Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation of SARS-CoV-2 in Viral Cell Culture in Immunocompromised Patients With Persistently Positive RT-PCR Results

Immunocompromised adults can have prolonged acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive RT-PCR results, long after the initial diagnosis of coronavirus disease 2019 (COVID-19). This study aimed to determine if SARS-CoV-2 virus can be recovered in viral cell culture from immunocompromised adults with persistently positive SARS-CoV-2 RT-PCR tests. We obtained 20 remnant SARS-CoV-2 PCR positive nasopharyngeal swabs from 20 immunocompromised adults with a positive RT-PCR test ≥14 days after the initial positive test. The patients’ 2nd test samples underwent SARS-CoV-2 antigen testing, and culture with Vero-hACE2-TMPRSS2 cells. Viral RNA and cultivable virus were recovered from the cultured cells after qRT-PCR and plaque assays. Of 20 patients, 10 (50%) had a solid organ transplant and 5 (25%) had a hematologic malignancy. For most patients, RT-PCR Ct values increased over time. There were 2 patients with positive viral cell cultures; one patient had chronic lymphocytic leukemia treated with venetoclax and obinutuzumab who had a low viral titer of 27 PFU/mL. The second patient had marginal zone lymphoma treated with bendamustine and rituximab who had a high viral titer of 2 x 106 PFU/mL. Most samples collected ≥7 days after an initial positive SARS-CoV-2 RT-PCR had negative viral cell cultures. The 2 patients with positive viral cell cultures had hematologic malignancies treated with chemotherapy and B cell depleting therapy. One patient had a high concentration titer of cultivable virus. Further data are needed to determine risk factors for persistent viral shedding and methods to prevent SARS-CoV-2 transmission from immunocompromised hosts.
Comparison of PK/PD Targets and Cutoff Values for Danofloxacin Against Pasteurella multocida and Haemophilus parasuis in Piglets

Danofloxacin is a synthetic fluoroquinolone with broad-spectrum activity developed for use in veterinary medicine. The aim of this study was to evaluate the pharmacokinetic/pharmacodynamic (PK/PD) targets, PK/PD cutoff values and the optimum doses of danofloxacin against P. multocida and H. parasuis in piglets. Single dose serum pharmacokinetics was determined in piglets after intravenous and intramuscular administration of 2.5 mg/kg. Danofloxacin was well absorbed and fully bioavailable (95.2%) after intramuscular administration of 2.5 mg/kg. The epidemiological cutoff (ECOFF) values of danofloxacin from 931 P. multocida isolates and 263 H. parasuis isolates were 0.03 and 4 mg/L, respectively. Danofloxacin MICs determined in porcine serum were markedly lower than those measured in artificial broth, with a broth/serum ratio of 4.33 for H. parasuis. Compared to P. multocida, danofloxacin exhibited significantly longer post-antibiotic effects (3.18–6.60 h) and post-antibiotic sub-MIC effects (7.02–9.94 h) against H. parasuis. The mean area under the concentration-time curve/MIC (AUC24h/MIC) targets of danofloxacin in serum associated with the static and bactericidal effects were 32 and 49.8, respectively, for P. multocida, whereas they were 14.6 and 37.8, respectively, for H. parasuis. Danofloxacin AUC24h/MIC targets for the same endpoints for P. multocida were higher than those for H. parasuis. At the current dose of 2.5 mg/kg, the PK/PD cutoff (COPD) values of danofloxacin against P. multocida and H. parasuis were calculated to be 0.125 and 0.5 mg/L, respectively, based on Monte Carlo simulations. The predicted optimum doses of danofloxacin for a probability of target attainment (PTA) of > 90% to cover the overall MIC population distributions of P. multocida and H. parasuis in this study were 2.38 and 13.36 mg/kg, respectively. These PK/PD-based results have potential relevance for the clinical dose optimization and evaluation of susceptibility breakpoints for danofloxacin in the treatment of swine respiratory tract infections involving these pathogens.
Increasing Diversity in Developmental Biology

The demographic profile of the scientific and biomedical workforce in the United States does not reflect the population at large (https://ncses.nsf.gov/pubs/nsf21321/data-tables; www.census.gov), raising concerns that there will be too few trained researchers in the future, the scope of research interests will not be broad enough, gaps in equity and social justice will continue to increase, and the safeguards to the integrity of the scientific enterprise could be jeopardized. To diversify the pool of scientists, the Society for Developmental Biology (SDB) developed the Choose Development! Program—a two-summer immersion for undergraduate students belonging to underrepresented (UR) populations in STEM to join the research laboratory of an established SDB member. This research-intensive experience was augmented by a multi-tier mentoring plan for each student, society-wide recognition, professional development activities and networking at national meetings. The strengths of the Choose Development! Program were leveraged to expand inclusion and outreach at the Society’s leadership level, the Board of Directors (BOD), which then led to significant changes that impacted the SDB community. The cumulative outcomes of the Choose Development! Program provides evidence that community-based, long-term advocacy, and mentoring of young UR scientists is successful in retaining UR students in scientific career paths and making a scientific society more inclusive.
Case studies on the safety management at construction site

Cases of construction site accidents always happen. In line with the efforts to reduce accidents at construction sites in Malaysia, the objectives of this research are to determine the current safety practices at construction sites, to identify the safety practices related problems, and to identify the strategies to reduce the safety practices related problems. Two case studies were conducted for data collection. Data were collected through semi-structured interviews with the safety officer of the respective project. It is concluded from the research findings that generally the construction site has good and structured as far as safety practices are concerned. Among the practices are safety policy, education and training, site safety inspection, safety auditing, safety meeting, site safety organization, personal protective equipments, emergency support and safety measuring devices, fall protective systems, and safety promotions. Nevertheless, several problems are encountered in the safety practices; the problems are ignorance of workers on work procedures, lack of financial allocation for safety management, lack of awareness among workers, and language barrier between supervisors and workers. Several strategies have been suggested to overcome the problems, the strategies are to provide effective safety training, allocation of budget for safety management, full commitment from the top management, and to provide safety booklets in various languages as the strategies to reduce problems in safety practices. The suggestion cover three aspects for the implementation of safety practices, i.e. awareness of workers, commitment of top management and the allocation of resources. The findings of this research would reduce the gap of understanding on the aspect of safety practices at construction site in Malaysia and can be used as construction practitioners as a source of reference in their site safety management.
Interferon Alpha Induces Cellular Autophagy and Modulates Hepatitis B Virus Replication

Hepatitis B virus (HBV) infection causes acute and chronic liver diseases, including severe hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). Interferon alpha 2a (IFNα-2a) is commonly used for treating chronic HBV infection. However, its efficacy remains relatively low. Yet, the immunological and molecular mechanisms for successful IFNα-2a treatment remain elusive. One issue is whether the application of increasing IFNα doses may modulate cellular processes and HBV replication in hepatic cells. In the present study, we focused on the interaction of IFNα signaling with other cellular signaling pathways and the consequence for HBV replication. The results showed that with the concentration of 6000 U/ml IFNα-2a treatment downregulated the activity of not only the Akt/mTOR signaling but also the AMPK signaling. Additionally, IFNα-2a treatment increased the formation of the autophagosomes by blocking autophagic degradation. Furthermore, IFNα-2a treatment inhibited the Akt/mTOR signaling and initiated autophagy under low and high glucose concentrations. In reverse, inhibition of autophagy using 3-methyladenine (3-MA) and glucose concentrations influenced the expression of IFNα-2a-induced ISG15 and IFITM1. Despite of ISGs induction, HBV replication and gene expression in HepG2.2. 15 cells, a cell model with continuous HBV replication, were slightly increased at high doses of IFNα-2a. In conclusion, our study indicates that IFNα-2a treatment may interfere with multiple intracellular signaling pathways, facilitate autophagy initiation, and block autophagic degradation, thereby resulting in slightly enhanced HBV replication.
Is the Peripheral Zone Thickness an Indicator of a Learning Curve in Bipolar Transurethral Plasma Enucleation of the Prostate?—A Single Center Cohort Study

Background We conducted this cohort study to assess the differences in the learning curve of bipolar transurethral plasma enucleation of the prostate (B-TUEP) associated with prostatic peripheral zone thickness (PZT) under MRI quantitative measurements. Methods For the study, 60 patients with benign prostatic hyperplasia (BPH) were involved. PZT are defined as “Thin” (<7 mm), “Thick” (>10 mm), and “Medium” (in between), with 20 patients in each group. Learning stages were defined as Group 1 (No. 1–20), Group 2 (No. 21–40), and Group 3 (No. 41–60). We measured parameters of the prostate, such as PZT and transitional zone thickness (TZT), with MRI. A learner with no experience in enucleation performed the operations. Statistical analyses were performed to compare the differences. Pearson correlation analysis and multiple linear regression analysis evaluated the relationship between characteristics of patients. P < 0.05 was deemed statistically significant. Results One-Way ANOVA revealed different enucleation efficiency (0.811 ± 0.18 vs. 0.748 ± 0.14 vs. 0.634 ± 0.16), prostate volume (58.9 ± 15.33 vs. 57.3 ± 15.58 vs. 46.6 ± 14.10), and thickness of transition zone (44.45 ± 7.60 vs. 42.45 ± 6.08 vs. 34.78 ± 6.04) among Thin, Medium, and Thick groups. The enucleation efficiency is different between groups divided by learning stages (Group 1 vs. Group 3, 0.658 vs. 0.783; Group 2 vs. Group 3, 0.751 vs. 0.783). Pearson correlation analysis reveals that PZT was negatively correlated with prostate volume (r = −0.427), resection weight (r = −0.35), enucleation efficiency (r = −0.445), and TZT (r = −0.533), and was positively correlated with Q-max (r = 0.301) and bladder outlet obstruction index (BOOI) (r = 0.388). The regression coefficients of PZT, TZT, prostate volume, and Q-max were −0.012, 0.008, 0.007, and 0.013, respectively (all P < 0.05). Conclusion Lower PZT is independent of higher enucleation efficiency, larger adenoma, and higher TZT. PZT may be an important factor on the learning curve of B-TUEP. Higher TZT, prostate volume. and Q-max may also relate to higher enucleation efficiency. For B-TUEP learners, it seems easier to perform the operation when the PZT is low, though more care should be taken with the capsule perforation. Further, the capsule plane should be maintained more attentively if the PZT is high.
Full Chromosomal Relationships Between Populations and the Origin of Humans

A comprehensive description of human genomes is essential for understanding human evolution and relationships between modern populations. However, most published literature focuses on local alignment comparison of several genes rather than the complete evolutionary record of individual genomes. Combining with data from the 1,000 Genomes Project, we successfully reconstructed 2,504 individual genomes and propose Divided Natural Vector method to analyze the distribution of nucleotides in the genomes. Comparisons based on autosomes, sex chromosomes and mitochondrial genomes reveal the genetic relationships between populations, and different inheritance pattern leads to different phylogenetic results. Results based on mitochondrial genomes confirm the “out-of-Africa” hypothesis and assert that humans, at least females, most likely originated in eastern Africa. The reconstructed genomes are stored on our server and can be further used for any genome-scale analysis of humans (http://yaulab.math.tsinghua.edu.cn/2022_1000genomesprojectdata/). This project provides the complete genomes of thousands of individuals and lays the groundwork for genome-level analyses of the genetic relationships between populations and the origin of humans.
On the Truncated Multidimensional Moment Problems in Cn

We consider the problem of finding a (non-negative) measure μ on B(Cn) such that ∫Cnzkdμ(z)=sk, ∀k∈K. Here, K is an arbitrary finite subset of Z+n, which contains (0,…,0), and sk are prescribed complex numbers (we use the usual notations for multi-indices). There are two possible interpretations of this problem. Firstly, one may consider this problem as an extension of the truncated multidimensional moment problem on Rn, where the support of the measure μ is allowed to lie in Cn. Secondly, the moment problem is a particular case of the truncated moment problem in Cn, with special truncations. We give simple conditions for the solvability of the above moment problem. As a corollary, we have an integral representation with a non-negative measure for linear functionals on some linear subspaces of polynomials.
Identification and Ontology Term Enrichment Analysis of Genes Associated with COVID-19 and Acute Kidney Disease

Acute kidney injury (AKI) is the main comorbidity of COVID-19, and the pathogenesis remains unclear. This study first performed a gene set enrichment analysis of 6 AKI-related Gene Expression Omnibus (GEO) studies and identified 3,876 AKI-associated genes. By incorporating COVID-19 related interactions from BioGRID, we further found 1,027 genes associated with both COVID-19 and AKI. Our Gene ontology (GO) enrichment analysis of these genes showed that viral and inflammation-related biological processes played important roles on COVID-19 related AKI. Furthermore, the COVID-19 pathways ranked second in the top 5 KEGG-enriched pathways, in which 66 enriched genes were all upregulated in the kidney tissue of the above 6 GEO studies. Ontology modeling is currently undergoing to systematically and logically represent the AKI pathogenesis process in COVID-19 patients. © 2021 Copyright for this paper by its authors.
Uma Abordagem Baseada em Especificação para Testes de Web Services RESTful

This paper presents an approach for RESTful Web Services test case generation. RESTful Web Services have features that are not fully covered by traditional software testing techniques. The proposed approach uses model transformation techniques to generate platform independent test cases from UML class models enriched with Object Constraint Language (OCL) constraints. These test cases are then transformed into platform specific test cases that can be used to verify the implementation of CRUD RESTful Web Services. Resumo. Este trabalho apresenta uma abordagem para geração de casos de teste para Web Services RESTful. Web Services RESTful possuem características que não são cobertas pelas técnicas tradicionais de teste de software. A abordagem proposta utiliza técnicas de transformação de modelos para gerar casos de teste independentes de plataforma a partir de modelos de classes UML enriquecidos com restrições Object Constraint Language (OCL). Tais casos de teste são, então, transformados em casos de teste específicos de plataforma que podem ser usados para verificar a implementação de Web Services RESTful do tipo CRUD.
Performance characteristics of a novel liquid-liquid contactor.

This thesis investigates the performance characteristics of a novel liquid-liquid contactor that employs woven screens as static mixing elements. The drag coefficient for single-phase flow was determined and compared to data reported in the literature. This showed that there is a relatively large discrepancy between the experimental data and the reported correlations, particularly for high fractional screen open area. Introduction of the dispersed phase to the main flow causes the drag coefficient to deviate slightly from its original value. The highest turbulence intensities and energy dissipation rates were found to occur immediately behind the screen and falls sharply with increasing downstream distance.
Cross-functional conflicts in new product launches in the food industry

This study explores the cross-functional conflicts in new product launches in the context of food industry, with particular focus to fast moving consumer goods setting. The purpose of this study is to develop an empirically grounded model of cross-functional conflicts in new product launches for the food industry. The theoretical approach taken in this study follows the resource based view of the firm. The theoretical framework was developed to make the conflict enablers, cross-functional conflicts and new product launches explicit for analysis. The empirical part of this study includes a qualitative single case study, which was geographically and culturally focused on Saudi Arabia. The research data was collected primarily through interviews from selected informants of the selected case company and representatives of two strategic partners and two competitors. The data was analyzed to empirically elaborate the theoretical framework. As a result of the data analysis, the cross-functional conflicts were categorized under task and relationship conflicts. The role of marketing resources in crossfunctional conflicts was found to be more complex than what had been reported in their earlier research. The results of the data analysis were used to revise the theoretical model of crossfunctional conflicts in the new product launches. The research provides several theoretical contributions and managerial implications in cross-functional conflicts in new product launches.
Active travel behaviour in the family environment: protocol for the mixed-methods cross-sectional ARRIVE study

Introduction Active travel is an important source of physical activity and a primary contributor to overall health among adolescents. To understand and promote active travel behaviour in adolescents, developing a more robust understanding of the predictors of active travel and its associated decision-making processes is needed. Situated within a theoretical socioecological framework for adolescent travel behaviour, the mixed-methods Active tRavel behavioR in the famIly enVironmEnt study aims to quantitatively assess the influence of several predictors of adolescent travel behaviour, and to qualitatively understand the associated decision-making processes of both adolescents and parents. Methods and analysis Our mixed-methods approach will feature online surveys and semistructured interviews. The online questionnaire, developed in accordance with a theoretical framework of adolescent active travel, will examine adolescent travel behaviour with respect to four different destinations while controlling for multiple relevant individual, social and physical environment factors. To enable the comparison of adolescent and parental perspectives, the questionnaire will be answered by a representative sample of German adolescents (11–15 years old) and their parents. Our semistructured interviews, likewise framed based on the central tenets of the theoretical framework of adolescent active travel, will seek to explore the decision-making process of families regarding travel mode choice via conducting interviews with each member (ie, father, mother, adolescent). To investigate travel decision-making processes, adolescents and their parents will be invited to talk about trips they undertook using both active and passive transport modes during the last week. Thematic analyses will be conducted to highlight the central concerns, priorities and values of participants’ decision-making processes. Ethics and dissemination This study has received ethical approval from the ethics commission of the Friedrich-Alexander-University Erlangen-Nuremberg. Study results will be disseminated at scientific conferences and published in peer-reviewed journals. Additionally, study findings will be made publicly available to relevant health, policy, and research stakeholders and groups.
Loneliness and mental well-being in the Polish population during the COVID-19 pandemic: a cross-sectional study

Objective There is a growing concern that the restrictions imposed due to the COVID-19 pandemic could lead to increased loneliness and mental disorders, which are considered a major public health problem. The aim of the study was to assess loneliness, anxiety, depression and irritability in the Polish population during the COVID-19 pandemic. Design A cross-sectional study. The study participants completed an online questionnaire using the computer-assisted web interview technique. Data were collected using Revised UCLA Loneliness Scale and Hospital Anxiety and Depression Scale. Setting Poland. Participants This study was conducted between 6 October and 12 October 2020, in a representative sample of 890 Polish residents. Primary outcome measures Self-reported loneliness; sociodemographic and COVID-19 pandemic factors associated with loneliness, anxiety, depression and irritability. Results The analyses showed a moderately high degree of loneliness in 22%, symptoms of anxiety in 27%, depression in 14% and irritability in 33% of the respondents. The increasing severity of anxiety, depression and irritation in the study group was accompanied by higher loneliness. Generally, younger people, both tested positive for SARS-CoV-2 and those who experienced home quarantine, scored higher in both scales. Conclusions It is necessary to identify those most vulnerable to loneliness, anxiety and depression during a crisis to assess health needs and proactively allocate resources during and after the pandemic. Loneliness, anxiety, depression and irritability are important factors to consider in a population of younger, disadvantaged people, who tested positive for SARS-CoV-2, people who were quarantined at home, and people who believe that their physical and mental health is worse than in the pre-pandemic period. It is important to cater for the mental health of individuals during the COVID-19 pandemic and to promote psychological interventions to improve mental well-being in potentially vulnerable social groups.