bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Map Construction and Functional Characterization of Genes within the Segregation Distortion Regions (SDRs) in the F2:3 Populations Derived from Wild Cotton Species of the D Genome
Authors: KIRUNGU Joy Nyangasi , MAGWANGA Richard Odongo , SHIRAKU Margaret Linyerera , Pu LU , MEHARI Teame Gereziher , Yuanchao XU , Yuqing HOU , AGONG Stephen Gaya , Yun ZHOU , Xiaoyan CAI , Zhou Zhongli , Kunbo WANG , Fang LIU 
Published: May 2020

Abstract
Background
Segregation distortion (SD) is a phenomenon common among stable or segregating populations, and the principle behind it still puzzles many researchers. The F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). A consensus map was developed between two maps from the four D genome, map A derived from an F2:3 progenies of Gossypium klotzschianum and G. davidsonii while Map B from G. thurberi and G. trilobum F2:3 generations. In each map 188 individual plants were used.
Results
The consensus linkage map had 1,492 markers across the 13 linkage groups; with a map size of 1,467.445 cM and average marker distance of 1.0370 cM. Chromosome D502 had the highest percentage of SD with 58.621% followed by Chromosome D507 with 47.887%. Six thousand and thirty eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus map. Within chromosome D502 and D507, 2,308 and 3,730 genes were mined, respectively and were found to belong to 1,117 domains out of which 622 domains were common across the two chromosomes. Moreover, the first 9 domains were members of the plant resistance genes (R genes), while Pkinase; Protein kinase domain (PF00069) was the dominant group with 188 genes. Further analysis on the dominant domains revealed that 287 miRNAs were found to target various genes, such as the gr-miR398, gra-miR5207, miR164a, miR164b, miR164c among others, which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, some of the stress responsive cis-regulatory elements were also detected. Furthermore, RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions in addition their higher expression at different stages fiber development.
Conclusion
The result obtained provided an indication of the important role of the SDRs in the evolution of significant genes in plants.
Brain tissue transcriptomic analysis of SIV-infected macaques identifies Poly (ADP-ribose) polymerases (PARPs) as potential biomarkers for neuropathogenesis.
Authors: Mavian Carla , Ramirez-Mata Andrea S , Dollar James Jarad , Nolan David J , Rich Shannan N , White Kevin , Magalis Brittany Rife , Cash Melanie N , Marini Simone , Prosperi Mattia , Amador David Moraga , Riva Alberto , Williams Kenneth C , Salemi Marco 
Published: May 2020

Abstract
Background. Despite improvements in antiretroviral therapy, human immunodeficiency virus type 1 (HIV-1)-associated neurocognitive disorders (HAND) remain prevalent in subjects undergoing therapy. HAND significantly affects individuals’ quality of life, as well as adherence to therapy, and, despite the increasing understanding of neuropathogenesis, no definitive diagnostic or prognostic marker has been identified.Results. We investigated transcriptomic profiles in frontal cortex tissues of Simian immunodeficiency virus (SIV)-infected Rhesus macaques sacrificed at different stages of infection. Gene expression was compared among SIV-infected animals (n=11), with or without CD8+ lymphocyte depletion, based on detectable (n=6) or non-detectable (n=5) presence of the virus in frontal cortex tissues. S ignificant enrichment in activation of monocyte and macrophage cellular pathways was found in animals with detectable brain infection, independently from CD8+ lymphocyte depletion . In addition, transcripts of four poly (ADP-ribose) polymerases ( PARPs) were up-regulated in the frontal cortex, which was confirmed by real-time polymerase chain reaction.Conclusions. Our results shed light on involvement of PARPs in SIV infection of the brain and their role in SIV-associated neurodegenerative processes. Inhibition of PARPs may provide an effective novel therapeutic target for HIV-related neuropathology .
A Composite Index Predicts Disease Progression in Early Stages of COVID-19: a Propensity Score-matched Cohort Study
Authors: Xu Jianjun , Hu Shaobo , Li Suzhen , Wang Weimin , Wu Yuzhe , Su Zhe , Zhou Xing , Cheng Xiang , Gao Yang , Zheng Qichang 
Published: May 2020

Abstract
Background: Thus far, studies on COVID-19 have focused on the epidemiology of the disease and clinical characteristics of patients (14-19), as well as on the risk factors associated with mortality during hospitalization in critical COVID-19 cases. However, no research has been performed on the prediction of progression in patients in the early stages of the disease. The aim of this work was to identify the early predictors of COVID-19 progression.Methods: The study included 338 patients with COVID-19 treated at two hospitals in Wuhan, Chian, from December, 2019 to March, 2020. Predictors of the progression of COVID-19 from mild to severe stages were selected by the logistic regression analysis. The predictive accuracy was evaluated further in the propensity score-matched cohort.Results: COVID-19 progression to severe and critical stages was confirmed in 78(23.1%) patients. The average value of the neutrophil-to-lymphocyte ratio (NLR) was higher in patients in the disease progression group than in the improvement group. Multivariable logistic regression analysis revealed that elevated NLR, LDH, and IL-10, were independent predictors of disease progression. The optimal cut-off value of NLR for predicting the progression of COVID-19 was 3.75. In the propensity score-matched cohort, NLR ≥ 3.75 was still an independent predictor of COVID-19 progression after multivariate analysis.Conclusions: The performed analysis demonstrates that NLR qualiﬁes as an independent predictor of disease progression in COVID-19 patients at the early stage of the disease. The combined evaluation of NLR and LDH improved the accuracy of the prediction of COVID-19 progression. Assessment of predictors might facilitate early identification of COVID-19 patients at high risk for disease progression and ensure timely administration of appropriate treatment to prevent mild cases from becoming severe.
Molecular Characterization of Plasmodium Falciparum DNA-3-Methyladenine Glycosylase
Authors: Pinthong Nattapon , Limudomporn Paviga , Vasuvat Jitlada , Adisakwattana Poom , Rattaprasert Pongruj , Chavalitshewinkoon-Petmitr Porntip 
Published: May 2020

Abstract
Background The emergence of artemisinin-resistant malaria parasite highlights the need for novel drugs and their targets. Alkylation in purine bases can hinder DNA replication if remained unsolved would eventually resulting in cell death. DNA-3-methyladenine glycosylase is an enzyme responsible for the repair of those alkylated lesions. Based on the AT-rich genome of Plasmodium falciparum and unexplored Plasmodium falciparum DNA-3-methyladenine glycosylase (PfMAG), therefore PfMAG should be characterized for its potential candidate for antimalarial drug development.Methods Bioinformatics analysis of PfMAG was performed. The native PfMAG from crude extract of chloroquine and pyrimethamine resistant Plasmodium falciparum strain K1 was partially purified using three columns. The existence of PfMAG activity leads to the cloning and expression of PfMAG for further characterization. The PfMAG was amplified, cloned to expression vector (pBAD202/D-TOPO), and expressed in Escherichia coli. The molecular weight of recombinant PfMAG was analyzed by SDS-PAGE and Western blot. Both functional and biochemical properties of the recombinant enzyme were characterized.Results PfMAG activity was most prominent in schizont. Native PfMAG was partially purified with a specific activity of 147.36 units/mg protein. The DNA sequence of amplified PfMAG showed an insertion of three nucleotides coding for asparagine compared to strain 3D7 and only 16% similarity compared to the human enzyme was observed. After cloning, the 74-kDa recombinant PfMAG was expressed and identified. PfMAG showed a larger size than its human counterpart twice. PfMAG preferred a double-stranded DNA substrate. Glycosylase activity was detected in a broad range of pH 5–8. The quite narrow optimal salt concentration was observed between 100–200 mM NaCl, whereas 250 mM NaCl reduces its activity. Divalent cations are not required for its glycosylase activity; on the contrary, they inhibited glycosylase activity in a concentration-dependent manner.Conclusion PfMAG activity increases according to parasite development. Native PfMAG was partially purified, the recombinant PfMAG was successfully expressed and characterized. An insertion of AAT coding for asparagine was found compared with that of strain 3D7. PfMAG differs from the human counterpart in a twice larger size and a wide range of optimal pH. Results obtained from this study will be a benefit for exploring and investigating of candidate targets toward antimalarial drug design in the future.
The Value and Feasibility of South-South Medical Elective Exchanges in Africa
Authors: Daniels Katy , Thomson Emma , Nawagi Faith , Flinkenflogel Maaike 
Published: May 2020

Abstract
Background
An elective is part of the curriculum where students have the flexibility to choose both the study topic and location. International medical electives are a well-established part of curricula at most medical schools in high-income countries. They are highly valued by students and have proven educational benefits, though do come with challenges, such as lack of reciprocity. Low and middle-income countries frequently host students from high-income countries providing learning opportunities, yet also carry the burden of supervision and resource consumption, whilst their students get few elective opportunities. This study explores the value and feasibility of South-South Medical Elective Exchanges (SSMEE), which creates elective opportunities for African medical students in other African countries to create reciprocity within the elective system.
Method
A qualitative evaluation of the South-South Medical Elective Exchanges was conducted using a case study approach. Four African medical schools, College of Medicine, Malawi; University of Rwanda, Rwanda; University of Witwatersrand, South Africa and Makerere University, Uganda participated in the pilot in 2017/18. Each institution selected two students to participate in a four-week elective to another participating institute. Participating students completed a pre-elective questionnaire and a post-elective interview exploring expectations, learning outcomes, challenges and how they are applying this learning. Data was analysed thematically.
Results
Data presented is from six of the eight participating students. All students found the elective a valuable experience and learning was demonstrated in four key areas: clinical knowledge and skills; attitudes; personal and professional development and global perspectives. For some, it challenged their assumptions of what an elective is because valuable learning can be achieved whilst remaining in Africa. The main challenge found related to funding the elective.
Conclusions
The SSMEE model is feasible and provides valuable learning for participating students and their peers/colleagues. Financing electives remains the biggest challenge. Since this pilot, SSMEE has become part of a regional elective exchange network in Africa with an additional four institutions in three other countries. As such SSMEE has resulted in increased opportunities for African medical students and better educational outcomes that are likely to have a positive effect on healthcare systems in Africa.
The effectiveness of antiviral treatment in severe COVID-19 patients in Wuhan: a retrospective cohort study
Authors: Zhou Xianlong , Ding Guoyong , Yang Luyu , Liu Ruining , Hou Haifeng , Wang Ping , Ma Min , Hu Zhuanzhuan , Huang Lei , Xu Xizhu , Hu Quan , Zhao Yan , Xing Weijia , Zhao Zhigang 
Published: May 2020

Abstract
Background Since the outbreak of COVID-19, the application of appropriate treatment strategy for COVID-19 patients, notably for the severe patients, was a huge challenge in case management. Therefore, we aimed to evaluate the effectiveness of antiviral treatment in severe COVID-19 patients.Methods A retrospective cohort study was conducted from January 8, 2020 to March 9, 2020 in four designated hospitals of COVID-19 in Wuhan, China. 138 severe COVID-19patients with above 18 years were included in this study. 109 patients receiving the antiviral treatment were selected in antiviral group. The remaining 29 patients were in control group. The primary outcome of the study was in-hospital death and length of hospitalization. Secondary outcomes included ICU admission, length of stays in ICU, use of mechanical ventilation, length of mechanical ventilation, and the development of complications. Univariate analysis and Kaplan-Meier curves were used to examined the association between antiviral treatment and the clinical outcomes of the COVID-19 patients.Results 48 (44.0%) and 15 (51.7%) deaths were occurred in antiviral and control groups, respectively. Antiviral treatment was not associated with the rate of fatal outcome in COVID-19 patients (P > 0.05). Among the survival patients, the median length of hospitalization was 11.0 days (IQR: 6.5–18.0) and 16.0 days (IQR: 8.5–26.0) in antiviral and control groups, respectively. No significant association was identified between the antiviral treatment and the length of hospitalization in survival patients (P > 0.05). Moreover, the antiviral treatment was not statistically associated with ICU admission, mechanical ventilation and length of mechanical ventilation (P > 0.05, respectively). However, the length of ICU stays in deaths was different both groups (P < 0.05). The median length of ICU stays in deaths was 7.0 days (IQR: 3.0-14.3) and 15.5 days (IQR: 8.3–21.8) in antiviral and control groups, respectively. The occurrence of majority of complications were similar both groups. Sepsis was the single complication in which the occurrence rates were statistical different between the antiviral group and control group (40.4% vs 13.8%, P < 0.01).Conclusion No benefit of antiviral treatment in severe COVID-19 patients was observed in our study. Clinical physicians should cautiously prescribe the antiviral drugs in severe COVID-19 patients.
Nasal Decolonization of Staphylococcus Aureus and the Risk of Surgical Site Infection After Surgery: A Meta-Analysis
Authors: Tang Jia , Hui Jiangjin , Ma Jing , Chen Mingquan 
Published: May 2020

Abstract
Aim: To assess the effects of nasal decontamination on preventing surgical site infections (SSIs) in people who are S aureus carriers undergoing different types of surgeries. Methods: Relevant randomized controlled trials (RCTs) were identified through systematic searches of the PubMed, Embase, Web of science, and the Cochrane Library databases. The risk ratios (RRs) and 95% confidence intervals (CIs) were calculated and the effects model was chosen according to the heterogeneity. Subgroup analyses were performed according to different types of surgeries that S aureus carriers were applied.Results: Twenty RCTs published between 1996 and 2019 involving 10526 patients were included. Pooled results showed that the overall SSIs and pulmonary surgery SSIs presented with a statistical difference in measures of nasal decontamination (RR=0.59 and 0.47, respectively, both p<0.01). However, the associations between nasal decolonization and increased risks of SSIs in orthopedics surgery or cardiovascular surgery remained insignificant in studies.Conclusion: It seems that nasal decolonization of Staphylococcus aureus may be associated with a reduction of SSI in these patients, especially in patients receiving pulmonary surgeries.
INSURE (INtubate, SURfactant and Extubate) method in preterm infants with respiratory distress syndrome: a retrospective study
Authors: Mohideen Mohamed Mubarak Shaik Kidur , Wagh Deepika , Athikarisamy Sam 
Published: May 2020

Abstract
Background: Preterm infants with severe respiratory distress syndrome (RDS) are usually managed with endotracheal intubation and surfactant administration followed by mechanical ventilation however this has immediate and long-term complications. Hence, INSURE (Intubate, surfactant administration and extubate) method combined with continuous positive airway pressure (CPAP) support has been accepted as an alternative method in eligible infants. Aim of this study is to look at our experience of administering INSURE and to look at the factors predisposing to the failure of INSURE. Methods: A retrospective chart review was done of all the babies who were born in a tertiary hospital between 1 st January 2014 to 31 st December 2015 (2 years) and received surfactant through INSURE method. Infants requiring reintubation and mechanical ventilation within 3 days post INSURE are considered as INSURE failure for our study purpose. Results: Eighty-five infants were included in the review with gestational age (GA) ranging from 26 +3 to 35 +5 weeks and birth weight ranging from 680 to 3340 grams. Of these, 22 infants (26%) had INSURE failure. INSURE failure rate was higher in infants born <30 weeks gestation (40%). Higher FiO2 requirement prior to INSURE (mean FIO 2 0.5 vs 0.3, P value <0.001) and preeclampsia in mothers of infants < 30 weeks of GA (P value 0.027) were strongly associated with INSURE failure. No mortality was noted in either group. Conclusion: We found that INSURE method may be useful in preventing the need for mechanical ventilation in late preterm infants with RDS. However, this method may be less successful in preterm infants with lower GA (<30 weeks) and higher FiO2 requirement (≥0.5). More prospective studies are needed to assess the effectiveness of INSURE method.
Time Spent Abroad Predicts Late Presentation for HIV among HIV-positive Tajikistani Migrants to the Russian Federation
Authors: Alaei Arash , Bromberg Daniel J , Tate Mary M , Alaei Kamiar , Karimov Saifuddin , Saidi Dilshod 
Published: May 2020

Abstract
Background Between 700 thousand and 1.2 million citizens of Tajikistan currently live in the Russian Federation, one of the only countries where the HIV epidemic continues to worsen. Given the previously reported barriers to healthcare access for migrants to the Russian Federation, and the rapidly expanding HIV epidemic in Eastern Europe and Central Asia, this present study set out to determine whether these barriers impact late presentation with HIV among Tajik migrants upon their return to Tajikistan. Method This study uses data from the Tajikistan Ministry of Health surveillance system (2006 – 2019). At time of diagnosis, patients are interviewed by staff of AIDS centers, and doctors complete routine intake forms and complete medical exam. Descriptive characteristics of HIV-positive migrant who had lived in the Russian Federation (n=503) were calculated and compared with those of HIV-positive non-migrants (n=9519). Missing data were imputed using a multiple imputation (predictive means matching, logistic regression imputation, and polytomous regression imputation). Two logistic models were created to model the probability of late presentation for HIV. The first model shows unadjusted associations between predictor variables and late presentation for HIV. The second model is shows multivariable associations between significant study variables identified in the univariate model, and late presentation. Results Compared to non-migrants, HIV-positive migrants are more likely to be from Gorno-Badakhshan region, are less likely to use illicit drugs, are more likely to have purchased the services of sex workers, and have more sexual partners on average. The unadjusted logistic model found that for every year spent in the Russian Federation, the risk of late presentation for an HIV-positive Tajikistani migrant increases by 4.0% (95% CI: 0.3-7.7). The multivariate model showed that when age, sex, and region of origin are held constant, the risk of late presentation for an HIV-positive Tajikistani migrant increases by 4.0% (95% CI: 0.1-7.8) for each year spent in the Russian Federation. Conclusion The results of this paper suggest that if the Russian Federation were loosen its restrictions of HIV care for foreign nationals, it might improve the treatment outcomes of migrant laborers. Further research is needed to explicate the causal pathways of the associations found in the present analysis.
Creating a ‘simulacrum’ of in-class learning environment employing distance learning modality during the COVID-19 pandemia: Quod Erat Demonstrandum
Authors: Azar Aida , Khamis Amar Hassan , Naidoo Nerissa , Lindsbro Marjam , Gonuguntla Suneetha , Banerjee Yajnavalka 
Published: May 2020

Abstract
Background The COVID-19 pandemic has forced medical schools to suspend on-campus live-sessions and shift to distance-learning (DL). This precipitous shift presented medical educators with a challenge, “to create a ‘simulacrum’ of the learning environment that students experience in classroom, in DL”. Aim We define a DL framework that provides a ‘simulacrum’ of classroom experience and can be effectively employed for course delivery in a competency-based curriculum during unprecedented times. Methodology The framework’s blueprint was designed amalgamating principles of: Garrison’s community inquiry, Siemens’ connectivism and Harasim’s online collaborative-learning; and improved using Anderson’s DL-model. Effectiveness of the designed framework in course delivery was demonstrated using the exemplar of fundamentals in epidemiology and biostatistics (FEB) course in our curriculum during COVID-19 lockdown. Virtual live-sessions integrated in the framework employed a blended-approach informed by instructional-design strategies of Gagne and Peyton. The efficiency of the framework was evaluated using first two levels of Kirkpatrick’s framework i.e. perception and cognitive development. Results Of 60 students, 51 (85%) responded to the survey assessing perception towards DL (Kirkpatrick’s Level:1). The survey-items, validated using exploratory factor analysis, were classified into four categories: computer expertise; DL flexibility; DL usefulness; and DL satisfaction. The overall mean (SD) score of 62.0 (9.0) for the four categories, highlighted respondents’ overall satisfaction with the framework. Scores for specific survey-items attested that students had an enriched learning experience, which promoted collaborative-learning and student-autonomy. For, Kirkpatrick’s Level:2 i.e. cognitive-development, performance in FEB’s summative-assessment of students experiencing DL was compared with students taught using traditional methods. Similar, mean-scores for both groups indicated that shift to DL didn’t have an adverse effect on students’ learning. Conclusion QED, we have demonstrated that the framework is an efficient pedagogical approach, pertinent for medical schools to adopt (elaborated using Bourdieu’s Theory of Practice) to address students’ learning trajectories during unprecedented times.