Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk factors for mortality among hospitalized patients with COVID-19

Objectives To develop a prognostic model to identify and quantify risk factors for mortality among patients admitted to the hospital with COVID-19. Design Retrospective cohort study. Patients were randomly assigned to either training (80%) or test (20%) sets. The training set was used to fit a multivariable logistic regression. Predictors were ranked using variable importance metrics. Models were assessed by C-indices, Brier scores, and calibration plots in the test set. Setting Optum de-identified COVID-19 Electronic Health Record dataset. Participants 17,086 patients hospitalized with COVID-19 between February 20, 2020 and June 5, 2020. Main outcome measure All-cause mortality during hospital stay. Results The full model that included information on demographics, comorbidities, laboratory results and vital signs had good discrimination (C-index = 0.87) and was well calibrated, with some overpredictions for the most at-risk patients. Results were generally similar on the training and test sets, suggesting that there was little overfitting. Age was the most important risk factor. The performance of models that included all demographics and comorbidities (C-index = 0.79) was only slightly better than a model that only included age (C-index = 0.76). Across the study period, predicted mortality was 1.2% for 18-year olds, 8.4% for 55-year olds, and 28.6% for 85-year olds. Predicted mortality across all ages declined over the study period from 21.7% by March to 13.3% by May. Conclusion Age was the most important predictor of all-cause mortality although vital signs and laboratory results added considerable prognostic information with oxygen saturation, temperature, respiratory rate, lactate dehydrogenase, and white blood cell count being among the most important predictors. Demographic and comorbidity factors did not improve model performance appreciably. The model had good discrimination and was reasonably well calibrated, suggesting that it may be useful for assessment of prognosis.
Immediate Early Gene Expression in Brain Regions Associated with the Social Behavioral Network After Male Competition in Medaka Fish

In this study, we used the immediate early gene, egr-1, as a marker for neural activation and examined whether egr-1 expression is affected in brain regions associated with the social behavioral network (SBN) when social rank is determined and changed in male medaka fish (Oryzias latipes). Based on the behavioral contest protocol used in this study, we obtained four types of males: social ascending, social descending, dominant, and subordinate. In some brain regions associated with the SBN, we detected higher egr-1 expression in ascending and descending males than in dominant and subordinate males. Social-rank stable males (i.e., dominant and subordinate male fish) showed a similar level of egr-1 expression as the control male fish, which were housed without social stimulus of encountering another conspecific. These findings suggested that the transitioning of social rank could enhance neural activity in some brain regions associated with the SBN in male medaka. The use of medaka fish has many advantages in various fields of research such as genetics, developmental biology, environmental biology, and behavioral neurology. The findings of this study would contribute to future research exploring the roles of the SBN regions in regulating physiological and behavioral events associated with social-rank transition.
Trade-off of sexual and asexual recruitment in a dominant weed Ligularia virgaurea (Maxim.) in Alpine grasslands (China)

Ligularia virgaurea (Maxim.) is a typical naturally-occurring native noxious weed, widely distributed in alpine grasslands of the Tibetan Plateau, China. Three field sampling plots (30 m ́ 50 m) dominated by L. virgaurea were selected to study its population colonization mode and the relationship between sexualand clonalrecruitment in alpine meadow of the QinghaiTibetan Plateau, NW China. Field investigations were conducted on its soil seed bank, seed rain and the individuals of new recruitment (seedlings and ramets) to study its sexual and asexual recruitment. And, 46 individuals which produced the seeds were selected randomly to study their relationship between seed production and ramet production. Results showed that there were more ramets (26.23 ramets m–2) and less seedlings (6.70 seedlings m–2) and a mean value of seed rain was close to 8.04 seeds m–2, but the soil seed bank for this species was not found in study sites. Significantly negative correlations (r = – 0.416, P <0.001) between seed number per individual and ramet number per adult individual were found for L. vrigaurea in studied alpine grasslands. Our results revealed that clonal reproduction was the main population colonization mode. In addition, there was a significantly negative relationship between seed production and ramets for this species.
SVIPEX: A Web Service for Discovering and Visualizing Instance Spanning Constraints based on Process Execution Logs

Instance spanning constraints (ISC) realize controls on the execution of multiple process instances of one or several process types. Examples include synchronization at critical resources and authorization across several instances. ISC leave marks in process execution logs, e.g., process tasks having the same time stamp. As ISC are not always known and might change over time, process execution logs provide a valuable resource for mining ISC. Algorithms for ISC discovery have been proposed in previous work. SVIPEX implements these algorithms and provides a novel visualization for discovered ISC through a lightweight web service. This way ISC mining becomes accessible. SVIPEX maturity is demonstrated based on case studies from manufacturing and higher education.
RegMiner: Taming the Complexity of Regulatory Documents for Digitalized Compliance Management

Business process compliance has become a crucial aspect for companies due to severe ﬁnes that can be imposed if constraints and rules emerging from regulatory documents are violated. Regulatory documents are often written in natural language and analyzing them is mainly done manually since only limited tool support is available. Therefore, we present RegMiner , a web service for discovering and visualizing constraints from regulatory documents. By employing NLP and data mining techniques, compliance constraints can be automatically extracted, grouped, and visualized leading to a separation of relevant and non-relevant document parts and insights into, e.g., duties of stakeholders. A case study based on a current document from the European parliament regarding the ﬁnancial domain demonstrates RegMiner’s maturity.
A molecular genetic survey of immune response genes and biodiversity of industrial and non-industrial chickens

The current practices in industrial poultry breeding developed specialized production lines from very few breeds, resulting in reducting in genetic diversity. “Free run/free range” production systems (non-industrial) are a more recent trend in the poultry sector. Non-industrial chicken populations may differ genetically and have more diversity in disease resistance genes than industrial populations. To test this hypothesis, six chicken populations from non-industrial source; Silkies (SK), Taiwanese Cross (TC), Shiqi (SQ), Yellow Shiqi (YSQ), Yellow Wai-Chow (YW), and Agassiz Cross (AC), and industrial populations; Lohmann White (LW) and Lohmann Brown (LB), were sampled and three related experiments were carried out. First, I used 18 microsatellite markers to study genetic diversity within and among the chicken populations. The industrial population LB and the experimental cross AC which shared some common ancestors, were closely related. Non-industrial chickens SK and TC, with Chinese breed ancestry, were related to SQ, YSQ and YW. LW with White Leghorn ancestry, was not related to the nonindustrial populations. Except for YSQ and SQ, STRUCTURE clustered these chicken populations to the genetically distinct groups. Secondly, I used microsatellite marker (LEI0258), situated within the Major Histocompatibility Complex (MHC) region, to reflect the genetic variability of the adaptive immune system. Results indicated that the industrial chicken populations may have less genetic variability in the MHC compared to non-industrial populations but industrial populations may have higher frequency of certain alleles that were part of their selection history against specific pathogens. Finally, I used SNP markers to examine the genetic variation in candidate genes associated with the innate immune system (ChB6, Casp-1, IAP-1, TGF-β3, BMP-7, TLR4, MD-2, IFN-γ, iNOS, IL-2, Mx1, and TVB). There was no difference between industrial and non-industrial populations in genetic variability in this immune system. The results provided partial support for the hypothesis that industrial populations may have higher resistance to specific diseases, while nonindustrial populations may have higher general disease resistance.
Imunodiagnóstico da toxocaríase humana com antígeno TES30 recombinante

The toxocariasis is a widespread zoonosis worldwide, thus becoming an important public health problem. The diversity of clinical conditions associated with the different sites (liver, lungs, brain, eyes, lymph nodes, etc.) of the Toxocara canis larvae in the human body, hamper the diagnosis of this disease. In this context, immunological methods for detecting anti-T. canis serum antibodies were developed. Currently, enzyme-linked immunosorbent assay (ELISA) associated with the excretorysecretory antigens of T. canis larvae (TES), and sera previously adsorved with somatic antigen of Ascaris spp. has been used as a standard method for testing of IgG anti-T. canis serum antibodies. The antigen TES is obtained from T. canis larvae cultivation and demand four months of expensive and laborious work. Given the above, recombinant antigens are being tested, aiming at improving the immunodiagnosis of human toxocariasis. The objective of this work was to produce recombinant excretion/secretion 30kDa T. canis larval antigen (TES30) in two heterologous protein expression systems, and evaluate them in the immunodiagnosis of human toxocariasis. The recombinants proteins rTES30E and rTES30P, respectively, produced in Escherichia coli and Pichia pastoris, were characterized by un indirect ELISA to detect anti-T. canis IgG in experimentally infected mice serum, which showed 100% effectiveness compared to native TES. For detecting anti-T. canis IgG antibodies in human sera, the rTES30E showed sensitivity and specificity (95% CI) of 95.8% and 82.6%, while rTES30P showed 95.4% and 92.8%, respectively, in comparison to native TES. Thus, we conclude that both recombinants proteins have antigenic potential, becoming an alternative to the use of native TES in immunodiagnosis of human toxocariasis. %%%%A toxocariase humana e uma zoonose difundida em todo o mundo, constituindo-se em um importante problema de saude coletiva, porem e negligenciada. A diversidade de quadros clinicos associada aos diferentes sitios (figado, pulmoes, cerebro, olhos, gânglios linfaticos, etc.) em que as larvas de Toxocara canis podem se alojar no organismo humano, dificulta o diagnostico desta parasitose. Neste contexto, metodos imunologicos para a deteccao de anticorpos anti-T. canis foram desenvolvidos. Atualmente, o ensaio imunoenzimatico (ELISA) associado ao antigeno de excrecao e secrecao de T. canis (TES), com adsorcao previa de soros com antigeno somatico de Ascaris spp. , tem sido utilizado como metodo padrao para pesquisa de anticorpos IgG sericos anti-T. canis. O antigeno TES e obtido a partir do cultivo de larvas de T. canis e demanda, aproximadamente, quatro meses de trabalho dispendioso e fastidioso. Diante do exposto, antigenos recombinantes estao sendo testados, visando o aperfeicoamento do imunodiagnostico da toxocariase humana. Assim, o objetivo deste trabalho foi produzir o antigeno de excrecao/secrecao de 30kDa de T. canis (TES30) em dois sistemas heterologos de expressao proteica, e avalia-los no imunodiagnostico da toxocariase humana. As proteinas…
EFFECT OF DIFFERENT SALINITY LEVELS ON MORPHO-PHYSIOLOGICAL CHARACTERS OF 8 WHEAT GENOTYPES (TRITICUM AESTIVUM L.)

For examining and producing salt tolerant wheat genotype based on morpho-physiological characteristics, a factorial experiment was set out in a green-house in a completely randomized design with three replications. The treatments included four saline solutions (0, 150, 200 and 250 mM NaCl) and 8 wheat genotypes: 3 hybrids (Cajema × Sette Cerros, Cajema × HO2 and Cajema × Lermaroja), 4 parents (Sette Cerros, HO2, Lermaroja, Cajema) and Axona as a control. Data for Na + , K + and Cl concentrations and Na /K ratio in the first leaf below the flag leaf yield and 1000 grain yield were measured. Based on analysis of variance, salinity had positive significant effect on Na + , Cl concentrations and Na /K ratio. As salinity levels increased, yield and 1000 grain weight and K + concentration declined. Based on Na /K ratio, the best physiological characteristic for recognizing sensitive and tolerant genotypes, Cajema was the most tolerant genotype. Hybrids produced in this study weren’t good for salinity condition and the hybrids didn’t show more feature than their parents.
Synaptic and extrasynaptic NMDA receptors in hippocampal neurons: regulation of nuclear shape and cell fate

Neuronal activity induces processes important for memory formation and cell survival by inducing calcium influx through synaptic NMDA receptors. Calcium subsequently activates the ERK-MAP kinase cascades that transmits the signal from the synapse to the nucleus. A second mode for synapse-to-nucleus communication involves a propagating calcium signal that invades the cell nucleus. Nuclear calcium is a key regulator of gene expression mediated by the transcription factor CREB. The nuclear architecture contains intranuclear structures that have been shown to facilitate calcium influx into the nucleus. This thesis describes a novel mechanism in which calcium influx through NMDA receptors induces morphological changes in the majority of hippocampal neurons by forming infoldings of the nuclear membrane. These infoldings are generated by an increase in the surface area of the nuclear membrane and require activation of the ERK-MAP kinase cascade as well as a nuclear calcium signal. Infoldings are formed rapidly within one hour and can be reversed by silencing of synaptic activity. The stability of infoldings increases within days after activation of synaptic NMDA receptors, suggesting the involvement of gene transcription in the stabilization process. Synaptic activity is counteracted by overactivation of extrasynaptic NMDA receptors. Calcium influx through these receptors leads to a rapid loss of nuclear infoldings. It also activates pathways leading to the shut-off of CREB and to cell death. I attempted to dissect the intracellular pathways downstream of synaptic and extrasynaptic NMDA receptors by designing a specific antagonist for extrasynaptic NMDA receptors. This should be achieved by coupling of Conantokin-G, a peptide antagonist against the NR2B subunit of NMDA receptors, to beads of a specific size. The peptide coupled to beads should allow blockade of extrasynaptic NMDA receptors and thereby block cell death pathways, leaving synaptic NMDA receptors unaffected.
A Revision of the Genera Stenopola and Cornops (Orthoptera, Acrididae, Leptysminae)

Illustrations, diagnoses and distributional records are given for the 18 species and sub- species, 8 of which are new, of the genus Stenopola and the 5 species and subspecies, two of which are new, of the genus Cornops, as here recognized. This report on these two genera is the first part of a continuing study of the Tetrataeniini, a Neotropical tribe of grasshoppers. Oxyblepta, Inusia, Heniola and Pseudoxyblepta are treated as congeneric with the genus Stenopola, thus becoming new junior synonyms. Twenty-three species names are treated as junior synonyms, most of which are new synonyms. Habitat information is given when available. (aquatic habitats, Cornops, grasshoppers, Neotropical, new taxa, Orthoptera, Stenopola, taxonomic revision)
Seasonal ultrastructural changes in apocrine gland cells in back skin of male brown bears (Ursus arctos)

Oily secretions from the back skin are involved in the marking behavior of male brown bears (Ursus arctos), and apocrine glands in back skin are activated during the breeding season. Here, we investigated seasonal changes in the intracellular organelles of apocrine gland cells in the back skin of male brown bears using transmission electron microscopy (TEM) and osmium‐maceration scanning electron microscopy (OM‐SEM). The morphological features of mitochondria and intracellular granules, and secretory mechanisms obviously differed between breeding and non‐breeding seasons. The TEM findings showed that contents of low‐density granules were released into the glandular lumen by frequent exocytosis, and sausage‐shaped mitochondria were located in the perinuclear region during the non‐breeding season. In contrast, high‐density granules appeared in the apical region and in projections during the breeding season, and swollen mitochondria and lysosome‐like organelles separating into high‐density granules were located in the perinuclear region. The OM‐SEM findings revealed swollen mitochondria with only a few partially developed cristae, and small mitochondria with cristae shaped like those in swollen mitochondria in the apical regions during the breeding season. These findings indicated that the small mitochondria corresponded to the high‐density granules identified by TEM. These findings suggested that mitochondria in apocrine gland cells swell, degenerate, fracture into small pieces, and are finally released by apocrine secretions during the breeding season. Small mitochondria released in this secretory manner might function as the source of chemical signals in the oily secretions of brown bears during the breeding season.
Effect of local cold application during exercise on gene expression related to mitochondrial homeostasis

Exercise training increases mitochondrial content in active skeletal muscle. Previous work suggests that mitochondrial-related genes respond favorably to exercise in cold environments. However, the impact of localized tissue cooling is unknown. The purpose of this study was to determine the impact of local muscle cooling during endurance exercise on human skeletal muscle mitochondrial-related gene expression. Twelve subjects (age, 28 ± 6 years) cycled at 65% peak power output. One leg was cooled (C) for 30 min before and during exercise with a thermal wrap while the other leg was wrapped but not cooled, room temperature (RT). Muscle biopsies were taken from each vastus lateralis before and 4 h after exercise for the analysis of gene expression. Muscle temperature was lower in the C (29.2 ± 0.7 °C) than the RT (34.1 ± 0.3 °C) condition after pre-cooling for 30 min before exercise (p < 0.001) and remained lower after exercise in the C (36.9 ± 0.5) than the RT (38.4 ± 0.2, p < 0.001) condition. PGC-1α and NRF1 mRNA expression were lower in the C (p = 0.012 and p = 0.045, respectively) than the RT condition at 4 h after exercise. There were no temperature-related differences in other genes (p > 0.05). These data suggest that local cooling has an inhibitory effect on exercise-induced PGC-1α and NRF1 expression in human skeletal muscle. Those considering using local cooling during exercise should consider other systemic cooling options. Novelty: Local cooling has an inhibitory effect on exercise-induced PGC-1α and NRF1 expression in human skeletal muscle. Local cooling may lead to a less robust exercise stimulus compared with standard conditions.
Repurposing drugs for treatment of SARS-CoV-2 infection: computational design insights into mechanisms of action

Abstract The COVID-19 pandemic has negatively affected human life globally. It has led to economic crises and health emergencies across the world, spreading rapidly among the human population and has caused many deaths. Currently, there are no treatments available for COVID-19 so there is an urgent need to develop therapeutic interventions that could be used against the novel coronavirus infection. In this research, we used computational drug design technologies to repurpose existing drugs as inhibitors of SARS-CoV-2 viral proteins. The Broad Institute’s Drug Repurposing Hub consists of in-development/approved drugs and was computationally screened to identify potential hits which could inhibit protein targets encoded by the SARS-CoV-2 genome. By virtually screening the Broad collection, using rationally designed pharmacophore features, we identified molecules which may be repurposed against viral nucleocapsid and non-structural proteins. The pharmacophore features were generated after careful visualisation of the interactions between co-crystalised ligands and the protein binding site. The ChEMBL database was used to determine the compound’s level of inhibition of SARS-CoV-2 and correlate the predicted viral protein target with whole virus in vitro data. The results from this study may help to accelerate drug development against COVID-19 and the hit compounds should be progressed through further in vitro and in vivo studies on SARS-CoV-2. Graphical Abstract Communicated by Ramaswamy H. Sarma
Nonopioid versus Opioid Based General Anesthesia Technique for Laparoscopic Cholecystectomy

Background: The choices of premedication and anesthetic techniques are able to influence the neurohormonal stress response by modulating the pathophysiological pathways. Various pharmacological agents like nitroglycerine, beta blocker, and opioids were used to decrease surgical stress of laparoscopic procedures to improve outcome, with their own limitations. Objective: It was to compare the effect of opioid-free (using dexmedetomidine and propofol) and opioid-based (using fentanyl and propofol) TIVA techniques on hemodynamic stability, sedation postoperative pain intensity and the incidence of side effects in patients scheduled for LC. Patients and Methods: Eighty patients who were scheduled for elective laparoscopic cholecystectomy were included in this study. Before induction of anesthesia, patients were randomly divided into two equal groups: (40 each). Dexmedetomidine group(Non-opioid group) received dexmedetomidine (1 µg/kg) over 10 minutes before induction of anesthesia followed by continuous infusion of 0.5 µg/kg/hr. till the end of surgery and Fentanyl group (Opioid group) received fentanyl (1.0 µg/kg) over 10 minutes before induction of anesthesia followed by continuous infusion of 0.4 µg/kg/hr. till the end of surgery. Results: The results of the present study showed that there were no significant differences between the two groups regarding HR and MAP except after loading dose of the studied drugs, after intubation, after pneumoperitoneum, 15 min, 30 min, 45 min, and 60 min after induction where it was lower in dexmedetomidine group than fentanyl group. There were no significant differences between two groups regarding intraoperative SPO2, postoperative SPO2 and blood glucose level (mg/dl). Conclusion: This study concluded that dexmedetomidine is better than fentanyl for patients who undergo elective laparoscopic cholecystectomy due to perioperative maintaining of hemodynamic stability, decrease dosages of postoperative analgesics, prolong the duration of postoperative analgesia and decrease postoperative nausea and vomiting.