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 , Yu Hai , Wang Kaihang , Chen Tingting , Ma Yue , Huang Yang , Li Jiajia , Liu Liqin , Li Yuqian , Kong Zhibo , Zheng Qingbing , Wang Yingbin , Gu Ying , Xia Ningshao , Li Shaowei 
Published: June 2020

Abstract
Background: The Escherichia coli ER2566 strain (NC_CP014268.2) was developed as a BL21 (DE3) derivative strain and had been widely used in recombinant protein expression. However, like many other current RefSeq annotations, the annotation of the ER2566 strain was 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 adapted under external pressure.Results: The reannotation included noteworthy corrections to all protein-coding genes, led to the exclusion of 190 hypothetical genes or pseudogenes, and resulted in the addition of 237 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 123 (63%) as coding genes. 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 lacI gene in the transcribed RNA, which was not detected at the genomic level by Sanger sequencing.Conclusion: The ER2566 strain was 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 be involved in the transcription and translation of genes encoding the lactose operon repressor. We proposed that our pipeline might offer a universal method for the reannotation of other bacterial genomes with high speed and accuracy. This study might facilitate a better understanding of gene function for the ER2566 strain under external burden and provided more clues to engineer bacteria for biotechnological applications.
Comparisons of Social and Demographic Determinants of Tobacco Use in the Democratic Republic of the Congo
Authors: Colwell Brian , Mosema Kizito , Bramble Matthew S. , Maddock Jay 
Published: June 2020

Abstract
Background: Worldwide, tobacco use has caused over 100 million deaths in the twentieth century and is projected to cause death in up to one billion people in the twenty-first century. It is a leading cause of early death and disability in over 100 countries and accounts for over 11% of global deaths, disproportionately affecting low- and middle-income countries. The purpose of the study was to examine a variety of social determinants of tobacco use in the Democratic Republic of the Congo, including region, sex, ethnicity, education, literacy, wealth index and place of residence, to gain insights with regard to tobacco use among sub-national groups. Methods: This project was a secondary data analysis of the 2013-2014 Demographics and Health Survey (DHS) for the Democratic Republic of the Congo. Logistic regressions predicting smoking, use of snuff and smoking cigars or natural tobacco as dichotomous variables were conducted. Independent variables included age, educational level, religion, rurality, literacy, wealth index, occupation and ethnicity. Results: Tobacco use is highest among those with less education and low literacy. It was also highest among the working poor. Older age and living in larger cities were predictive of smoking, although the relationship between age and smoking was not linear. There was a strong linear effect for wealth. Being in a professional, technical or managerial position was highly protective against smoking while being engaged in services, skilled and unskilled manual labor, and the army had significantly greater odds of smoking. Conclusions: Data indicate that tobacco use in the DRC, as is common in the developing world, is heavily concentrated in the working poor with lower educational status. Higher educational status is consistently predictive of avoiding tobacco use. Additionally, examining only national-level data to ascertain tobacco use levels and patterns may lead to mistaken conclusions that can lead to inefficient and ineffective allocation of resources aimed at controlling tobacco use.
Intracellular expression of arginine deiminase activates the mitochondrial apoptosis pathway through inhibiting cytosolic ferritin and inducing chromotin autophagy
Authors: Feng Qingyuan , Bian Xuzhao , Liu Xuan , Wang Ying , Zhou Huiting , Ma Xiaojing , Quan Chunju , Yao Yi , Zheng Zhongliang 
Published: June 2020

Abstract
Background：Based on its low toxicity, arginine starvation therapy has the potential to treat those malignant tumors that can’t be treated by surgery. Arginine deiminase (ADI) gene is indicated to be an ideal cancer-suppressor gene. ADI expressed in cytosol displays higher oncolytic efficiency than ADI-PEG20 (Pegylated Arginine Deiminase by PEG 20,000). However, it is still unknown whether cytosolic ADI has the same function mechanism as ADI-PEG20 or other underlying mechanisms in cells.Methods: The interaction of ADI and other protein factors was screened by yeast hybrid, and verified by co-immunoprecipitation and immunofluorescent staining. The effect of ADI inhibiting ferritin light-chain domain (FTL) on mitochondrial damage was evaluated by site-directed mutation and flow cytometry. The apoptosis pathway of mitochondria control was analyzed by Western Blot and real-time PCR experiments. The effect of p53 expression on cancer cell death was assessed by siTP53 transfection. The chromatin autophagy was explored by immunofluorescent staining and Western Blot.Results: ADI expressed in cytosol inhibited the activity of cytosolic ferritin through interacting with FTL. The inactive mutant of ADI still induced the apoptosis in certain cell lines of ASS- through mitochondrial damage. Arginine starvation also induced the increased expression of p53 and p53AIP1, which aggravate cellular mitochondrial damage. Chromatin autophagy appeared at the later stage of arginine starvation. DNA damage came along with the whole process of arginine starvation. Histone 3 (H3) was found in autophagosomes, which implied that cancer cells try to utilize the arginine in histones to survive during arginine starvation. Conclusions: Mitochondrial damage is the major mechanism of cell death induced by cytosolic ADI. Chromatophagy accumulations not only drive cancer cell to utilize histone arginine but also speed up cancer cell death at the later time point of arginine starvation.
HiCoP, a simple and robust method for detecting interactions of regulatory regions
Authors: Zhang Yan , Li Zhaoqiang , Bian Shasha , Zhao Hao , Feng Delong , Chen Yanhong , Hou Yuhe , Liu Qifa , Hao Bingtao 
Published: June 2020

Abstract
Background: Chromatin physical interactions provide essential information for understanding the regulation of cis-elements like enhancers, promoters, and insulators in cell development and differentiation. The Hi-C assay is a technique detecting chromatin structures of the whole genome but not sensitive to interactions of regulatory elements. Several methods, like HiChIP, DNase-C, and OCEAN-C, have been developed for enriching interactions of regulatory regions, but all of them have some shortcomings. New simple, efficient, and robust methods are still in need of detecting interactions of regulatory regions. Results: We developed a new, simple, and robust assay called CoP (Column Purified chromatin) for profiling of open chromatin regions by directly purifying fragmentized crosslinked chromatin with a DNA purification column. The accessible chromatin regions, including active enhancers, promoters, and insulators, were significantly enriched in CoP chromatin. The CoP-seq assay can efficiently detect open chromatin regions, especially active promoters, with a high signal-to-noise ratio. We integrated the CoP-seq and Hi-C technique (HiCoP) to detect interactions of accessible chromatin regions, which represent active cis-regulatory elements in cells. We observed that the HiCoP captured the peaks in the promoters-associated enhancer regions. HiCoP detected more promoter-enhancer (P-E), promoter-promoter (P-P), and enhancer-enhancer (E-E) interactions within 20kb-5Mb than Hi-C. Most of the loops identified by HiCoP are associated with the expressed genes. Conclusion: CoP assay can efficiently enrich open chromatin regions. When CoP assay was integrated with Hi-C assay, it provides a simple, robust, alternative technique for profiling accessible chromatin regions and chromatin conformation simultaneously.
Cognitive, language and behavioral outcomes in children and adolescents with autism spectrum disorders exposed to early comprehensive treatment models: A meta-analysis and meta-regression
Authors: Shi Bijun , Wu Weijia , Dai Meixia , Zeng Jingjing , Luo Jingyin , Cai Li , Wan Bin , Jing Jin 
Published: June 2020

Abstract
Background Early comprehensive treatment models (CTMs) have been developed as effective treatments for children with autism spectrum disorder (ASD). Numerous studies have suggested that CTMs can improve short-term outcomes, but little is known about outcomes in mid-childhood and adolescence. The current meta-analysis reviewed studies reporting broader outcomes in children and adolescents with ASD who had ever participated in a CTM and examined the predictors of developmental gains.Methods We searched eight databases up to June 13, 2019, for relevant trials and natural experiments. Longitudinal studies were selected if they investigated the outcomes of CTMs. Two meta-analyses were undertaken to provide a summary estimate of change in treatment outcomes and to evaluate the effect of CTMs; one used the standardized mean change between the pretest and posttest, and the other was a classical meta-analysis. Stratified and random-effects meta-regression analyses were performed to search for outcome differences among studies. Results Eighteen intervention studies (involving 495 children with ASD) met all the inclusion criteria: 12 used early intensive behavioral intervention (EIBI), and two used the Early Start Denver Model (ESDM). Outcomes were categorized into three parts: cognitive, language and behavioral (e.g., adaptive functioning and symptomatology). Overall, most children with ASD who had ever participated in an early CTM made gains in many areas of functioning, especially in terms of symptom- and language-related outcomes. Stratified analyses indicated that the ESDM displayed the largest effect on IQ improvement (ES=1.37, 95% CI: 0.95-1.80), while EIBI was more effective for symptom reduction (ES=-1.27, 95% CI: -1.96 to -0.58). Further meta-regression suggested that interventions with parent involvement and longer treatment hours yielded greater improvements in IQ and social adaptive functioning, respectively.Conclusion The results demonstrate a positive association between CTMs and better prognosis in mid-childhood and adolescence, especially regarding symptoms and language. However, most extant research involves small, nonrandomized studies, preventing definitive conclusions from being drawn. Clearly, the outcomes of children with ASD are still far from normal, especially with respect to adaptive functioning, and the three mediating variables pertaining to treatment elements can affect their gains, including approach, implementer and total treatment hours.
A focused netnographic study exploring experiences associated with counterfeit and contaminated anabolic androgenic steroids
Authors: Frude Evelyn , McKay Fiona , Dunn Matthew 
Published: June 2020

Abstract
Background: A primary consequence of illicit drug markets and the absence of regulation is the variable quality or purity of the final product. Analysis of anabolic-androgenic steroid seizures shows that these products can contain adulterated products, product not included on the label, or product of unsatisfactory standard. While the potential negative effects of counterfeit AAS use is a recognised risk associated with use, no study has explored personal experiences associated with use. The aim of the present study was to use online discussion forums to investigate and explore the experiences associated with the purchase and consumption of counterfeit AAS among consumers. Methods: An online search was conducted to identify online forums that discussed counterfeit or contaminated AAS; three were deemed suitable for the study. The primary source of data for this study were the ‘threads’ from these online forums, identified using search terms including ‘counterfeit’, ‘tampered’, and ‘fake’. Threads were thematically analysed for overall content, leading to the identification of themes. Results: Data from 134 threads (2743 posts from 875 unique avatars) was included. Two main themes were identified from the analysis: 1) Experiences with counterfeit product; and 2) Harms and benefits associated with counterfeit product.Conclusions: The use of counterfeit or contaminated substances represents a public health concern. Those who report using PIEDs such as AAS for non-medical purposes report consuming these substances, and experiencing harm as a result. Consumers take steps to limit coming into contact with counterfeit or contaminated product, though recognise that many of these have limitations. The implementation of accessible drug safety checking services may provide an opportunity to provide consumers with information to assist them with making healthier choices.
Experimental Pain and Fatigue Induced by Excessive Chewing
Authors: Sayegh Samaa Al , Vasilatou Ioanna , Kumar Abhishek , Barwari Ceva Al , Fredriksson Lars , Grigoriadis Anastasios , Christidis Nikolaos 
Published: June 2020

Abstract
Background: The study was aiming to optimize excessive gum chewing as an experimental model to induce jaw muscle pain and fatigue similar to those in painful TMDs with durations that would allow immediate investigations of jaw-motor function. Further, if any sex differences would be detected in the expression of pain.
Methods: This randomized, double blinded study included 31 healthy participants of both sexes. A standardized chewing protocol of either 40- or 60-minutes of chewing was used with a wash-out period of one week. Subjective fatigue, pain characteristics and functional measures were assessed. For statistical analyses, Wilcoxon Signed Rank test, Mann–Whitney Rank Sum test and Friedman’s ANOVA with Tukey post-hoc test were used.
Results: High subjective fatigue scores that lasted up to 20 minutes after the end of the trial were significantly induced both in the 40- and 60-minute chewing trials (P<0.001*). Significant but mild pain was induced only in the 60-minute trial (P=0.004*) and only in men (P=0.04*). Also, the induced pain area was significantly bigger in the 60-minute trial (P=0.009*). However, this increase in pain and pain area did not last to the first 10-minute follow-up. There were no significant differences neither between the 40- and 60-minute chewing trials, except regarding the pain area (P=0.008*), nor between the sexes.
Conclusion: Taken together, excessive chewing in its current form does not seem to be a proper pain experimental model. The model needs further adjustments in order to mimic TMD-pain especially in women and to prolong the pain duration.
Trends and seasonality in cause-specific mortality among children under 15 years in Guangzhou, China, 2008-2018
Authors: Xu Xiao-Han , Dong Hang , Li Li , Liu Wen-Hui , Lin Guo-Zhen , Ou Chun-Quan 
Published: June 2020

Abstract
Background: This study analyzed the trends and seasonality in mortality among children aged 0-14 years in Guangzhou, China during 2008-2018. Understanding the epidemiology of this public health problem can guide policy development for children mortality prevention.
Methods: A population-based epidemiological retrospective study was conducted. 7,265 individual data of children mortality were obtained from the Guangzhou Center for Disease Control and Prevention. The Poisson regression was used to quantify the annual average reduction rate and the difference in mortality rate between sex and age groups. Incidence ratio with 95% confidence interval (CI) was estimated to determine the temperaol variations in mortality by month, season, school term, day of the week and between holidays and other days.
Results: Between 2008 and 2018, the children mortality rate in Guangzhou decreased from 54.0 to 34.3 per 100,000 children, with an annual reduction rate of 4.6% (95% CI: 1.1%-8.1%), especially the under-5 mortality rate decreased by 8.3% (95% CI: 4.8%-11.6%) per year. Decline trends varied by causes of death, even with an upward trend for the mortality of asphyxia and neurological diseases. The risk of death among males children was 1.33 times (95% CI: 1.20-1.47) of that of females. The distribution of causes of death differed by age group. Maternal and perinatal, congenital and pneumonia were the top three causes of death in infants and cancer accounted for 17% of deaths in children aged 1-14 years. Moreover, the injury-related mortality showed significant temporal variations with higher risk during the weekend. And there was a summer peak for drowning and a winter peak for asphyxia.
Conclusions: Guangzhou has made considerable progress in reducing mortality over the last decade. The findings of characteristics of children mortality would provide important information for the development and implementation of integrated interventions targeted specific age groups and causes of death.
Surgery combined with antibiotics for the treatment of endogenous endophthalmitis caused by liver abscess
Authors: Wang Yue , Wang Xue , Di Yu 
Published: June 2020

Abstract
Backgrounds: Endogenous endophthalmitis is a serious disease caused by intraocular infection that can rapidly progress to cause blindness. This study evaluated the clinical features, surgical and antibiotics treatment strategies, and treatment outcomes in patients with endophthalmitis caused by liver abscess.Methods: Between April 2014 and April 2019, the clinical data of 16 patients (19 eyes) with endophthalmitis associated with liver abscess who underwent surgery at Shengjing Hospital were retrospectively analyzed. Furthermore, we evaluated the final visual outcomes in the patients to determine the efficacy of surgeryResults: Fifteen patients (18 eyes) underwent intravitreal injection followed by vitrectomy after admission. One patient (1 eye) only underwent intravitreal injection. Of the 16 patients, 3 patients (3 eyes) had recurrent intraocular inflammation and eventually underwent evisceration. Systemic antibiotics were administered for all patients based on the results of vitreous humor culture, blood culture, and antibiotic susceptibility tests. Outpatient follow-ups were performed until the patients were stable (6 months). Of the 19 eyes, 1 eye (5%) had visual acuity restored to 20/200, 6 eyes (31%) had visual acuity restored to counting fingers (CF), 2 eyes (11%) had visual acuity restored to hand motion (HM), 4 eyes (22%) showed only light perception (LP), and the remaining 6 eyes (31%) showed no light perception (NLP). Drug susceptibility tests suggested that the carbapenems exhibited significant effects in the inflammatory reaction.Conclusion: Endogenous endophthalmitis caused by liver abscess is a very serious condition, and the final visual outcome is poor. Timely surgical intervention combined with antibiotic treatment is essential, and the primary disease must be treated to control disease progression at the earliest.
Influence of Participation in a Quality Improvement Collaborative on Staff Perceptions of Organizational Sustainability
Authors: II James H Ford , Gilson Aaron 
Published: June 2020

Abstract
Background: Organizational sustainability capacity (SC) – the ability to implement and maintain change – is influenced by internal attributes, environmental contextual influencers, and intervention attributes. Dissemination and implementation research has generally not explored temporal changes in staff SC perceptions, and how quality improvement collaborative (QIC) participation influences those changes. This project addresses the gap, using the British National Health Services sustainability index, to measure staff SC perceptions at four time points (baseline and every 9 months) for participating clinics in the NIATx200 QIC initiative.Methods: Respondent demographic information allowed matching individual survey responses, so all analyses comprise responses from the same staff members (n=908, representing 2,329 total cases) across the evaluation timeframe. A mixed linear model repeated measures analysis fit three separate statistical models to assess potential predictors of SC perceptions: Time (Models I-III); NIATx200 intervention, staff job function, and tenure (Models II &III); and NIATx200 participation hours (Model III).Results: Model I yielded strong overall predictive significance for Time (F=7.270, p<.0001), with staff perceptions of overall SC increasing throughout most of the study (t1,4=-6.74, p<.0001; t2,4=-3.100, p<.036; t3,4=-0.23, p=ns). Model II did not change the overall Time effect from Model I, but the assigned NIATx200 intervention – combined services, (t=-3.28, p=.026), staff job function and organizational administrators, (t=-3.50, p=.001) became significantly associated with greater perceptions of SC. The addition of participation levels in Model III demonstrated the importance of a higher participation dose (t=-3.73, p<.0001) on staff perceptions about overall SC. Conclusion: Although there was minimal staff exposure to sustainability principals within NIATx200, staff perceptions about their organization’s SC significantly differed over time. However, an organization’s participation level in a QIC became the principal predictor of staff SC perceptions, regardless of other factors. Given these findings, it is possible to develop and introduce specific sustainability content within the structure of a QIC to assess the impact on staff SC perceptions over time and the sustainment of organizational change.Trial Registration: ClinicalTrials.gov, NCT00934141 Registered July 6, 2009. Retrospectively registered. https://clinicaltrials.gov/ct2/show/NCT00934141