Miracle-dz/UniFAR-FTUs huggingface dataset:
The expression of hemagglutinin by a recombinant Newcastle disease virus causes structural changes and alters innate immune sensing

Recombinant Newcastle disease viruses (rNDV) have been used as bivalent vectors for vaccination against multiple economically important avian pathogens. NDV-vectored vaccines expressing the immunogenic H5 hemagglutinin (rNDV-H5) are considered attractive candidates to protect poultry from both highly pathogenic avian influenza (HPAI) and Newcastle disease (ND). However, the impact of the insertion of a recombinant protein, such as H5, on the biological characteristics of the parental NDV strain has been little investigated to date. The present study compared a rNDV-H5 vaccine and its parental NDV LaSota strain in terms of their structural and functional characteristics, as well as their recognition by the innate immune sensors. Structural analysis of the rNDV-H5 demonstrated a decreased number of fusion (F) and a higher number of hemagglutinin-neuraminidase (HN) glycoproteins compared to NDV LaSota. These structural differences were accompanied by increased hemagglutinating and neuraminidase activities of rNDV-H5. During in vitro rNDV-H5 infection, increased mRNA expression of TLR3, TLR7, MDA5, and LGP2 was observed, suggesting that the recombinant virus is recognized differently by sensors of innate immunity when compared with the parental NDV LaSota. Given the growing interest in using NDV as a vector against human and animal diseases, these data highlight the importance to thoroughly understand the recombinant vaccines structural organization, functional characteristics, and the immune responses elicited.
An Upper Bound on Magnitude Error of Voltage Drop Phasors in Distribution Lines Due to Phase Transposition Assumption

Abstract A renewed interest in comprehensive modeling of distribution system components arose in recent literature. This trend can be attributed to, aside from the inherent imbalance of such systems, the rapid and system-wide integration of technologies, e.g. non-linear loads and distributed generators, which further increase grid imbalance effects. Such phenomena, in turn, demand sufficiently detailed models for their proper assessment. Despite the described scenario, it remains reasonable to inquire whether approximate component models can still be used for simplifying computations without causing exceedingly high modeling error. In this context, an approximation of particular interest is assuming phase transposition for distribution lines, due to its property of impedance matrix decoupling on the symmetric component frame. In this paper, the derivation of a closed-form upper bound for voltage drop magnitude error, due to assuming transposition in a general M-phase line, is carried out. The bound is validated by means of a case study based on the IEEE 4-bus feeder considering generalized feeder geometries. Obtained results suggest that the upper bound is tight with respect to actual error and thus provides a practical means of estimating voltage drop error yielded by the assumption of distribution line transposition.
The role of quenched-in disorder in polycrystalline bulk and melt-spun ribbons of Ni50Mn29Ga21

ABSTRACT Investigations on the properties of polycrystalline bulk and melt-spun ribbons of composition Ni50Mn29Ga21 are contrasted. Both samples are subjected to quenching after melting and then were homogenized at the same temperature. Though the electron per atom ratio is unchanged, the quenched-in disorder has caused the structural and magnetic transformations to occur in close proximity in the ribbon giving rise to magnetic entropy change of –9.2 J/kg-K at the martensitic transformation. The bulk alloy showed significantly high magnetic field-induced strain of 0.7% at 5 kOe magnetic field and an apparent compressive strain of 5.3% at 40 MPa compression stress, without training the sample. Large grain size and micro-twinning are observed in the bulk, while nano-scale twinning is seen in the ribbon. The variations in the process altered the degree of ordering, which modified the transformation temperatures, the crystal structure, the microstructures of the ribbon and the mechanical properties of the bulk specimen significantly.
Ischemia-Reperfusion Injury Reduces Kidney Folate Transporter Expression and Plasma Folate Levels

Acute or chronic kidney disease can cause micronutrient deficiency. Patients with end-stage renal disease, kidney transplantation or on dialysis have reduced circulating levels of folate, an essential B vitamin. However, the molecular mechanism is not well understood. Reabsorption of folate in renal proximal tubules through folate transporters is an important process to prevent urinary loss of folate. The present study investigated the impact of acute kidney injury (AKI) on folate transporter expression and the underlying mechanism. AKI was induced in Sprague-Dawley rats that were subjected to kidney ischemia (45 min)-reperfusion (24 h). Both male and female rats displayed kidney injury and low plasma folate levels compared with sham-operated rats. The plasma folate levels were inversely correlated to plasma creatinine levels. There was a significant increase in neutrophil gelatinase-associated lipocalin (NGAL) and IL-6 mRNA expression in the kidneys of rats with ischemia-reperfusion, indicating kidney injury and increased inflammatory cytokine expression. Ischemia-reperfusion decreased mRNA and protein expression of folate transporters including folate receptor 1 (FOLR1) and reduced folate carrier (RFC); and inhibited transcription factor Sp1/DNA binding activity in the kidneys. Simulated ischemia-reperfusion through hypoxia-reoxygenation or Sp1 siRNA transfection in human proximal tubular cells inhibited folate transporter expression and reduced intracellular folate levels. These results suggest that ischemia-reperfusion injury downregulates renal folate transporter expression and decreases folate uptake by tubular cells, which may contribute to low folate status in AKI. In conclusion, ischemia-reperfusion injury can downregulate Sp1 mediated-folate transporter expression in tubular cells, which may reduce folate reabsorption and lead to low folate status.
Analysis of the Impact of Medical Features and Risk Prediction of Acute Kidney Injury for Critical Patients Using Temporal Electronic Health Record Data With Attention-Based Neural Network

Acute kidney injury (AKI) is one of the most severe consequences of kidney injury, and it will also cause or aggravate the complications by the fast decline of kidney excretory function. Accurate AKI prediction, including the AKI case, AKI stage, and AKI onset time interval, can provide adequate support for effective interventions. Besides, discovering how the medical features affect the AKI result may also provide supporting information for disease treatment. An attention-based temporal neural network approach was employed in this study for AKI prediction and for the analysis of the impact of medical features from temporal electronic health record (EHR) data of patients before AKI diagnosis. We used the publicly available dataset provided by the Medical Information Mart for Intensive Care (MIMIC) for model training, validation, and testing, and then the model was applied in clinical practice. The improvement of AKI case prediction is around 5% AUC (area under the receiver operating characteristic curve), and the AUC value of AKI stage prediction on AKI stage 3 is over 82%. We also analyzed the data by two steps: the associations between the medical features and the AKI case (positive or inverse) and the extent of the impact of medical features on AKI prediction result. It shows that features, such as lactate, glucose, creatinine, blood urea nitrogen (BUN), prothrombin time (PT), and partial thromboplastin time (PTT), are positively associated with the AKI case, while there are inverse associations between the AKI case and features such as platelet, hemoglobin, hematocrit, urine, and international normalized ratio (INR). The laboratory test features such as urine, glucose, creatinine, sodium, and blood urea nitrogen and the medication features such as nonsteroidal anti-inflammatory drugs, agents acting on the renin–angiotensin system, and lipid-lowering medication were detected to have higher weights than other features in the proposed model, which may imply that these features have a great impact on the AKI case.
Modeling Spatial Interaction in Stochastic Frontier Analysis

We compare farm level efficiency rankings derived from non-spatial and a variety of spatial model specifications that account for unobserved heterogeneity in both the production and the efficiency sides of the stochastic frontier model in an empirical application on rice farming in the Philippines. We show how not accounting for unobserved spatial heterogeneity affects efficiency estimates and farm efficiency rankings. When not accounting for unobserved spatial heterogeneity efficiency, models show farms to be relatively more inefficient than they actually are (i.e., once unobserved spatial heterogeneity is incorporated in the models). More importantly from a policy perspective, the rankings of the farms in terms of efficiency are altered once unobserved spatial heterogeneity is incorporated in efficiency models. We recommend the use of unobserved effects in both production and efficiency within the stochastic frontier analysis framework to avoid making any misleading recommendations to farmers and policymakers.
Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model Reconstruction

Since their initial discovery in 1976, mesenchymal stem cells (MSCs) have been gathering interest as a possible tool to further the development and enhancement of various therapeutics within regenerative medicine. However, our current understanding of both metabolic function and existing differences within the varying cell lineages (e.g., cells in either osteogenesis or adipogenesis) is severely lacking making it more difficult to fully realize the therapeutic potential of MSCs. Here, we reconstruct the MSC metabolic network to understand the activity of various metabolic pathways and compare their usage under different conditions and use these models to perform experimental design. We present three new genome-scale metabolic models (GEMs) each representing a different MSC lineage (proliferation, osteogenesis, and adipogenesis) that are biologically feasible and have distinctive cell lineage characteristics that can be used to explore metabolic function and increase our understanding of these phenotypes. We present the most distinctive differences between these lineages when it comes to enriched metabolic subsystems and propose a possible osteogenic enhancer. Taken together, we hope these mechanistic models will aid in the understanding and therapeutic potential of MSCs.
Automatic Bayesian Weighting for SAXS Data

Small-angle X-ray scattering (SAXS) experiments are important in structural biology because they are solution methods, and do not require crystallization of protein complexes. Structure determination from SAXS data, however, poses some difficulties. Computation of a SAXS profile from a protein model is expensive in CPU time. Hence, rather than directly refining against the data, most computational methods generate a large number of conformers and then filter the structures based on how well they satisfy the SAXS data. To address this issue in an efficient manner, we propose here a Bayesian model for SAXS data and use it to directly drive a Monte Carlo simulation. We show that the automatic weighting of SAXS data is the key to finding optimal structures efficiently. Another key problem with obtaining structures from SAXS data is that proteins are often flexible and the data represents an average over a structural ensemble. To address this issue, we first characterize the stability of the best model with extensive molecular dynamics simulations. We analyse the resulting trajectories further to characterize a dynamic structural ensemble satisfying the SAXS data. The combination of methods is applied to a tandem of domains from the protein PTPN4, which are connected by an unstructured linker. We show that the SAXS data contain information that supports and extends other experimental findings. We also show that the conformation obtained by the Bayesian analysis is stable, but that a minor conformation is present. We propose a mechanism in which the linker may maintain PTPN4 in an inhibited enzymatic state.
An Immersive Investment Game to Study Human-Robot Trust

As robots become more advanced and capable, developing trust is an important factor of human-robot interaction and cooperation. However, as multiple environmental and social factors can influence trust, it is important to develop more elaborate scenarios and methods to measure human-robot trust. A widely used measurement of trust in social science is the investment game. In this study, we propose a scaled-up, immersive, science fiction Human-Robot Interaction (HRI) scenario for intrinsic motivation on human-robot collaboration, built upon the investment game and aimed at adapting the investment game for human-robot trust. For this purpose, we utilize two Neuro-Inspired COmpanion (NICO) - robots and a projected scenery. We investigate the applicability of our space mission experiment design to measure trust and the impact of non-verbal communication. We observe a correlation of 0.43 ( p = 0.02 ) between self-assessed trust and trust measured from the game, and a positive impact of non-verbal communication on trust ( p = 0.0008 ) and robot perception for anthropomorphism ( p = 0.007 ) and animacy ( p = 0.00002 ). We conclude that our scenario is an appropriate method to measure trust in human-robot interaction and also to study how non-verbal communication influences a human’s trust in robots.
Financing Advantage of Green Corporate Asset-Backed Securities and its Impact Factors: Evidence in China

As an innovative green financial tool, green corporate asset-backed securities can effectively solve the problems of narrow financing channels and maturity mismatches for green projects, which can help achieve green and low-carbon development, carbon peaking, and carbon neutrality goals. In this paper, we examine the financing cost advantages of green corporate asset-backed securities and the related impact factors through a combination of empirical and case studies. Empirical research based on the propensity score matching method (PSM) shows that China’s green corporate asset-backed securities issuance rates are 36.97°bps lower than traditional corporate asset-backed securities on average. Credit rating, issuance scale, issuance interest rate, issuance period, and green factors have become the main impact factors of green corporate asset-backed securities financing advantages.
Effects of Bacillus amyloliquefaciens Instead of Antibiotics on Growth Performance, Intestinal Health, and Intestinal Microbiota of Broilers

The aim of this study was to evaluate the dietary effects of Bacillus amyloliquefaciens SC06 (SC06) instead of antibiotics on the growth performance, intestinal health, and intestinal microbiota of broilers. A total of 360 30-day-old Lingnan yellow broilers were randomly allocated into two groups with six replicates per group (30 birds per replicate). The broilers were fed either a non-supplemented diet or a diet supplemented with 108 colony-forming units lyophilized SC06 per kilogram feed for 30 days. Results showed that SC06 supplementation had no effect on the growth performance compared with that of the control group. SC06 treatment significantly (P <0.05) increased the total antioxidant capacity (T-AOC), total superoxide dismutase (T-SOD) activity in the liver, and the activities of trypsin, α-amylase (AMS), and Na+K+-ATPase in the ileum, whereas it decreased (P < 0.05) lipase, gamma glutamyl transpeptidase (γ-GT), and maltase activities in the ileum. Meanwhile, SC06 treatment also improved the immune function indicated by the significantly (P < 0.05) increased anti-inflammatory cytokine [interleukin (IL)-10] level and the decreased (P < 0.05) pro-inflammatory cytokine [IL-6 and tumor necrosis factor (TNF)-α] levels in the ileum. Furthermore, we also found that SC06 enhanced the intestinal epithelial intercellular integrity (tight junction and adhesion belt) in the ileum. Microbial analysis showed that SC06 mainly increased the alpha diversity indices in the jejunum, ileum, and cecum. SC06 treatment also significantly (P < 0.05) increased the abundances of Bacteroidetes, Bacteroidales, Bacteroides, Fusobacteria, Clostridiaceae, and Veillonellaceae in the cecum and simultaneously decreased the abundances of Planococcaceae in the duodenum, Microbacteriaceae in the jejunum, and Lachnospiraceae, [Ruminococcus] and Ruminococcus in cecum. In conclusion, these results suggested that B. amyloliquefaciens instead of antibiotics showed a potential beneficial effect on the intestinal health of broilers.
A Methodological Advance of Tobacco Rattle Virus-Induced Gene Silencing for Functional Genomics in Plants

As a promising high-throughput reverse genetic tool in plants, virus-induced gene silencing (VIGS) has already begun to fulfill some of this promise in diverse aspects. However, review of the technological advancements about widely used VIGS system, tobacco rattle virus (TRV)-mediated gene silencing, needs timely updates. Hence, this article mainly reviews viral vector construction, inoculation method advances, important influential factors, and summarizes the recent applications in diverse plant species, thus providing a better understanding and advice for functional gene analysis related to crop improvements.
The Mediating Roles of Core Self-Evaluation and Career Exploration in the Association Between Proactive Personality and Job Search Clarity

In recent years, university students’ employment has become an increasingly prominent problem worldwide. Improving the job search clarity of students is a great way to boost job-hunting success. Proactive personality may predict job search clarity through the mediating effects of core self-evaluation and career exploration. However, few studies have explored this relationship and the mediating roles of core self-evaluation and career exploration. To identify the relationship between a proactive personality and job search clarity and the mediating roles of core self-evaluation and career exploration, a cross-sectional survey was conducted. A total of 495 students majoring in nursing completed the questionnaire which consisted of the proactive personality scale, core self-evaluation scale, career exploration survey, and job search clarity scale. Correlation analyses and mediation analyses were conducted using SPSS 24.0 and AMOS 24.0 respectively. This study showed that students higher on the proactive personality scale were more likely to perform better on job search clarity. Core self-evaluation and career exploration have fully mediating effects on the relationship between a proactive personality and job search clarity. Therefore, interventions concentrated on cultivating proactive personality, improving core self-evaluation, and strengthening career exploration would be necessary for increasing job search clarity.
Transcatheter Mitral Valve Replacement and Thrombosis: A Review

Mitral regurgitation is the most prevalent form of moderate or severe valve disease in developed countries. Surgery represents the standard of care for symptomatic patients with severe mitral regurgitation, but up to 50% of patients are denied surgery because of high surgical risk. In this context, different transcatheter options have been developed to address this unmet need. Transcatheter mitral valve replacement (TMVR) is an emergent field representing an alternative option in high complex contexts when transcatheter mitral valve repair is not feasible or suboptimal due to anatomical issues. However, TMVR is burdened by some device-specific issues (device malposition, migration or embolization, left ventricular outflow tract obstruction, hemolysis, thrombosis, stroke). Here we discuss the thrombotic risk of TMVR and current evidence about anticoagulation therapy after TMVR.
A Staphylococcus aureus clpX Mutant Used as a Unique Screening Tool to Identify Cell Wall Synthesis Inhibitors that Reverse β-Lactam Resistance in MRSA

Staphylococcus aureus is a leading cause of bacterial infections world-wide. Staphylococcal infections are preferentially treated with β-lactam antibiotics, however, methicillin-resistant S. aureus (MRSA) strains have acquired resistance to this superior class of antibiotics. We have developed a growth-based, high-throughput screening approach that directly identifies cell wall synthesis inhibitors capable of reversing β-lactam resistance in MRSA. The screen is based on the finding that S. aureus mutants lacking the ClpX chaperone grow very poorly at 30°C unless specific steps in teichoic acid synthesis or penicillin binding protein (PBP) activity are inhibited. This property allowed us to exploit the S. aureus clpX mutant as a unique screening tool to rapidly identify biologically active compounds that target cell wall synthesis. We tested a library of ∼50,000 small chemical compounds and searched for compounds that inhibited growth of the wild type while stimulating growth of the clpX mutant. Fifty-eight compounds met these screening criteria, and preliminary tests of 10 compounds identified seven compounds that reverse β-lactam resistance of MRSA as expected for inhibitors of teichoic acid synthesis. The hit compounds are therefore promising candidates for further development as novel combination agents to restore β-lactam efficacy against MRSA.
Crops for Carbon Farming

Agricultural cropping systems and pasture comprise one third of the world’s arable land and have the potential to draw down a considerable amount of atmospheric CO2 for storage as soil organic carbon (SOC) and improving the soil carbon budget. An improved soil carbon budget serves the dual purpose of promoting soil health, which supports crop productivity, and constituting a pool from which carbon can be converted to recalcitrant forms for long-term storage as a mitigation measure for global warming. In this perspective, we propose the design of crop ideotypes with the dual functionality of being highly productive for the purposes of food, feed, and fuel, while at the same time being able to facilitate higher contribution to soil carbon and improve the below ground ecology. We advocate a holistic approach of the integrated plant-microbe-soil system and suggest that significant improvements in soil carbon storage can be achieved by a three-pronged approach: (1) design plants with an increased root strength to further allocation of carbon belowground; (2) balance the increase in belowground carbon allocation with increased source strength for enhanced photosynthesis and biomass accumulation; and (3) design soil microbial consortia for increased rhizosphere sink strength and plant growth-promoting (PGP) properties.