bluuebunny/crossref_metadata_2025_split huggingface dataset:
A plasmid-encoded papB paralogue modulates autoaggregation of Escherichia coli transconjugants
Authors: Monarrez Ruben , Okeke Iruka 
Published: June 2020

Abstract
Objective: Plasmids are key to the transmission of antimicrobial resistance among enteric bacteria. It is becoming increasingly clear that resistance genes alone do not account for the selective advantage of plasmids and bacterial strains that harbor them. Deletion of a 32 Kb fitness-conferring region of pMB2, a conjugative resistance plasmid, produced a hyper­autoaggregation phenotype in laboratory Escherichia coli. This study sought to determine the genetic basis for hyper-autoaggregation conferred by the pMB2-derived mini-plasmid.Results: The 32 Kb fragment deleted from pMB2 included previously characterized nutrient acquisition genes as well as putative transposase and integrase genes, a 272 bp papB/ pefB-like gene, and several open-reading frames of unknown function. We cloned the papB/ pefB paralogue and found it sufficient to temper the hyper-autoaggregation phenotype. Hyper­autoaggregation conferred by the mini-plasmid did not occur in a fim-negative background. This study has identified and characterized a gene capable of down-regulating host adhesins and has shown that trans-acting papB/pefB paralogues can occur outside the context of an adhesin cluster. This plasmid-mediated modification of a bacterial host’s colonization program may optimize horizontal transfer of the mobile element bearing the genes.
Results Following Surgical Resection of Recurrent Chordoma Of the Spine: Experience in a Single Institution
Authors: Chanplakorn Pongsthorn , Lertudomphonwanit Thamrong , Homcharoen Wittawat , Suwanpramote Prakrit , Laohacharoensombat Wichien 
Published: June 2020

Abstract
Background: Chordoma of the spine is a low-grade malignant tumor with vague and indolentsymptoms thus large tumor mass is encountered at the time of diagnosis in almost cases and makes a difficult for En-bloc free-margin resection. Salvage therapyfor recurrent chordoma is very challenging due to its relentless nature and refractory to adjuvant therapies. The aim of this present study was to report the oncologic outcome following surgical resection of chordoma of the spine.Materials and Methods:Retrospective review of 10 consecutive cases of recurrent chordoma patients who underwent surgical treatment between 2003 and 2018atone tertiary-care center was conducted.Results: There were 10 patients, 4 females and 6 males were included in this study. Eight patients had local recurrence. The recurrence was encountered at the muscle, surrounding soft tissue and remaining bony structure. Distant metastaseswere found in 2 patients. The average time of recurrence was 28 months after first surgery. Conclusion:En-bloc free margin resection is mandatory toprevent recurrent. The clinical vigilance and investigation to identify tumor recurrent should be obtained periodically,in the first 28 months. Detection of recurrent in early stage with a small mass may be the best chance to perform an En-Bloc margin free resection to prevent further recurrent.
Semi-Embedded Valve Anastomosis: a New Anti-reflux Anastomotic Method After Proximal Gastrectomy for Adenocarcinoma of Esophagogastric Junction
Authors: Wang Baohua , Wu Yupeng , Wang Haijun , Zhang Haiqiang , Wang Liting , Zhang Zhanxue 
Published: June 2020

Abstract
Background
There is a high probability of gastroesophageal reflux after laparoscopic proximal gastrectomy of SiewertⅡAEG. Various anti-reflux anastomotic methods are emerging in clinical practice, however, none of them is widely accepted. We have innovated a new type of anti-reflux anastomotic method, named semi-embedded valve anastomosis. The aim of this study is to explore the feasibility and anti-reflux effect of the new anastomotic method.
Methods
The clinical data of 28 patients with SiewertⅡAEG were collected in this study, who were treated by semi-embedded valve anastomosis. The key point of operation is to reconstruct a simulated valve and form a similar anti-reflux barrier under physiological mechanism. GerdQ gastroesophageal reflux questionnaire and classification of gastroesophageal reflux under electron microscope were used to evaluate gastroesophageal reflux after operation.
Results
The mean time of operation was 164.3 ± 19.0 min, the median intraoperative hemorrhage was 65 ml, the average number of lymph nodes dissected was 23 ± 2.6, the time of making valve was 15.8 ± 3.2 min, the time of anastomotic reconstruction was 35.4 ± 4.8 min, the median time of first exhaust was 3d, the median time of hospitalization was 12 days, one case with postoperative anastomotic stenosis. GerdQ score, median (range) : 2 (0–6), preoperation; 0 (0–8), 1 months postoperation; 2 (0–12), 3 months postoperation; 3 (0–12), 6 months postoperation. Wilcoxon signed rank sum test was carried out at different time after operation and the day before operation respectively, the differences were not statistically significant, P < 0.05. There was one case of grade B according to LA classification system of gastroesophageal reflux among the gastrofiberscope reexamination reports of 28 cases.
Conclusion
Semi-embedded valve anastomosis is safe and feasible after the proximal gastrectomy of Siewert Ⅱ AEG, and has good anti-reflux effect.
Spie charts for quantifying treatment effectiveness and safety in multiple outcome network meta-analysis: A proof-of-concept study
Authors: Daly Caitlin , Mbuagbaw Lawrence , Thabane Lehana , Straus Sharon E , Hamid Jemila S 
Published: June 2020

Abstract
Background
Network meta-analysis (NMA) simultaneously synthesises direct and indirect evidence on the relative efficacy and safety of at least three treatments. A decision maker may use the coherent results of an NMA to determine which treatment is best for a given outcome. However, this evidence must be balanced across multiple outcomes. This study aims to provide a framework that permits the objective integration of the comparative effectiveness and safety of treatments across multiple outcomes.
Methods
In the proposed framework, measures of each treatment’s performance are plotted on its own pie chart, superimposed on another pie chart representing the performance of a hypothetical treatment that is the best across all outcomes. This creates a spie chart for each treatment, where the coverage area represents the probability a treatment ranks best overall. The angles of each sector may be adjusted to reflect the importance of each outcome to a decision maker. The framework is illustrated using two published NMA datasets comparing dietary oils and fats and psoriasis treatments. Outcome measures are plotted in terms of the surface under the cumulative ranking curve. The use of the spie chart was contrasted with that of the radar plot.
Results
In the NMA comparing the effects of dietary oils and fats on four lipid biomarkers, the ease of incorporating the lipids’ relative importance on spie charts was demonstrated using coefficients from a published risk prediction model on coronary heart disease. Radar plots produced two sets of areas based on the ordering of the lipids on the axes, while the spie chart only produced one set. In the NMA comparing psoriasis treatments, the areas inside spie charts containing both efficacy and safety outcomes masked critical information on the treatments’ comparative safety. Plotting the areas inside spie charts of the efficacy outcomes against measures of the safety outcome facilitated simultaneous comparisons of the treatments’ benefits and harms.
Conclusions
The spie chart is more optimal than a radar plot for integrating the comparative effectiveness or safety of a treatment across multiple outcomes. Formal validation in the decision-making context, along with statistical comparisons with other recent approaches are required.
Design and Optimization for Uav-enabled Two-way Relaying System With Swipt
Authors: Wang Jinlong , Wang Gang , Chen Guanyi , Li Bo , Zhou Ruofei , Zhang Ruoyu 
Published: June 2020

Abstract
In this paper, we investigate the resource allocation scheme for an unmanned-aerial-vehicle-enable (UAV-enabled) two-way relaying system with simultaneous wireless information and power transfer (SWIPT), where two user equipments (UEs) exchange information with the help of UAV relay and harvest energy through power splitting (PS) scheme. Under the transmission power constraints at UEs and UAV relay, a non-convex intractable optimization problem is formulated which maximizes the sum retained energy of two UEs while satisfying the minimum signal-to-noise ratio requirement. We decouple the complicated beamforming and PS factors optimization problem into three solvable subproblems and propose an efficient alternating optimization scheme. Subsequently, in order to reduce the complexity, a robust scheme based on generalized singular value decomposition (GSVD) is designed. Finally, numerical results verify the robustness and effectiveness of two proposed schemes.
Compensation Models for Community Health Workers: Comparison of Legal Frameworks across Five Countries
Authors: Ballard Madeleine , Westgate Carey , Alban Rebecca , Choudhury Nandini , Adamjee Rehan , Schwarz Ryan , Bishop Julia , McLaughlin Meg , Flood David , Finnegan Karen , Rogers Ash , Olsen Helen , Johnson Ari , Palazuelos Daniel , Schechter Jennifer 
Published: June 2020

Abstract
Background
Despite the life-saving work they perform, community health workers (CHWs) have long been subject to global debate about their remuneration. There is now, however, an emerging consensus that CHWs should be paid. As the discussion evolves from whether to financially remunerate CHWs to how to do so, there is an urgent need to better understand the types of CHW payment models and their implications.
Methods
This study examines the legal framework on CHW compensation in five countries: Brazil, Ghana, Nigeria, Rwanda, and South Africa. In order to map the characteristics of each approach, a standardized questionnaire was developed and targeted at local law firms. The questionnaire covered legal structures and requirements for compensation of CHWs, CHW compensation mechanisms, CHW legal protections and benefits, and alignment of national CHW policies with global guidelines.
Results
The five countries profiled represent possible archetypes for CHW compensation: Brazil (public), Ghana (volunteer-based), Nigeria (private), Rwanda (cooperatives with performance based incentives) and South Africa (hybrid public/private). Advantages and disadvantages of each model with respect to (i) CHWs, in terms of financial protection, and (ii) the public sector, in terms of ease of implementation, are outlined.
Conclusions
While a strong legal framework does not necessarily translate into high-quality implementation, it is the first necessary step. While certain approaches to CHW compensation - particularly public-sector or hybrid models with public sector wage floors - best institutionalize recommended CHW protections, political will and long-term financing often remain obstacles. Removing ecosystem barriers - such as multilateral and bilateral restrictions on the payment of salaries - can help governments institutionalize CHW payment.
Pre-existing liver disease is associated with poor outcome in patients with SARS CoV2 infection; The APCOLIS Study (APASL COVID-19 Liver Injury Spectrum Study)
Authors: Sarin Shiv Kumar , Choudhury Ashok , Lau George K , Zheng Ming-Hua , Ji Dong , Abd-Elsalam Sherief , Hwang Jaeseok , Qi Xiaolong , Cua Ian Homer , Suh Jeong Ill , Park Jun Gi , Putcharoen Opass , Kaewdech Apichat , Piratvisuth Teerha , Treeprasertsuk Sombat , Park Sooyoung , Wejnaruemarn Salisa , Payawal Diana A. , Baatarkhuu Oidov , Ahn Sang Hoon , Yeo Chang Dong , Alonzo Uzziel Romar , Chinbayar Tserendorj , Loho Imelda M. , Yokosuka Osamu , Jafri Wasim , Tan Soeksiam , Soo Lau Ing , Tanwandee Tawesak , Gani Rino , Anand Lovkesh , Esmail Eslam Saber , Khalaf Mai , Alam Shahinul , Lin Chun-Yu , Chuang Wan-Long , Soin A S , Garg Hitendra K , Kalista Kemal , Batsukh Badamnachin , Purnomo Hery Djagat , Dara Vijay Pal , Rathi Pravin , Mahtab Mamun Al , Shukla Akash , Sharma Manoj K , Omata Masao 
Published: June 2020

Abstract
Background and Aims: COVID-19 is a dominant pulmonary disease, with multisystem involvement, depending upon co morbidities. Its profile in patients with pre-existing chronic liver disease (CLD) is largely unknown. We studied the liver injury patterns of SARS-Cov-2 in CLD patients, with or without cirrhosis. Methods: Data was collected from 13 Asian countries on patients with CLD, known or newly diagnosed, with confirmed COVID-19. Result: Altogether, 228 patients [185 CLD without cirrhosis and 43 with cirrhosis] were enrolled, with comorbidities in nearly 80%. Metabolism associated fatty liver disease (113, 61%) and viral etiology (26, 60%) were common. In CLD without cirrhosis, diabetes [57.7% vs 39.7%, OR=2.1(1.1-3.7), p=0.01] and in cirrhotics, obesity, [64.3% vs. 17.2%, OR=8.1(1.9-38.8), p=0.002) predisposed more to liver injury than those without these. Forty three percent of CLD without cirrhosis presented as acute liver injury and 20% cirrhotics presented with either acute-on-chronic liver failure [5(11.6%)] or acute decompensation [4(9%)]. Liver related complications increased (p<0.05) with stage of liver disease; a Child-Turcotte Pugh score of 9 or more at presentation predicted high mortality [AUROC-0.94, HR=19.2(95CI 2.3-163.3), p<0.001, sensitivity 85.7% and specificity 94.4%). In decompensated cirrhotics, the liver injury was progressive in 57% patients, with 43% mortality. Rising bilirubin and AST/ALT ratio predicted mortality among cirrhosis. Conclusions: SARS-Cov-2 infection causes significant liver injury in CLD patients, decompensating one fifth of cirrhosis, and worsening the clinical status of the already decompensated. The CLD patients with diabetes and obesity are more vulnerable and should be closely monitored.
Accelerated Partial Breast Irradiation in the Elderly:8-year Oncological Outcome and Prognostic Factors
Authors: Sumodhee Shakeel , PUJALTE-MARTIN Marc , Gal Jocelyn , Kee Daniel Lam Cham , Gautier Mathieu , Schiappa Renaud , Chand Marie-Eve , Hannoun-Levi Jean-Michel 
Published: June 2020

Abstract
Introduction: To evaluate long term clinical outcome and prognostic factors after accelerated partial breast irradiation (APBI) in the elderly using high-dose-rate interstitial multi-catheter brachytherapy (HIBT).Material and methods: Between 2005 and 2018, 109 patients underwent APBI using HIBT (34 Gy/10f/5d or 32 Gy/8f/4d). Based on a prospective database, outcomes were retrospectively analyzed (local relapse-free survival (LRFS), metastatic-free survival (MFS), specific survival (SS) and overall survival (OS). Prognostic factors were investigated. Late toxicity and cosmetic evaluation were reported.Results: With a median follow-up of 97 months [7–159], median age was 81.7 years [58-89]. According to the GEC-ESTRO APBI classification, 72.5%, 11.9% and 15.6% were classified as low, intermediate and high-risk respectively. The histological type was mainly invasive ductal carcinoma (87.1%). The median tumor size was 10 mm [range 1-35]. Eight-year LRFS, SS and OS were 96.7% [95% CI [0.923; 1]), 96.7% [95% CI [0.924; 1] and 72%[95% CI [0.616; 0.837] respectively. In univariate analysis, APBI classification was not cosidered as prognostic factor, whilemolecular classification was prognostic factor for OS (p<0.0001), SS (p=0.007) and MFS (p=0.009) but not for LR (p=0.586). No Grade ³3 late toxicity was observed while 61 patients (88.4%) and 8 patients (11.6%) presented grade 1 and 2 toxicities respectively. Cosmetic outcome was excellent/good for 96.4%.Conclusion: Long-term follow-up confirms that HIBT is safe and effective for elderly early breast cancer. Our results suggest that selected elderly women presenting with high-risk breast cancer could be also considered for APBI.
Potential research ethics violations against an indigenous tribe in Ecuador: a mixed methods approach
Authors: Ortiz-Prado Esteban , Simbana-Rivera Katherine , Gomez-Barreno Lenin , Tamariz Leonardo , Lister Alex , Baca Juan Carlos , Norris Alegria , Adana-Diaz Lila 
Published: June 2020

Abstract
Background
Biomedical and ethnographic studies among indigenous people are common practice in health and geographical research. Prior health research misconduct has been documented, particularly when obtaining genetic material. The objective of this study was to crossmatch previously published data with the perceptions of the Waorani peoples about the trading of their genetic material and other biological samples.
Methods
We conducted a mixed methods study design using a tailored 15-item questionnaire and in-depth interviews with 72 participants belonging to 20 Waorani communities about their experiences and perceptions of participating in biomedical research projects. Additionally, we conducted a systematic review of the literature in order to crossmatch the published results of studies stating the approval of an ethics committee and individual consent within their work.
Results
A total of 40 men (60%) and 32 women (40%), with a mean age of 57 ± 15 years agreed to be interviewed for inclusion. Five main categories around the violation of good clinical practices were identified, concerning the obtention of blood samples from a recently contacted Waorani native community within the Amazonian region of Ecuador. These themes are related to the lack of adequate communication between community members and researchers as well as the voluntariness to participate in health research. Additionally, over 40 years, a total of 38 manuscripts related to the use of biological samples in Waorani indigenous people were published. The majority of the studies (68%) did not state within their article obtaining research ethics board approval, and 71% did not report obtaining the informed consent of the participants prior to the execution of the project.
Conclusion
Clinical Research on the Waorani community in the Ecuadorian Amazon basin has been performed on several occasions. Unfortunately, the majority of these projects did not follow the appropriate ethical and professional standards in either reporting the results or fulfilling them. The results of our investigation suggest that biological material, including genetic material, has been used by researchers globally, with some omitting the minimum information required to guarantee transparency and good clinical practices. We highlight the importance of stating ethics within research to avoid breaches in research transparency.
Urinary sediments could differentiate the endocapillary proliferative lupus nephritis and endocapillary proliferative IgA nephrology
Authors: Yuan Mo , Li Jing-zi , Yu Xiao-juan , Zhang Hong , Tan Ying 
Published: June 2020

Abstract

Background: The role of manual urine sediment examination in the diagnosis and prognostication of endocapillary proliferative glomerulonephritis remains to be elucidated. This study aims to investigated the differences of urinary sediment findings between lupus nephritis and IgA nephropathy with endocapillary proliferative glomerulonephritis and further evaluated associations of leukocyturia with disease activity, pathological features and prognosis.Methods: The urinary sediment of 126 patients, including 92 patients with lupus nephritis and 34 patients with IgA nephropathy, with a renal biopsy-proven endocapillary proliferative glomerulonephritis were examined in the morning before renal biopsy according to a standardized method. The urinary elements investigated including various cells, casts and crystals. The associations of the level of leukocyturia and disease activity, pathological features and prognosis were further analyzed.Results: In the patients with endocapillary proliferative glomerulonephritis, normal to mild leukocyturia (≤12/HPF), and moderate to severe leukocyturia (>12/HPF) were found in 52(41.27%) and 74 (58.73%) patients, respectively. The proportion of moderate to severe leukocyturia, the frequency of urinary white blood cells casts and waxy casts were significantly higher in endocapillary proliferative lupus nephritis patients compared with endocapillary proliferative IgA nephropathy patients (P<0.001, P=0.020, P=0.010, respectively). In the proliferative lupus nephritis group, the levels of leukocyturia was significantly correlated with serum creatinine (r=0.288, P=0.005), eGFR (r=-0.284, P= 0.006), serum C3 (r=-0.275, P= 0.009) , SLEDAI scores (r=0.383, P=＜0.001) and glomerular leukocyte infiltration (r=0.285, P= 0.002). A multivariate analysis showed that leukocyturia was identified as an independent risk factor for renal outcome in proliferative lupus nephritis (HR: 1.456, 95% CI: 1.083-1.957, P=0.013) but not in IgA nephropathy (HR: 1.069, 95% CI: 0.494-2.312, P=0.866).Conclusions: Urinary sediments of the endocapillary proliferative lupus nephritis and endocapillary proliferative IgA nephrology differed in many aspects. Leukocyturia could reflect the disease activity and prognosis of endocapillary proliferative glomerulonephritis, especially in lupus nephritis.
ProfKin: A Comprehensive Web Server for Structure-based Kinase Selectivity Profiling
Authors: Shen Zihao , Yan Yu-Hang , Yang Shuo , Zhu Sang , Yuan Yuan , Qiu Zhiqiang , Jia Huan , Wang Ruiqiong , Li Guo-Bo , Li Honglin 
Published: June 2020

Abstract
Protein kinases are central mediators of signal-transduction cascades and attractive drug targets for therapeutic intervention. Since kinases are structurally and mechanistically related to each other, kinase inhibitor selectivity is often investigated by kinase profiling and considered as an important index for drug discovery. We here describe a versatile web server termed ProfKin for structure-based kinase selectivity profiling, which is based on a kinase-ligand focused database (KinLigDB). It provides all ready-to-use 3D structure coordinates of 4,219 kinase-ligand complex structures covering 297 human kinases and the associated information, particularly including binding site type, binding ligand type, interaction fingerprints, downstream molecules and related human diseases. The web server works via predicting possible binding modes for the query molecule, prioritizing the binding modes guided by an interaction fingerprint analysis method, and giving a list of ranked kinases by a comprehensive index. Users can freely select entire or part of the KinLigDB database, e.g. via subfamily and binding site type, to customize the profiling contents. The superimpositions of the predicted binding poses of the query molecule with reference binding modes can be visually inspected on the website. For each top-ranked kinase, the additional classification attributes and the phylogenetic tree are given simultaneously.