Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Analysis of a Novel Phage Infecting the Turkey Pathogen Escherichia coli APEC O78 and Its Endolysin Activity

Due to the increasing spread of multidrug-resistant (MDR) bacteria, phage therapy is considered one of the most promising methods for addressing MDR bacteria. Escherichia coli lives symbiotically in the intestines of humans and some animals, and most strains are beneficial in terms of maintaining a healthy digestive tract. However, some E. coli strains can cause serious zoonotic diseases, including diarrhea, pneumonia, urinary tract infections, and hemolytic uremic syndrome. In this study, we characterized a newly isolated Myoviridae phage, vB_EcoM_APEC. The phage vB_EcoM_APEC was able to infect E. coli APEC O78, which is the most common MDR E. coli serotype in turkeys. Additionally, the phage’s host range included Klebsiella pneumoniae and other E. coli strains. The genome of phage vB_EcoM_APEC (GenBank accession number MT664721) was 35,832 bp in length, with 52 putative open reading frames (ORFs) and a GC content of 41.3%. The genome of vB_EcoM_APEC exhibited low similarity (79.1% identity and 4.0% coverage) to the genome of Acinetobacter phage vB_AbaM_IME284 (GenBank no. MH853787.1) according to the nucleotide Basic Local Alignment Search Tool (BLASTn). Phylogenetic analysis revealed that vB_EcoM_APEC was a novel phage, and its genome sequence showed low similarity to other available phage genomes. Gene annotation indicated that the protein encoded by orf11 was an endolysin designated as LysO78, which exhibited 64.7% identity (91.0% coverage) with the putative endolysin of Acinetobacter baumannii phage vB_AbaM_B9. The LysO78 protein belongs to glycoside hydrolase family 19, and was described as being a chitinase class I protein. LysO78 is a helical protein with 12 α-helices containing a large domain and a small domain in terms of the predicted three-dimensional structure. The results of site-directed mutagenesis indicated that LysO78 contained the catalytic residues E54 and E64. The purified endolysin exhibited broad-spectrum bacteriolytic activity against Gram-negative strains, including the genera Klebsiella, Salmonella, Shigella, Burkholderia, Yersinia, and Pseudomonas, as well as the species Chitinimonas arctica, E. coli, Ralstonia solanacearum, and A. baumannii. An enzymatic assay showed that LysO78 had highly lytic peptidoglycan hydrolases activity (64,620,000 units/mg) against E. coli APEC O78, and that LysO78 had lytic activity in the temperature range of 4–85 °C, with an optimal temperature of 28 °C and optimal pH of 8.0, and was active at pH 3.0–12.0. Overall, the results suggested that LysO78 might be a promising therapeutic agent for controlling MDR E. coli APEC O78 and nosocomial infections caused by multidrug-resistant bacteria.
The Quorum Sensing Auto-Inducer 2 (AI-2) Stimulates Nitrogen Fixation and Favors Ethanol Production over Biomass Accumulation in Zymomonas mobilis

Autoinducer 2 (or AI-2) is one of the molecules used by bacteria to trigger the Quorum Sensing (QS) response, which activates expression of genes involved in a series of alternative mechanisms, when cells reach high population densities (including bioluminescence, motility, biofilm formation, stress resistance, and production of public goods, or pathogenicity factors, among others). Contrary to most autoinducers, AI-2 can induce QS responses in both Gram-negative and Gram-positive bacteria, and has been suggested to constitute a trans-specific system of bacterial communication, capable of affecting even bacteria that cannot produce this autoinducer. In this work, we demonstrate that the ethanologenic Gram-negative bacterium Zymomonas mobilis (a non-AI-2 producer) responds to exogenous AI-2 by modulating expression of genes involved in mechanisms typically associated with QS in other bacteria, such as motility, DNA repair, and nitrogen fixation. Interestingly, the metabolism of AI-2-induced Z. mobilis cells seems to favor ethanol production over biomass accumulation, probably as an adaptation to the high-energy demand of N2 fixation. This opens the possibility of employing AI-2 during the industrial production of second-generation ethanol, as a way to boost N2 fixation by these bacteria, which could reduce costs associated with the use of nitrogen-based fertilizers, without compromising ethanol production in industrial plants.
Sodium sulfite causes gastric mucosal cell death by inducing oxidative stress

Abstract Sulfites are commonly used as a preservative and antioxidant additives in the food industry. Sulfites are absorbed by the gastrointestinal tract and distributed essentially to all body tissues. Although sulfites have been believed to be safe food additives, some studies have shown that they exhibit adverse effects in various tissues. In this study, we examined the cytotoxic effect of sodium sulfite (Na2SO3) against rat gastric mucosal cells (RGM1) and further investigated its underlying molecular mechanism. We demonstrated that exposure to Na2SO3 exerts significant cytotoxicity in RGM1 cells through induction of oxidative stress. Exposure of RGM1 cells to Na2SO3 caused a significant formation of protein carbonyls and 8-hydroxy-2'-deoxyguanosine, major oxidative stress markers, with a concomitant accumulation of carbonylated protein-related aggregates. Furthermore, we found that incubation of lysozyme with Na2SO3 evokes protein carbonylation and aggregation via the metal ion-catalyzed free radical formation derived from Na2SO3. Our results suggest that Na2SO3 might lead to gastric tissue injury via induction of oxidative stress by the formation of Na2SO3-related free radicals.
A Systematic Review and Meta-Analysis of Fall Prevention Programs for Pediatric Inpatients

Falls account for a high proportion of the safety accidents experienced by hospitalized children. This study aims to analyze the contents and effects of fall prevention programs for pediatric inpatients to develop more adaptable fall prevention programs. A literature search was performed using PubMed (including Medline), Science Direct, CINAHL, Embase, and Cochrane. We included articles published from the inception of each of the databases up to 31 March 2019. A total of 1725 results were reviewed according to the inclusion and exclusion criteria, and nine studies were selected. Data were analyzed using descriptive statistics and the Comprehensive Meta-Analysis program. Four of the nine studies divided their participants into a high-risk fall group and a low-or medium-risk fall group, and all studies used a high-risk sign/sticker as a common protocol guideline for its high-risk fall group. The odds ratio of 0.95 (95% Cl 0.550–1.640) for the fall prevention program in seven studies was not statistically significant. To develop a standardized fall prevention program in the future, randomized control trial studies that can objectively measure the fall rate reduction effect of the integrated fall prevention program need to be expanded.
Interaction of Poly L-Lactide and Tungsten Disulfide Nanotubes Studied by In Situ X-ray Scattering during Expansion of PLLA/WS2NT Nanocomposite Tubes

In situ synchrotron X-ray scattering was used to reveal the transient microstructure of poly(L-lactide) (PLLA)/tungsten disulfide inorganic nanotubes (WS2NTs) nanocomposites. This microstructure is formed during the blow molding process (“tube expansion”) of an extruded polymer tube, an important step in the manufacturing of PLLA-based bioresorbable vascular scaffolds (BVS). A fundamental understanding of how such a microstructure develops during processing is relevant to two unmet needs in PLLA-based BVS: increasing strength to enable thinner devices and improving radiopacity to enable imaging during implantation. Here, we focus on how the flow generated during tube expansion affects the orientation of the WS2NTs and the formation of polymer crystals by comparing neat PLLA and nanocomposite tubes under different expansion conditions. Surprisingly, the WS2NTs remain oriented along the extrusion direction despite significant strain in the transverse direction while the PLLA crystals (c-axis) form along the circumferential direction of the tube. Although WS2NTs promote the nucleation of PLLA crystals in nanocomposite tubes, crystallization proceeds with largely the same orientation as in neat PLLA tubes. We suggest that the reason for the unusual independence of the orientations of the nanotubes and polymer crystals stems from the favorable interaction between PLLA and WS2NTs. This favorable interaction leads WS2NTs to disperse well in PLLA and strongly orient along the axis of the PLLA tube during extrusion. As a consequence, the nanotubes are aligned orthogonally to the circumferential stretching direction, which appears to decouple the orientations of PLLA crystals and WS2NTs.
‘All My Animals Are Equal, but None Can Survive without the Horse’. The Contribution of Working Equids to the Livelihoods of Women across Six Communities in the Chimaltenango Region of Guatemala

Simple Summary Working equids are often absent from higher level policy interventions, and the global standard of their welfare is low. Understanding the social and cultural context of their contributions to human livelihoods generates evidence supporting the importance of their inclusion in livestock welfare programmes. Although there is increasing evidence globally that working equids contribute to women’s livelihoods and that women facilitate equid welfare, there is a well recognised gender gap in access to extension services. This study aims to investigate how working equids contribute to women’s livelihoods in six communities in Guatemala, using information from 34 face-to-face interviews. Results show that working equids support women’s livelihoods by generating income, saving time, feeding livestock and reducing domestic drudgery. Thirty-two women played a major role in the daily husbandry of working equids, and 31 expressed an interest in gaining more knowledge in equid care. This study explores the relationship between working equids and women in a local context, using the concept of ‘One Welfare’, and investigates the knowledge gaps that exist in the daily husbandry of horses, donkeys and mules. It emphasises the need for equid welfare organisations to understand women’s roles in their target communities and recognise what prevents women from accessing educational resources. Abstract It is widely assumed that working equid husbandry is carried out by men, and women are often not recognised as facilitating equid welfare. The aim of this study is to investigate how working equids contribute to women’s livelihoods in six of the World Horse Welfare programme target communities in Guatemala and determine what roles women have in their care. Thirty-four face-to-face interviews were carried out and data were analysed using both quantitative and qualitative methods. This study found that working equids support women by reducing domestic drudgery, generating income, feeding livestock and saving time. Thirty-two women played a major role in the care of one or more equids, and overall, women did not feel that they knew enough about equid husbandry. Thirty-one women said they would attend training opportunities if the advertising was clear and they felt that women were able to join. This study recognises the contribution of working equids to women’s livelihoods, describes the roles women play in equid husbandry and addresses the discrepancies between women’s roles and their capacity to undertake these tasks. This emphasises the need for extension services to include and cater for women, improving equid welfare and their ability to continue supporting women’s livelihoods.
Magnesium Isoglycyrrhizinate Reduces Hepatic Lipotoxicity through Regulating Metabolic Abnormalities

The excessive accumulation of lipids in hepatocytes induces a type of cytotoxicity called hepatic lipotoxicity, which is a fundamental contributor to liver metabolic diseases (such as NAFLD). Magnesium isoglycyrrhizinate (MGIG), a magnesium salt of the stereoisomer of natural glycyrrhizic acid, is widely used as a safe and effective liver protectant. However, the mechanism by which MGIG protects against NAFLD remains unknown. Based on the significant correlation between NAFLD and the reprogramming of liver metabolism, we aimed to explore the beneficial effects of MGIG from a metabolic viewpoint in this paper. We treated HepaRG cells with palmitic acid (PA, a saturated fatty acid of C16:0) to induce lipotoxicity and then evaluated the antagonistic effect of MGIG on lipotoxicity by investigating the cell survival rate, DNA proliferation rate, organelle damage, and endoplasmic reticulum stress (ERS). Metabolomics, lipidomics, and isotope tracing were used to investigate changes in the metabolite profile, lipid profile, and lipid flux in HepaRG cells under different intervention conditions. The results showed that MGIG can indeed protect hepatocytes against PA-induced cytotoxicity and ERS. In response to the metabolic abnormality of lipotoxicity, MGIG curtailed the metabolic activation of lipids induced by PA. The content of total lipids and saturated lipids containing C16:0 chains increased significantly after PA stimulation and then decreased significantly or even returned to normal levels after MGIG intervention. Lipidomic data show that glycerides and glycerophospholipids were the two most affected lipids. For excessive lipid accumulation in hepatocytes, MGIG can downregulate the expression of the metabolic enzymes (GPATs and DAGTs) involved in triglyceride biosynthesis. In conclusion, MGIG has a positive regulatory effect on the metabolic disorders that occur in hepatocytes under lipotoxicity, and the main mechanisms of this effect are in lipid metabolism, including reducing the total lipid content, reducing lipid saturation, inhibiting glyceride and glycerophospholipid metabolism, and downregulating the expression of metabolic enzymes in lipid synthesis.
Chemical Characterization and Source Apportionment of Atmospheric Particles Across Multiple Sampling Locations in Faisalabad, Pakistan

Author(s): Javed, W; Wexler, AS; Murtaza, G; Iqbal, MM; Zhao, Y; Naz, T | Abstract: © 2016 WILEY-VCH Verlag GmbH a Co. KGaA, Weinheim. Atmospheric particles (total suspended particles, TSPs) mass samples (288) were collected by high volume samplers at nine sampling locations in Faisalabad, Pakistan from May 2012 to April 2013. These TSP mass samples were subjected to gravimetric and quantitative chemical analyses for determining trace elements (Pb, Cd, Ni, Zn, Cu, Fe) using atomic absorption spectroscopy and water-soluble cations (Ca2+, Mg2+, Na+ and K+, NH4+) and anions (Cl−, SO42−, and NO3−) by ion chromatography. The average TSP mass and elemental concentrations at all locations were found to be highest during the dry and lowest during the wet season. The crustal elements Ca, Fe, Mg, and Na were the largest contributors to TSP mass while elements of anthropogenic origin Pb, Cd, Ni, Cu, and Zn had relatively lower concentrations and also showing a high spatial variation. The concentration of TSP and elements exhibited the maxima at the sampling locations characterized by intensive industrial and vehicular activities. The wind rose analysis and the UNMIX model applied to chemical speciation data both identified the same three primary sources of TSP: power plant/refinery, brick kilns, and roadways. The normalized dot product was successfully used to quantify the similarity between different source profiles extracted from UNMIX model. The coupling of UNMIX with wind direction analysis complemented each other and provided a complete assessment of source contributions and locations.
A Multi-Phase Based Multi-Application Mapping Approach for Many-Core Networks-on-Chip

More and more attention is being paid to the use of massive parallel computing performed on many-core Networks-on-Chip (NoC) in order to accelerate performance. Simultaneously deploying multiple applications on NoC is one feasible way to achieve this. In this paper, we propose a multi-phase-based multi-application mapping approach for NoC design. Our approach began with a rectangle analysis, which offered several potential regions for application. Then we mapped all tasks of the application into these potential regions using a genetic algorithm, and identified the one which exhibited the strongest performance. When the packeted regions for each application were identified, a B*Tree-based simulated annealing algorithm was used to generate the optimal placement for the multi-application mapping regions. The experiment results show that the proposed approach can achieve a considerable reduction in network power consumption (up to 23.45%) and latency (up to 24.42%) for a given set of applications.
Intracellular Na+ Modulates Pacemaking Activity in Murine Sinoatrial Node Myocytes: An In Silico Analysis

Background: The mechanisms underlying dysfunction in the sinoatrial node (SAN), the heart’s primary pacemaker, are incompletely understood. Electrical and Ca2+-handling remodeling have been implicated in SAN dysfunction associated with heart failure, aging, and diabetes. Cardiomyocyte [Na+]i is also elevated in these diseases, where it contributes to arrhythmogenesis. Here, we sought to investigate the largely unexplored role of Na+ homeostasis in SAN pacemaking and test whether [Na+]i dysregulation may contribute to SAN dysfunction. Methods: We developed a dataset-specific computational model of the murine SAN myocyte and simulated alterations in the major processes of Na+ entry (Na+/Ca2+ exchanger, NCX) and removal (Na+/K+ ATPase, NKA). Results: We found that changes in intracellular Na+ homeostatic processes dynamically regulate SAN electrophysiology. Mild reductions in NKA and NCX function increase myocyte firing rate, whereas a stronger reduction causes bursting activity and loss of automaticity. These pathologic phenotypes mimic those observed experimentally in NCX- and ankyrin-B-deficient mice due to altered feedback between the Ca2+ and membrane potential clocks underlying SAN firing. Conclusions: Our study generates new testable predictions and insight linking Na+ homeostasis to Ca2+ handling and membrane potential dynamics in SAN myocytes that may advance our understanding of SAN (dys)function.
Simulating Peptide Monolayer Formation: GnRH-I on Silica

Molecular dynamics (MD) simulations can provide a detailed view of molecule behaviour at an atomic level, which can be useful when attempting to interpret experiments or design new systems. The decapeptide gonadotrophin-releasing hormone I (GnRH-I) is known to control fertility in mammals for both sexes. It was previously shown that inoculation with silica nanoparticles (SiNPs) coated with GnRH-I makes an effective anti-fertility vaccine due to how the peptide adsorbs to the nanoparticle and is presented to the immune system. In this paper, we develop and employ a protocol to simulate the development of a GnRH-I peptide adlayer by allowing peptides to diffuse and adsorb in a staged series of trajectories. The peptides start the simulation in an immobile state in solution above the model silica surface, and are then released sequentially. This facile approach allows the adlayer to develop in a natural manner and appears to be quite versatile. We find that the GnRH-I adlayer tends to be sparse, with electrostatics dominating the interactions. The peptides are collapsed to the surface and are seemingly free to interact with additional solutes, supporting the interpretations of the GNRH-I/SiNP vaccine system.
The Moderating Role of Corporate Social Responsibility in the Association of Internal Corporate Governance and Profitability; Evidence from Pakistan

At present, climate and other environmental problems are arising because of the development of the industrial sector at a large level. The industrial sector is supposed to be a major cause of climate change problems that lead to global warming. Therefore, corporate social responsibility (CSR) with the help of corporate governance is an imperative approach to control these social problems. Consequently, in the context of the organizational and management theory, agency theory, and the stakeholder theory, this study focuses on important factors of internal corporate governance such as chief executive officer (CEO) power, the board size, independence, ownership concentration, managerial ownership, and audit quality for improving the profitability of firms. Moreover, this study considers corporate social responsibility as a controlling and moderating factor for firm performance and internal corporate governance. We employed ordinary least square (OLS) for endogeneity testing, fixed effect (FE), generalized method of moments (GMM), and feasible generalized least square (FGLS) on data of Pakistani firms for the period of 2010–2019. The results of this study demonstrate the following outcomes: firstly, all internal corporate governance factors are positively linked with firm performance; secondly, corporate social responsibility (CSR) is the most valuable tool for improving profitability. Importantly, this study suggests that all internal corporate governance factors are positively linked with firm performance because of the interactive role of corporate social responsibility (CSR). This study practically contributes to the literature by suggesting the imperative role of corporate social responsibility (CSR) for internal corporate governance, which may help to reduce climate and social problems.
Modeling of cesium sorption on biotite using cation exchange selectivity coefficients

Abstract For the modeling of cesium sorption on biotite, samples of natural biotite separated from gneissic rocks were converted into monoionic potassium, sodium, and calcium forms, and sorption isotherms for Cs/K, Cs/Na and Cs/Ca exchange were determined at pH 6 and 8 in E-4–E-8 M Cs solutions. Selectivity coefficients for Cs/K, Cs/Na, and Cs/Ca ion exchange reactions were calculated from the isotherm data, using the Gaines-Thomas convention. At Cs loadings below 1% of the total ion exchange capacity, the overall selectivity coefficient for Cs/Ca exchange was approximately five and seven orders of magnitude higher than those for Cs/Na and Cs/K exchange, respectively. Based on the selectivity coefficients, the ion exchange isotherms were modeled with the U.S. Geological Survey PhreeqC program, assuming three different types of ion exchange site: sites on the basal planes on biotite crystal surfaces with 95% site abundance, probable interlayer sites on crystal edges [frayed edge sites (FESs)] (0.02%) and third-type sites (5%), the physical background of which is unclear. Of these three types, the FES sites were superior in Cs selectivity, while the planar sites exhibited the lowest selectivity, and the third-type sites had selectivity between these two. The functionality of the model was successfully verified by modeling the Cs sorption isotherms on crushed mica gneiss rock in saline groundwater. Determination of the exchangeable ions K, Na, Ca, and Cs on the basal plane and edge surfaces by scanning electron microscopy-energy-dispersive x-ray spectroscopy (SEM-EDX) supports the results of modeling: edge sites highly prefer Cs ions and also Ca and Na ions but not K ions.