bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome re-sequencing and reannotation of the Escherichia coli ER2566 strain and transcriptome sequencing under overexpression conditions
Authors: Zhou Lizhi , Wang Kaihang , Chen Tingting , Ma Yue , Huang Yang , Li Jiajia , Liu Liqin , Li Yuqian , Kong Zhibo , Zheng Qingbing , Wang Yingbin , Gu Ying , Yu Hai , Li Shaowei , Xia Ningshao 
Published: March 2020

Abstract
Background

The Escherichia coli ER2566 strain (NC_CP014268.2) was developed as a BL21 (DE3) derivative strain and has been widely used in recombinant protein expression. However, like many other current RefSeq annotations, the annotation of the ER2566 strain is incomplete, with missing gene names and miscellaneous RNAs, as well as uncorrected annotations of some pseudogenes. Here, we performed a systematic reannotation of the ER2566 genome by combining multiple annotation tools with manual revision to provide a comprehensive understanding of the E. coli ER2566 strain, and used high-throughput sequencing to explore how the strain adapts under external pressure.

Results

The reannotation included noteworthy corrections to all protein-coding genes, led to the exclusion of 120 hypothetical genes or pseudogenes, and resulted in the addition of 65 coding sequences and 230 miscellaneous noncoding RNAs and 2 tRNAs. In addition, we further manually examined all 194 pseudogenes in the Ref-seq annotation and directly identified 144 (74%) as coding genes. The remaining pseudogenes without explicit function were removed. We then used whole-genome sequencing and high-throughput RNA sequencing to assess mutational adaptations under consecutive subculture or overexpression burden. Whereas no mutations were detected in response to consecutive subculture, overexpression of the human papillomavirus 16 type capsid led to the identification of a mutation (position 1,094,824 within the 3’ non-coding region) positioned 19-bp away from the lac I gene in the transcribed RNA, which was not detected at the genomic level by Sanger sequencing.

Conclusion

The ER2566 strain is used by both the general scientific community and the biotechnology industry. Reannotation of the E.coli ER2566 strain not only improved the RefSeq data but uncovered a key site that might involve in the transcription and translation of genes encoding the lactose operon repressor. We propose that our pipeline might offer a universal method for the reannotation of other bacterial genomes with high speed and accuracy. This study may facilitate a better understanding of gene function for the ER2566 strain under external burden and provide more clues to engineer bacteria for biotechnological applications.
Prevalence and Correlates of Bullying in Physiotherapy Education in Nigeria
Authors: Mbada Chidozie Emmanuel , Ogunseun Idowu Phebean , Fasuyi Francis Oluwafunso , Adegbemigun Oluwafemi David , Fatoye Clara Toyin , Idowu Opeyemi Ayodiipo , Johnson Olubusola Esther , Odole Adesola Christiana , Okonji Adaobi Margaret , Kaka Basir , Fatoye Francis 
Published: March 2020

Abstract
Background: Bullying is an unexpressed part and parcel of medical education but it is largely unexplored in physiotherapy. This study assessed the prevalence and socio-demographic correlates of bullying in physiotherapy education in Nigeria.
Methods: Two hundred and nineteen clinical physiotherapy students from three purposively selected Federal Universities in Nigeria participated in this study. Following a cross-sectional design, the Students Perception of Professor Bullying Questionnaire (SPPBQ) was used to obtain information on bullying. The SPPBQ includes a working definition of lecturer bullying followed by two sections inquiring about lecturers bullying experiences. Data was collected on socio-demographic characteristics, availability of adequate policy and support and the different forms of bullying experienced. Descriptive and inferential statistics were used analyze data. Alpha level was set at p<0.05.
Results: Lifetime and point prevalence of bullying in physiotherapy education was 98.6% and 99.1% respectively. 94.5% of the respondents had witnessed physiotherapy students bullying and there was a 100% rate of ‘no attempt’ to stop a physiotherapy lecturer from bullying. There was no significant association between bullying and each of age (𝜒2=0.117, p=0.943), gender (𝜒2=0.001,p=0.974), university (𝜒2=1.343,p=0.511) and level of study (𝜒2=0.000,p=0.995).
Conclusion: There is high lifetime and point prevalence of bullying in physiotherapy education in Nigeria, which are largely unchallenged or redressed. Also, being a clinical physiotherapy student makes prone to bullying without necessary contributions of other intrinsic and extrinsic factors.
Genome-wide analysis of Jatropha curcas MADS-box gene family and functional characterization of the JcMADS40 gene in transgenic rice
Authors: Tang Yuehui , Wang Jian , Bao Xinxin , Wu Qian , Yang Tongwen , Li Han , Wang Wenxia , Zhang Yizhen , Bai Nannan , Guan Yaxin , Dai Jiaxi , Xie Yanjie , Li Shen , Huo Rui , Cheng Wei 
Published: March 2020

Abstract
Background: Physic nut (Jatropha curcas), a non-edible oilseed plant, is among the most promising alternative energy sources because of its high seed oil content, rapid growth and extensive adaptability. Proteins encoded by MADS-box genes are important transcription factors involved in the regulation of plant growth, seed development and responses to abiotic stress. However, there has been no in-depth research on the MADS-box genes and their roles in physic nut. Results: In the present study, 63 MADS-box genes (JcMADSs) were identified in the physic nut genome, and classed into five groups (MIKC, Mα, Mβ, Mγ, MIKC*) based on phylogenetic comparison with Arabidopsis homologs. Expression profile analysis based on RNA-seq suggested that many JcMADS genes were expressed most strongly in seeds, and seven of them responded in leaves to at least one abiotic stressor (drought and/or salinity) at one or more time points. Transient expression analysis and a transactivation assay indicated that JcMADS40 is a nucleus-localized transcriptional activator. Plants overexpressing JcMADS40 did not show altered plant growth, but the overexpressing plants did exhibit reductions in grain size, grain length, grain width, 1000-seed weight and yield per plant. Further data on the reduced grain size in JcMADS40-overexpressing plants supported the putative role of JcMADS genes in seed development. Conclusions: This study will be useful in understanding the involvement of MADS-box genes in growth and development in addition to their functions in abiotic stress resistance, and will ultimately form the basis for functional characterization and the exploitation of candidate genes for the genetic engineering of physic nut.
Toluene Biodegradation using a Lab-Scale Biofilter Inoculated with Pseudomonas Putida PTCC 1694
Authors: Ghasemi Roohollah , Golbabaei Farideh , Pourmand Mohammad Reza , Rezaei Sasan , Jafari Mohammad Javad , Nabizadeh Ramin , Masoorian Ensieh 
Published: March 2020

Abstract
Biomanipulation is reliable method for treating volatile organic compounds (VOCs) in polluted air. The performances of two biofilters in the removal of toluene vapors from air stream were compared. Two identical biofilters designed in parallel configuration were operated in lab-scale for 20 days; one of them was filled by sterilized media (compost and wood charcoal 2:1 v/v) and another was filled by the same media inoculated with Pseudomonas putida PTCC 1694, as a native strain. Moreover, batch tests were performed to determine the biodegradation rate of toluene. The results showed that, in comparison with the sterilized BF (89% vs 58%), the inoculated BF could effectively eliminate toluene from air stream. The pressure drop across the inoculated BF and the sterilized BF were 0.66±0.28 and 0.47±0.27 mm water respectively. The batch test results showed that loss of toluene in the control bottles was greater than the blanks. Based on the experimental results, inoculated BFs can effectively treat toluene vapors from gaseous streams.
Association between malaria-related health service readiness and malaria mortality in under 5-year-old children in Burkina Faso
Authors: Millogo Ourohiré , Doamba Jean Edouard Odilon , Sié Ali , Utzinger Juerg , Vounatsou Penelope 
Published: March 2020

Abstract
Background: The Service Availability and Readiness Assessment (SARA) surveys generate data on the readiness of health facility services. We constructed a readiness index related to malaria services and determined the association between health facility malaria readiness and malaria mortality in children under the age of 5 years in Burkina Faso. Methods: Data on malaria-related visits and deaths in under 5-year-old children were extracted from the national Health Management Information System (HMIS) in Burkina Faso. Bayesian geostatistical models with variable selection were fitted to malaria mortality data. The most important facility readiness indicators related to general and malaria-specific services were determined. Multiple correspondence analysis (MCA) was used to construct a composite facility readiness score based on multiple factorial axes. The analysis was carried out separately for 112 medical centers and 546 peripheral health centers. Results: Malaria mortality rate in medical centres was 4.8 times higher than that of peripheral health centres (3.46 vs 0.72%, p<0.0001). Essential medicines was the domain with the lowest readiness (only 0.1% of medical centres and 0% of peripheral health centres had the whole set of essential medicines tracer indicators). Basic equipment readiness was the highest. The composite readiness score explained 30% and 53% of the original indicators for medical centers and peripheral health centers, respectively. Mortality rate ratio (MRR) was by 59% (MRR = 0.41, 95% Bayesian credible interval (BCI): 0.19-0.91) lower in the high readiness group of peripheral health centers, compared to the low readiness group. Medical centers readiness was not related to malaria mortality. The geographical distribution of malaria mortality rate showed that regions with high mortality rate have also high proportion of health facilities with low readiness and vice versa. Conclusion: Performant health services in Burkina Faso are associated with lower malaria mortality rates. Health system readiness should be strengthened in the regions of Sahel, Sud-Ouest and Boucle du Mouhoun. Emphasis should be given to improving the management of essential medicines and to reducing delays of emergency transportation between the different levels of the health system.
Transbronchial Lung Cryobiopsy May be of Value for Nonresolving Acute Respiratory Distress Syndrome: Case series and Systematic literature Review
Authors: Zhou Guowu , Feng Yingying , Wang Shiyao , Zhang Yi , Tian Ye , Wu Xiaojing , Zhao Ling , Wang Dan , Li Yi , Tian Zheng , Zhan Qingyuan 
Published: March 2020

Abstract
Background: Identifying pathologic features is helpful for the management of nonresolving acute respiratory distress syndrome (ARDS). Transbronchial lung cryobiopsy (TBLC) is a novel biopsy technique that may have comparable utility to surgical biopsy. The aim of this study was to assess the value of TBLC in patients with nonresolving ARDS.
Methods: All patients with nonresolving ARDS who underwent TBLC from January 2019 to August 2019 in a tertiary medical ICU were included. In addition, a literature search of TBLC for ARDS was performed by searching PubMed, EMBASE, ATS/ERS/APSR meeting abstracts, clinicaltrial.gov, and Google Scholar. Data on complications, histologic diagnosis, management changes, and outcomes were analyzed.
Results: Five patients (three women and two men) underwent TBLC. None of the patients developed pneumothorax although in two patients massive bleeding occurred, which was controlled by continuous occlusion using bronchial blockers. There were no procedure-related deaths. Diffuse alveolar damage (DAD) and alternative histologic patterns were found in two and three patients, respectively, resulting in management changes in all cases. Literature search yielded four studies, which together with the present study resulted in data from 25 cases in which TBLC was used in nonresolving ARDS. The summary diagnostic yield was 92% (23/25). Only 44% (11/25) of cases were proven to be DAD. TBLC contributed to management changes in 80% of patients (20/25). Procedure-related complications consisted of pneumothorax (16%, 4/25), significant bleeding (12%, 3/25), and persistent air leak (8%, 2/25). There were no procedure-related deaths. The follow-up survival rate was 61.9% (13/21).
Conclusions: Given its acceptable safety profile and high diagnostic yield, TBLC may be of value in selected patients with nonresolving ARDS.
An Integrated Humanities–Social Sciences Course in Health Sciences Education: Its Proposed Design, Effectiveness and Associated Factors
Authors: Lee Jihyun , Lee Jueyeun , Jung Ilyoung 
Published: March 2020

Abstract
BackgroundPrevious research has not provided enough direction regarding effective content design of courses integrating humanities and social sciences in medical and dental education This study aims at exploring how an Integrated Medical/Dental Humanities–Social Medicine/Dentistry course can be designed; how effective it can be in terms of students’ growth in knowledge, attitudes, skills, and aspirations; and what can be associated factors. MethodsThe course was designed by distilling commonalities in the international standards for medical/dental education proposed by seven major health organizations. This analysis resulted in a curriculum covering eight major topics (history; professionalism; communication; ethics; management; policy; insurance; law; and research methodology). During the 2017 calendar year, data was collected and statistically analyzed from 68 third-year pre-doctoral students enrolled in the resulting MDHS 13-week course. ResultsParticipants showed growth in skills, aspirations, knowledge, and attitudes, with the greatest change occurring in skills, then aspirations, knowledge, and attitude. However, knowledge growth was the only variable significantly related to student achievement of course objectives ( β = 0.635, t (63) = 3.394, p = 0.001). The topics that students perceived as most critical were insurance, policy, management, and law. Perceived importance of research was the most common and was significantly related to all types of learning outcomes (For knowledge, β =0.213, t (63) = 2.203, p = 0.031; for attitudes, β = 0.784, t (63) = 10.257, p = 0.000; for skills, β = 0.769, t (63) = 9.772, p = 0.000; and aspirations β = 0.639, t (63) = 7.595, p = 0.000). ConclusionsThis study proposed a framework for a humanities-social sciences education for health sciences education, and analyzed its implementation. The empirical evaluation of its effectiveness and factors related to successful outcomes found that students perceived gains in their knowledge, attitudes, skills, and aspirations for humanistic and social aspects of dentistry/medicine, and that recognized importance of research was associate with the greatest growth in all four areas of learning outcomes. This study hopes to contribute to the improved design of integrated humanities–social sciences courses.
Genetic basis analysis for indica germinability under low temperature using a new RILs population genotyping by whole-genome resequencing
Authors: Wang Peng , Wu Guangliang , Luo Xin , Liu Ruiqi , Zhou Andong , Cai Yicong , Zhou Dahu , Tan Jingai , Tong Shan , Zhang Xiangyu , Li Caijin , Li Cuijuan , Wang Yanning , Cheng Qin , He Haohua , Jianmin Bian 
Published: March 2020

Abstract
Background : Improving the cold tolerance of rice at germination stage is an important objective to maintain rice yields. However, less analyses were carried out to detect the quantitative trait loci (QTLs) associated with cold tolerance using indica/indica population. Therefore, the genetic basis of cold tolerance of the indica varieties should be provided considerable attentionResults: In this study, a recombinant inbred lines (RILs) population comprising 126 lines derived from two widely used double-cropped indica rice varieties Wufeng B (WFB) and Changhui T025 (CHT025) was used to construct a high-density linkage map based on whole-genome resequencing. The high-density genetic map included 2,578 bins on 12 linkage groups and was 1762.80 cM in length, with an average interlocus distance of 0.68 cM. On the basis of newly constructed high-density genetic map, a total of 18 additive QTLs ranging from 34.55 to 315.21 kb on Nipponbare genome and two pairs of epistatic QTLs associated with cold stress at germination stage were detected, which indicated that the genetic basis of cold tolerance of WFB and CHT025 at germination stage is manly due to additive effects of several QTLs. Otherwise, the phylogenetic analysis showed that WFB is a typical indica variety while CHT025 is an interphyletic rice variety. Most of the favorable QTLs harbouring in indica WFB showed different chromosomal region from the QTLs associating with cold stress from japonica rice in previous studies, which indicated that indica might have different cold stress genetic mechanism comparing to japonica subspecies. Furthermore, we can incorporate these favorable QTLs existing in WFB into rice varieties to breed new cold tolerance indica male sterile maintenance line via marker-assisted selection; CHT025 is a better source of these cold tolerance favorable QTLs only only for the improvement of indcia but also for japonica restorer line germinability under low temperature via marker-assisted selection.Conclusion : This population with high density genetic map will serve as better choice for identifying important quantitative traits of these two good indica germplasms, and these favorable QTLs exist in WFB and CHT025 can be used to breed new cold tolerance indica varieties via marker-assisted selection. These authors have contributed equally to this work
A hypoxia-related signature for clinically predicting diagnosis, prognosis and immune microenvironment of hepatocellular carcinoma patients.
Authors: Zhang Baohui , Tang Bufu , Gao Jianyao , Li Jiatong , Kong Lingming , Qin Ling 
Published: March 2020

Abstract
Background Hypoxia plays an indispensable role in the development of hepatocellular carcinoma (HCC). However, there are few studies on the application of hypoxia molecules in the prognosis predicting of HCC. We aimed to identify the hypoxia-related genes in HCC and construct reliable models for diagnosis, prognosis and recurrence of HCC patients as well as exploring the potential mechanism.Methods Differentially expressed genes (DEGs) analysis was performed using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database and four clusters were determined by a consistent clustering analysis. Three DEGs closely related to overall survival（OS）were identified using Cox regression and LASSO analysis and the hypoxia-related signature was developed and validated in TCGA and International Cancer Genome Consortium (ICGC) database. Then the Gene Set Enrichment Analysis (GSEA) was performed to explore signaling pathways regulated by the signature and the CIBERSORT was used for estimating the fractions of immune cell types.Results A total of 397 hypoxia-related DEGs were detected and three genes (PDSS1, CDCA8 and SLC7A11) were selected to construct a prognosis, recurrence and diagnosis model. Then patients were divided into high- and low-risk groups. Our hypoxia-related signature was significantly associated with worse prognosis and higher recurrence rate. The diagnostic model also accurately distinguished HCC from normal samples and nodules. Furthermore, the hypoxia-related signature could positively regulate immune response and the high-risk group had higher fractions of macrophages, B memory cells and follicle-helper T cells, and exhibited higher expression of immunocheckpoints such as PD1and PDL1.Conclusions Altogether, our study showed that hypoxia-related signature is a potential biomarker for diagnosis, prognosis and recurrence of HCC, and it provided an immunological perspective for developing personalized therapies.
Rectal douching before sexual intercourse and inappropriate douching tool use associated with increased HIV infection among men who have sex with men: a cross-sectional study from Shenyang, China
Authors: Chu ZhenXing , Shen Guangquan , Hu Qinghai , Wang Hongyi , Zhang Jing , Dong Willa , Jiang Yongjun , Geng Wenqing , Shang Hong , Xu Junjie 
Published: March 2020

Abstract
Background: Rectal douching (RD) is widely practiced by men who have sex with men (MSM), and is correlated with increased risk of HIV infection. However, the mechanism of how RD increases the risk of HIV infection is not well understood, and there is limited data on RD behavior in MSM practicing anal sex in China. We examine the purpose of RD, its timing in relation to anal sex, the types of RD products used, and risky sexual behaviors among MSM reporting anal sex.Methods: Between August 2017 and December 2018, a cross-sectional study was conducted among adult MSM in Shenyang, China. Data were collected on demographics, sexual behaviors, and RD for the most recent sexual intercourse by means of interviewer-administered face-to-face questionnaires. Blood samples were collected to test for antibodies to HIV and syphilis. Multivariable logistic regression models were used to assess the risk factors associated with HIV infection.Results: A total of 515 eligible MSM participated in this survey (median age: 31 years). During the most recent anal intercourse, 28.3% (146/515) had condomless receptive anal intercourse (CRAI), 21.4% (110/515) practiced serosorting, and more than half (61.6%, 317/515) reported RD before or after anal sex. Of those practicing RD, 96.8% (307/317) conducted RD before sex, while 62.5% (198/317) conducted RD after sex. The douching devices used were primarily shower hoses (85.3%, 262/307), and relatively few MSM used commercial RD products (8.1%). The prevalence of HIV-1 and syphilis was 11.7% and 13.2%, respectively. HIV infection was positively associated with RD (adjusted odds ratio (AOR), 2.8; 95% confidence interval (CI), 1.4-5.5), practicing RD before sex (AOR, 2.3; 95% CI, 1.2–4.3), practicing RD after sex (AOR, 1.8; 95% CI, 1.0–3.1), using a shower hose for RD (AOR, 3.5; 95% CI, 1.1–13.0), condomless receptive anal intercourse (CRAI) (AOR, 2.9; 95% CI, 1.6–5.5), and using nitrite inhalants (AOR, 2.8; 95 % CI, 1.6-5.1) in the most recent anal intercourse.Conclusions: RD is popular among Chinese MSM. Improper noncommercial RD tools increase the rates of HIV infection. Public health workers and the MSM community should publicize scientific knowledge and prevention approaches relating to RD and HIV transmission to MSM, and we recommend that better tools be offered to assist in RD in order to decrease the risk of acquiring HIV.