriamycin (ADR) NS rat model. Method: All male rats were divided into three groups: control group, model group, and ARB group. The rats in the model group were induced by ADR, and the rats in the ARB group received losartan after induction of renal injury for 4 weeks. The changes in parameters related to renal dysfunction, and glomerular and podocyte structural damage, such as AngⅡ, AngⅡ type I receptor (AT1R), TRPC6, CaN, Caspase-3, Nephrin, and Podocin, were analyzed. Furthermore, the kidneys were isolated for study via transmission electron microscopy (TEM), immunohistochemistry, and western blot (WB) after the rats were sacrificed. In vitro, immortalized mouse MPC5 podocytes were used to investigate the regulatory effect of flufenamic acid (Flu) and SAR7334 (SAR) on the AngⅡ-TRPC6 signaling axis. Flow cytometry and WB were conducted to determine the relationship between podocyte injury and AngⅡ-TRPC6. Results: In vivo results showed that NS rats developed massive albuminuria and abnormal renal function, accompanied by abnormally increased levels of AngⅡ, TRPC6, AT1R, and CaN and a decreased expression of actin molecules in podocytes, extensive fusion of foot processes (FP), loss of glomerular structural integrity, collapse of podocyte structure, and skeletal reorganization. In vitro experiments indicated that both AngⅡ and Flu (the specific agonist of TRPC6) stimulated the expressions of TRPC6, AT1R, and Caspase-3 in podocytes. The AngⅡ receptor–blocker losartan and TRPC6-specific inhibitor SAR blocked the overexpression of the aforementioned proteins. In addition, SAR also attenuated the degradation of podocyte structural proteins and inhibited the fluorescence intensity of intracellular calcium (Ca2+) and cell apoptosis. Conclusion: The involvement of AngⅡ in the occurrence of NS proteinuria may be related to podocyte injury induced by activated TRPC6.
Beluga (Delphinapterus leucas) response to personal watercraft and motorized whale watching vessels in the Churchill River estuary

As interest in tourism and conservation grows worldwide, whale-watching has become a popular means of educating the public about wildlife conservation. The short-term impact of ecotourism industries on observed species has been widely studied with findings that indicate responses are most often behavior alterations or avoidance. Close vessel interactions with beluga whales (Delphinapterus leucas) are a major draw for whale-watching ecotourism in Churchill, Manitoba, Canada. As the Churchill River estuary and surrounding waters are assessed for a Marine Protected Area, information on the response of belugas to vessels are needed to inform management. To assess this, an oblique time-lapse camera system with a 5-minute photo interval was set up overlooking a section of the Churchill River estuary that is shared by belugas and tourist vessels. Measurements calculated from photos were used to compare the distance between belugas and kayaks, paddleboards, motorboats, and Zodiac whale-watching vessels. These distances were compared to an expected distribution generated from locations of belugas in photos without the presence of vessels. We found evidence that belugas are attracted to kayaks, avoid paddleboards, and are neutral regarding motorboats and Zodiacs. This is the first study to quantify the behavioral response of cetaceans to tourist vessels using a camera system and a distance-based analysis. Results could inform the development of a site-specific management system that accounts for beluga-vessel relationships.
Salt-tolerant endophytic bacterium Enterobacter ludwigii B30 enhance bermudagrass growth under salt stress by modulating plant physiology and changing rhizosphere and root bacterial community

Osmotic and ionic induced salt stress suppresses plant growth. In a previous study, Enterobacter ludwigii B30, isolated from Paspalum vaginatum, improved seed germination, root length, and seedling length of bermudagrass (Cynodon dactylon) under salt stress. In this study, E. ludwigii B30 application improved fresh weight and dry weight, carotenoid and chlorophyll levels, catalase and superoxide dismutase activities, indole acetic acid content and K+ concentration. Without E. ludwigii B30 treatment, bermudagrass under salt stress decreased malondialdehyde and proline content, Y(NO) and Y(NPQ), Na+ concentration, 1-aminocyclopropane-1-carboxylate, and abscisic acid content. After E. ludwigii B30 inoculation, bacterial community richness and diversity in the rhizosphere increased compared with the rhizosphere adjacent to roots under salt stress. Turf quality and carotenoid content were positively correlated with the incidence of the phyla Chloroflexi and Fibrobacteres in rhizosphere soil, and indole acetic acid (IAA) level was positively correlated with the phyla Actinobacteria and Chloroflexi in the roots. Our results suggest that E. ludwigii B30 can improve the ability of bermudagrass to accumulate biomass, adjust osmosis, improve photosynthetic efficiency and selectively absorb ions for reducing salt stress-induced injury, while changing the bacterial community structure of the rhizosphere and bermudagrass roots. They also provide a foundation for understanding how the bermudagrass rhizosphere and root microorganisms respond to endophyte inoculation.
The association of Curcuma and Scutellaria plant extracts improves laying hen thermal tolerance and egg oxidative stability and quality under heat stress conditions

Chronic exposure to high ambient temperatures is detrimental to laying hen performance and egg quality. Plant secondary metabolites may alleviate effects, partly due to their antioxidant activities. Herein, we investigated the effects of dietary supplementation with a phytonutrient solution (PHYTO) consisting of a plant extract combination of Scutellaria baicalensis and Curcuma longa on young layers (25–32 wk of age) raised under naturally elevated temperature conditions. Four hundred, 24-wk-old Lohmann hens were allocated in 50 cages and, after a week of adaptation, were offered a diet either containing 2 g/kg of PHYTO or not, for 8 wk. Hen BW was measured at the beginning and end of the trial, and egg production and feed intake were recorded weekly. At week 32, four eggs per cage were collected to determine egg quality characteristics as well as the rate of lipid and albumen oxidation in fresh eggs. At the end of the trial, two hens per cage were blood sampled for assessment of biochemical markers, one of which was euthanized for histopathological evaluation of the liver and intestine and assessment of intestinal histomorphometry. The herbal mixture supplementation significantly increased egg production rate at weeks 28 and 29 and for the overall production period, and feed efficiency at weeks 26–29. In addition, the degree of liver necrosis and microvascular thrombosis was lower (P < 0.05) whereas intestinal villosity was greater in duodenal and jejunal segments (P < 0.05) in the PHYTO compared to the control group. Supplementation also reduced (P < 0.05) blood concentrations of corticosterone, alanine aminotransferase activity, and TBARS, and a reduction in catalase activity was observed. Egg quality characteristics were not affected, except for eggshell thickness, egg diameter, and eggshell breaking strength that were superior in the PHYTO group (P < 0.05). PHYTO supplementation significantly improved egg lipid oxidation status of fresh eggs. In conclusion, supplementation with PHYTO improved laying hen productivity and egg quality, which was associated with an improvement in laying hen thermotolerance.
Construction and Immunogenicity of a Recombinant Pseudorabies Virus Expressing SARS-CoV-2-S and SARS-CoV-2-N

Coronavirus (CoV) is an important pathogen of humans and animals, which can infect humans or animals through the respiratory mucosal route. Syndrome coronavirus 2 (SARS-CoV-2) is quite similar to syndrome coronavirus (SARS-CoV) with the same receptor, angiotensin-converting enzyme 2 (ACE2). The S and N proteins are the most important protective antigens of the SARS-CoV-2. The S protein on the viral membrane mediates the virus attachment with the host cells, and the N protein is the most abundant expression during infection. In this study, the recombinant viruses expressing the S and N proteins of SARS-CoV-2 were successfully constructed by Red/ET recombinant technology using Pseudorabies virus (PRV) strain Bartha-K61 as a vector. Genetic stability and growth kinetics analysis showed that the recombinant viruses rPRV-SARS-CoV-2-S and rPRV-SARS-CoV-2-N had similar genetic stability and proliferation characteristics to the parental PRV. The immunoassay results showed that mice immunized with recombinant viruses could produce total IgG antibodies. Therefore, PRV is feasible and promising as a viral vector to express SARS-CoV-2-S and SARS-CoV-2-N genes. This study can provide a reference for future research on live vector vaccines for domestic animals, pets, and wild animals.
Effect of a tailored upper extremity strength training intervention combined with direct current stimulation in chronic stroke survivors: A Randomized Controlled Trial

Strengthening exercises are recommended for managing persisting upper limb (UL) weakness following a stroke. Yet, strengthening exercises often lead to variable gains because of their generic nature. For this randomized controlled trial (RCT), we aimed to determine whether tailoring strengthening exercises using a biomarker of corticospinal integrity, as reflected in the amplitude of motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS), could optimize training effects in the affected UL. A secondary aim was to determine whether applying anodal transcranial direct current stimulation (tDCS) could enhance exercise-induced training effects. For this multisite RCT, 90 adults at the chronic stage after stroke (>6 months) were recruited. Before training, participants underwent TMS to detect the presence of MEPs in the affected hand. The MEP amplitude was used to stratify participants into three training groups: (1) low-intensity, MEP <50 μV, (2) moderate-intensity, 50 μV < MEP < 120 μV, and (3) high-intensity, MEP>120 μV. Each group trained at a specific intensity based on the one-repetition maximum (1 RM): low-intensity, 35–50% 1RM; moderate-intensity, 50–65% 1RM; high-intensity, 70–85% 1RM. The strength training targeted the affected UL and was delivered 3X/week for four consecutive weeks. In each training group, participants were randomly assigned to receive either real or sham anodal tDCS (2 mA, 20 min) over the primary motor area of the affected hemisphere. Pre-/post-intervention, participants underwent a clinical evaluation of their UL to evaluate motor impairments (Fugl-Meyer Assessment), manual dexterity (Box and Blocks test) and grip strength. Post-intervention, all groups exhibited similar gains in terms of reduced impairments, improved dexterity, and grip strength, which was confirmed by multivariate and univariate analyses. However, no effect of interaction was found for tDCS or training group, indicating that tDCS had no significant impact on outcomes post-intervention. Collectively, these results indicate that adjusting training intensity based on the size of MEPs in the affected extremity provides a useful approach to optimize responses to strengthening exercises in chronic stroke survivors. Also, the lack of add-on effects of tDCS applied to the lesioned hemisphere on exercise-induced improvements in the affected UL raises questions about the relevance of combining such interventions in stroke. Clinical trial registry number NCT02915185. https://www.clinicaltrials. gov/ct2/show/NCT02915185.