Miracle-dz/UniFAR-FTUs huggingface dataset:
Urea, Uric Acid, and Creatinine in Postmortem Blood, Vitreous Humor, and Synovial Fluid: A Comparative and Correlation Study ,

Urea, uric acid, and creatinine have been demonstrated to be relatively stable in postmortem blood (BL), thus being useful for diagnostic purposes. However, no studies have explored their levels in BL, vitreous humor (VH), and synovial fluid (SF) concurrently. Therefore, we measured and compared their levels in these fluids. We also determined the effects of various factors on their levels. The results indicated that BL urea, uric acid, and creatinine levels were significantly higher than VH and SF levels. VH and SF urea levels and SF creatinine levels had a strong correlation with BL urea and creatinine levels, respectively. BL creatinine levels were higher in men than in women. BL and SF creatinine levels were negatively correlated with age. SF uric acid and BL, VH, and SF creatinine levels exhibited a positive correlation with weight. Only VH creatinine levels were positively correlated with body mass index. None of urea, uric acid, and creatinine levels were correlated with postmortem interval.
Saiph, a domain specific language for computational fluid dynamics simulations

Nowadays, High-Performance Computing (HPC) is assuming an increasingly central role in scientific research while computer architectures are becoming more and more hetero-geneous and using different parallel programming models and techniques. Under this scenario, the only way to successfully exploit an HPC system requires that computer and domain scientists work closely towards producing applications to solve domain problems, ensuring productivity and performance at the same time. Facing such purpose, Saiph is a Domain Specific Language designed to ease the task of solving couple and uncouple Partial Differential Equations (PDE’s), with a primary focusing on Computational Fluid Dynamics (CFD) applications. Saiph allows to model complex physical phenomena featured by PDE’s, easing the use of numerical methods and optimizations on different computer architectures to the users.
Solar Radiation Exposure Has Diurnal Effects on Thermoregulatory Responses During High-Intensity Exercise in the Heat Outdoors.

Otani, H, Goto, T, Goto, H, Hosokawa, Y, and Shirato, M. Solar radiation exposure has diurnal effects on thermoregulatory responses during high-intensity exercise in the heat outdoors. J Strength Cond Res XX(X): 000-000, 2019-This study investigated the diurnal effects of variations in solar radiation associated with changing solar elevation angle on thermoregulatory responses during high-intensity exercise in the heat outdoors. Ten male high school soccer players completed two 2-hour soccer training sessions under a clear sky in the heat of summer. These sessions were commenced at 0900 hours (AM) and 1600 hours (PM) on separate days. Solar radiation and elevation angle were higher in AM (820-1,070 W·m and 45-69°) than PM (620-110 W·m and 34-10°: both p < 0.001). Neither ambient temperature (AM 29-32° C; PM 31-31° C) nor wet-bulb globe temperature was different between trials. Although mean skin temperature was not different between trials, infrared tympanic temperature was higher at the end of exercise in AM than PM (p < 0.001). Heart rate (p < 0.01) and body heat gain from the sun (p < 0.001) were greater during exercise in AM than PM. Dry heat loss was smaller, but evaporative heat loss was greater in AM than PM (both p < 0.001). Thermal sensation and rating of perceived exertion were similar between trials, but GPS measurements showed a less total distance and distance covered by walking, jogging, and running in AM than PM (p < 0.01). This study demonstrates a greater thermoregulatory strain in AM than PM during 2-hour high-intensity soccer training in the heat under a clear sky. This observation is accompanied by a progressive increase in environmental heat stress with rising solar radiation and elevation angle in AM and a greater body heat gain from the sun in AM compared with PM.
Clinical usefulness of prethymectomy plasmapheresis in patients with myasthenia gravis: a systematic review and meta-analysis.

OBJECTIVES Our goal was to evaluate, through a systematic review, the efficacy of plasmapheresis in the preoperative preparation of the patient for a thymectomy for the treatment of myasthenia gravis. METHODS MEDLINE, Embase, LILACS, Scopus and CENTRAL databases were searched. The following outcomes were evaluated: myasthenic crisis, mortality, pneumonia, bleeding, use of mechanical ventilation, length of hospital stay and intensive care unit (ICU) stay. RevMan 5.3 software provided by the Cochrane Collaboration was used for the meta-analysis. RESULTS The total number of patients evaluated in the 7 included studies was 360. Plasmapheresis during the preoperative period did not decrease the myasthenic crisis [risk ratio (RR) 0.36, 95% confidence interval (CI) 0.08-1.66; I2 = 44%; 5 studies, 243 patients]. There was also no change in the mortality rate (RR 0.7, 95% CI 0.11-4.62; I2 = 0%; 3 studies, 172 patients) or pneumonia cases (RR 0.28, 95% CI 0.07-1.09; I2 = 27%; 5 studies, 272 patients). Bleeding was greater in patients who underwent plasmapheresis (mean difference 34.34 ml; 95% CI 24.93-43.75; I2 = 0%). We evaluated the following outcomes: need for mechanical ventilation, hospital stay, ICU stay and mechanical ventilation, but these outcomes were not adequate to perform the meta-analysis due to the high heterogeneity among the studies. Subgroup analysis showed that plasmapheresis performed during the preoperative period in patients with severe disease (Osserman III and IV) decreased the myasthenic crisis postoperatively (RR 0.12, 95% CI 0.02-0.65; I2 = 63%). CONCLUSIONS Plasmapheresis may reduce the myasthenic crisis during the postoperative period in patients with severe disease but may produce little or no difference in patients with mild clinical expression of the disease.
Protective effect of coenzyme Q10 against bisphenol-A-induced toxicity in the rat testes

The present study was conducted to investigate the antioxidant, histomorphometric, histochemical, immunohistochemical, biochemical, and cytological effects of coenzyme Q10 (CoQ10) against bisphenol-A (BPA)-induced testicular toxicity in rats. A total of 40 adult male Wistar rats were divided into five equal groups. The control group remained untreated. The vehicle control group was administered corn oil (2 ml/kg/day), the BPA group was given BPA (100 mg/kg/day), the CoQ10 group was supplemented with CoQ10 (10 mg/kg/day), and the rats in the CoQ10-BPA group received CoQ10 (10 mg/kg/day) followed by BPA (100 mg/kg/day) 1 h later. The treatments were administered by oral gavage for 14 days. Results showed that the seminiferous tubule diameters (STDs) and seminiferous epithelium heights (SEHs) at stages VII–VIII and XII–XIV, number of undifferentiated embryonic cell transcription factor-1 (UTF-1) positive cells per tubule, UTF-1 positive tubules (%), plasma glutathione (GSH), and serum superoxide dismutase activities, testicular GSH activity and sperm viability (%) decreased whereas the number of terminal dUTP nick end labeling (TUNEL) positive cells per tubule, TUNEL positive tubules (%), testicular and serum malondialdehyde (MDA) levels, and the rate of mid-piece sperm abnormality increased in the BPA administered group. However, while the STDs at stages VII–VIII and XII–XIV, SEHs at stages VII–VIII, plasma GSH, and serum SOD activities increased, serum MDA level decreased in the CoQ10-BPA group. In conclusion, these results suggest a protective effect of CoQ10 against BPA-induced testicular toxicity in rats.
A multibiomarker approach to evaluate the effect of polyaromatic hydrocarbon exposure on oxidative and genotoxic damage in tandoor workers

We conducted a cohort study of tandoor workers to evaluate the relationship between the biomarkers of oxidative and genotoxic damage and exposure to polyaromatic hydrocarbons. A series of oxidative and genotoxic damage biomarkers, including urinary 8-hydroxy-2′-deoxyguanosine (8-OHdG), malondialdehyde (MDA) content, and tail moment (TM) by comet assay, was studied. A total of 76 tandoor workers and 79 demographically matched healthy individuals as controls were included. Our results showed that the tandoor workers had significantly higher urinary levels of 1-hydroxypyrene, urinary 8-OHdG, MDA content, and TM compared with the control population. The concentration of all these biomarkers increased with age in the control population as well as tandoor workers. In tandoor workers, significant variation in MDA, 8-oxodG (8-oxo-2′-deoxyguanosine) and TM concentration was detected between smokers (5.08 ± 1.72 nmol/mL, 16.01 ± 4.94 ng/mg creatinine, and 5.87 ± 0.98 µm, respectively) and nonsmokers (3.84 ± 0.98 nmol/mL, 13.74 ± 3.60 ng/mg creatinine, and 5.32 ± 0.69 µm, respectively). A similar pattern was obtained for the control population. We did not obtain significant variations for alcoholics and tobacco chewers. A significant increase in all these three biomarkers was observed with the increase in the period of work exposure in tandoor workers. Multivariate regression analysis also revealed that urinary 8-oxodG, MDA, and TM were statistically significantly related to age and period of work exposure. Overall, the present study showed that the exposure to wood smoke in tandoor workers under occupational conditions led to increased DNA damage because of oxidative stress and genotoxicity. These biomarkers, therefore, are good indices to assess oxidative DNA damage in these workers exposed to occupational genotoxicants. It is also necessary to make preventive changes in work conditions and lifestyle, which will help these occupational workers to lead a healthy life.
Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature

The number of published materials science articles has increased manyfold over the past few decades. Now, a major bottleneck in the materials discovery pipeline arises in connecting new results with the previously established literature. A potential solution to this problem is to map the unstructured raw-text of published articles onto structured database entries that allows for programmatic querying. To this end, we apply text-mining with named entity recognition (NER) for large-scale information extraction from the published materials science literature. The NER model is trained to extract summary-level information from materials science documents, including: inorganic material mentions, sample descriptors, phase labels, material properties and applications, as well as any synthesis and characterization methods used. Our classifier achieves an accuracy (f1) of 87%, and is applied to information extraction from 3.27 million materials science abstracts. We extract more than 80 million materials-science-related named entities, and the content of each abstract is represented as a database entry in a structured format. We demonstrate that simple database queries can be used to answer complex ``meta-questions" of the published literature that would have previously required laborious, manual literature searches to answer. All of our data and functionality has been made freely available (https://github.com/materialsintelligence/matscholar), and we expect these results to accelerate the pace of future materials science discovery.
IMPACT OF LES TURBULENCE SUBGRID MODELS IN THE JET RELEASE SIMULATION

The right choice of sub-grid scale (SGS) models in any simulation scenario plays an important role, since it can lead to more accurate results. This paper aims to investigate SGS models in order to perform jet release simulation accurately. Fire Dynamics Simulation (FDS) code is used for this propose. Preliminary results for jet centreline velocity profile are obtained considering four different SGS models. Findings are compared with analytical model. Three of four SGS models investigated let to excellent results.
The antimicrobial peptide database provides a platform for decoding the design principles of naturally occurring antimicrobial peptides

This article is written for the 2020 tool issue of Protein Science. It briefly introduces the widely used antimicrobial peptide database, initially online in 2003. After a description of the main features of each database version and some recent additions, the focus is on the peptide design parameters for each of the four unified classes of natural antimicrobial peptides (AMPs). The amino acid signature in AMPs varies substantially, leading to a variety of structures for functional and mechanistic diversity. Also, Nature is a master of combinatorial chemistry by deploying different amino acids onto the same structural scaffold to tune peptide functions. In addition, the single‐domain AMPs may be posttranslationally modified, self‐assembled, or combined with other AMPs for function. Elucidation of the design principles of natural AMPs will facilitate future development of novel molecules for various applications.
Psychometric properties of the Georgian version of Hospital Survey on Patient Safety Culture: a cross-sectional study

Objectives To study the psychometric properties of the Georgian version of the Hospital Survey on Patient Safety Culture (HSPSC-GE). Design Cross-sectional study. Setting Three Georgian hospitals. Participants Staff of participating hospitals (n=579 responses, response rate 41.6%). Primary and secondary outcome measures Psychometric properties (Model fit, internal consistency, construct validity) of the instrument, factor structure derived from the data. Results HSPSC-GE demonstrated acceptable construct validity but highly limited internal consistency (Cronbach’s alpha 0.35–0.87). Confirmatory factor analysis with the original 12-factor model resulted in poor model fit (root mean square error of approximation (RMSEA)=0.06; standardised root mean square residuals (SRMR)=0.08; comparative fit index (CFI)=0.74; goodness of fit index (GFI)=0.81; Tucker-Lewis Index (TLI)=0.70). Accounting for reversed item bias resulted in improved fit indices. Exploratory factor analysis resulted in an alternative five-factor model including only 19 items, but with satisfactory model fit (RMSEA=0.07; SRMR=0.07; CFI=0.90; GFI=0.89; TLI=0.88). Conclusions The HSPSC-GE as a whole demonstrated poor psychometric properties. However, a number of dimensions demonstrated acceptable internal consistency and reliability. Our results indicated presence of reversed item bias, which may be inherent to the original instrument design of the HSPSC and should be taken into account while interpreting or comparing results, as well as in analyses of psychometric properties of the instrument. Nevertheless, the HSPSC-GE provides first insights in hospital patient safety culture (PSC) in Georgia and we recommend using it in its full form to facilitate deeper analysis and further development of PSC in Georgian healthcare.
Deep Learning Frameworks on Apache Spark: A Review

ABSTRACT Deep Learning is undergoing intense study as it continues to attain outstanding results because of multiple levels of abstractions. Currently, deep learning algorithms are trained and executed on a single machine with multiple Graphics Processing Units (GPUs). To achieve better results, a large amount of data need to be trained in deep neural network with expensive GPUs and General Purpose GPU (GPGPUs). Training complex deep learning models take weeks and sometimes even months. In order to converge faster without comprising in accuracy percentage, distributed and parallel nature of Apache Spark comes into play. Spark has an advantage of in-memory and fast processing of data. Recent researchers involve the integration of deep learning and Apache Spark to exploit computation power and scalability. In this paper, all the recent deep learning frameworks are reviewed exhaustively with a detailed assessment and comparison. Experimentation results are provided to evaluate which frameworks are more suitable for deep models. We also discussed the open issues related to each deep learning framework.
Multilocus Analysis Resolves the European Finch Epidemic Strain of Trichomonas gallinae and Suggests Introgression from Divergent Trichomonads

Abstract In Europe, Trichomonas gallinae recently emerged as a cause of epidemic disease in songbirds. A clonal strain of the parasite, first found in the United Kingdom, has become the predominant strain there and spread to continental Europe. Discriminating this epidemic strain of T. gallinae from other strains necessitated development of multilocus sequence typing (MLST). Development of the MLST was facilitated by the assembly and annotation of a 54.7 Mb draft genome of a cloned stabilate of the A1 European finch epidemic strain (isolated from Greenfinch, Chloris chloris, XT-1081/07 in 2007) containing 21,924 protein coding genes. This enabled construction of a robust 19 locus MLST based on existing typing loci for Trichomonas vaginalis and T. gallinae. Our MLST has the sensitivity to discriminate strains within existing genotypes confidently, and resolves the American finch A1 genotype from the European finch epidemic A1 genotype. Interestingly, one isolate we obtained from a captive black-naped fruit dove Ptilinopsus melanospilus, was not truly T. gallinae but a hybrid of T. gallinae with a distant trichomonad lineage. Phylogenetic analysis of the individual loci in this fruit dove provides evidence of gene flow between distant trichomonad lineages at 2 of the 19 loci examined and may provide precedence for the emergence of other hybrid trichomonad genomes including T. vaginalis.
Physical Abuse Explains Sex Differences in the Link Between Psychopathy and Aggression

Psychopathy has long been associated with aggression. However, few studies have looked at differences between men and women. Studies that do exist demonstrate that psychopathy differentially relates to aggression in men and women and indicate that environmental factors may play a significant role in influencing these associations. A key environmental factor is a history of lifetime physical abuse (LPA), which has been linked to aggressive behavior in both men and women. The aim of the present study was to test if psychopathy differentially predicted physical, verbal, and indirect aggression in men and women, and if these associations were moderated by LPA. In a large community sample of men (n = 369) and women (n = 204), we assessed the 4-facet model of psychopathy (Interpersonal, Affective, Lifestyle, Antisocial) with the Psychopathy Checklist: Screening Version, LPA with the Addiction Severity Index, and self-report aggression with the Aggression Questionnaire. Results revealed sex differences and similarities. Physical aggression was associated with the affective facet of psychopathy in both men and women, though in different directions based on the moderating effects of LPA. Verbal aggression was associated with higher antisocial facet scores and LPA for men and not women. Finally, indirect aggression was associated with the antisocial facet of psychopathy for men, and the interpersonal facet for women, and these associations were not moderated by LPA. In women, low antisocial facet scores and no LPA were found to be protective for indirect aggression. These results show that LPA and psychopathy generally increase the risk of aggression, but the interaction between LPA and psychopathy differentiates the risk of aggression forms for men and women. These sex differences highlight the need for female-responsive interventions to target sex-specific risk factors for aggressive behavior.
Pseudouridine synthase 7 impacts Candida albicans rRNA processing and morphological plasticity

RNA can be modified in over 100 distinct ways, and these modifications are critical for function. Pseudouridine synthases catalyse pseudouridylation, one of the most prevalent RNA modifications. Pseudouridine synthase 7 modifies a variety of substrates in Saccharomyces cerevisiae including tRNA, rRNA, snRNA, and mRNA, but the substrates for other budding yeast Pus7 homologues are not known. We used CRISPR‐mediated genome editing to disrupt Candida albicans PUS7 and find absence leads to defects in rRNA processing and a decrease in cell surface hydrophobicity. Furthermore, C. albicans Pus7 absence causes temperature sensitivity, defects in filamentation, altered sensitivity to antifungal drugs, and decreased virulence in a wax moth model. In addition, we find C. albicans Pus7 modifies tRNA residues, but does not modify a number of other S. cerevisiae Pus7 substrates. Our data suggests C. albicans Pus7 is important for fungal vigour and may play distinct biological roles than those ascribed to S. cerevisiae Pus7.
Amphotericin B loaded nanostructured lipid carriers for parenteral delivery: Characterization, antifungal and in vitro toxicity assessment.

BACKGROUND Amphotericin B (AmB) is one of the gold standards for the treatment of systemic fungal infections. Nowadays, only intravenous administration (IV) of AmB has been available due to its low aqueous solubility. Two forms of AmB are available. The first is Fungizone®, a mixture of AmB and sodium deoxcycholate that produces severe nephrotoxicity. The second is lipid-based formulations that found to reduce nephrotoxicity, but they are costly and require higher dose than Fungizone®. Thus, the cheaper delivery system with reduced AmB toxicity is needed. OBJECTIVE To develop and characterize AmB loaded-nanostructured lipid carriers (AmB-loaded NLCs) for IV administration to reduce AmB toxicity. METHODS AmB-loaded NLCs with different solid lipids were prepared by the high-pressure homogenization technique. Their physicochemical properties and the drug release profile were examined. The molecular structure of the AmB, antifungal and hemolysis activities of developed AmB-loaded NLCs were also evaluated. RESULTS AmB-loaded NLCs of ~110 to ~140 nm in diameter were successfully produced with a zeta potential of ~-19 mV and entrapment efficiency of ~75%. In vitro release showed fast release characteristics. AmB-loaded NLCs reduced AmB molecular aggregation and Peak I/IV ratio showed a partial aggregation of AmB, suggesting that less nephrotoxicity compared to Fungizone®. The AmB-loaded NLCs displayed very low toxicity in hemolysis compared to the free drug and Fungizone®. In vitro antifungal activity of AmB-loaded NLCs showed MIC of 0.25 µgmL-1. CONCLUSION AmB-loaded NLCs present high potential carriers for effective IV treatment with prolonged circulation time and reduced toxicity.
A Quantum Ant Colony Multi-Objective Routing Algorithm in WSN and Its Application in a Manufacturing Environment

In many complex manufacturing environments, the running equipment must be monitored by Wireless Sensor Networks (WSNs), which not only requires WSNs to have long service lifetimes, but also to achieve rapid and high-quality transmission of equipment monitoring data to monitoring centers. Traditional routing algorithms in WSNs, such as Basic Ant-Based Routing (BABR) only require the single shortest path, and the BABR algorithm converges slowly, easily falling into a local optimum and leading to premature stagnation of the algorithm. A new WSN routing algorithm, named the Quantum Ant Colony Multi-Objective Routing (QACMOR) can be used for monitoring in such manufacturing environments by introducing quantum computation and a multi-objective fitness function into the routing research algorithm. Concretely, quantum bits are used to represent the node pheromone, and quantum gates are rotated to update the pheromone of the search path. The factors of energy consumption, transmission delay, and network load-balancing degree of the nodes in the search path act as fitness functions to determine the optimal path. Here, a simulation analysis and actual manufacturing environment verify the QACMOR's improvement in performance.