Takshan/R1 huggingface dataset:
Review of attacks on health care facilities in six conflicts of the past three decades.

Background: In the ongoing conflicts of Syria and Yemen, there have been widespread reports of attacks on health care facilities and personnel. Tabulated evidence does suggest hospital bombings in Syria and Yemen are far higher than reported in other conflicts but it is unclear if this is a reporting artefact. Objective: This article examines attacks on health care facilities in conflicts in six middle- to high- income countries that have occurred over the past three decades to try and determine if attacks have become more common, and to assess the different methods used to collect data on attacks. The six conflicts reviewed are Yemen (2015-Present), Syria (2011- Present), Iraq (2003-2011), Chechnya (1999-2000), Kosovo (1998-1999), and Bosnia and Herzegovina (1992-1995). Methods: We attempted to get the highest quality source(s) with summary data of the number of facilities attacked for each of the conflicts. The only conflict that did not have summary data was the conflict in Iraq. In this case, we tallied individual reported events of attacks on health care. Results: Physicians for Human Rights (PHR) reported attacks on 315 facilities (4.38 per month) in Syria over a 7-year period, while the Monitoring Violence against Health Care (MVH) tool launched later by the World Health Organization (WHO) Turkey Health Cluster reported attacks on 135 facilities (9.64 per month) over a 14-month period. Yemen had a reported 93 attacks (4.65 per month), Iraq 12 (0.12 per month), Chechnya > 24 (2.4 per month), Kosovo > 100 (6.67 per month), and Bosnia 21 (0.41 per month). Methodologies to collect data, and definitions of both facilities and attacks varied widely across sources. Conclusion: The number of reported facilities attacked is by far the greatest in Syria, suggesting that this phenomenon has increased compared to earlier conflicts. However, data on attacks of facilities was incomplete for all of the conflicts examined, methodologies varied widely, and in some cases, attacks were not defined at all. A global, standardized system that allows multiple reporting routes with different levels of confirmation, as seen in Syria, would likely allow for a more reliable and reproducible documentation system, and potentially, an increase in accountability.
Palliative care for the management of chronic illness: a systematic review study protocol.

INTRODUCTION: Chronic illnesses are marked by fluctuations and variations over time. Individuals with chronic illness experience pain and other symptoms that are not always adequately managed. Their caregivers often have to deal with enormous burden as the illness progresses. Palliative care can serve as an intervention to manage chronic illness, not just at the end of life but also in the early phases of illness. METHODS AND ANALYSIS: Randomised and non-randomised studies will be included in the systematic review. The focus will be on non-cancer chronic illness. Sources of data will be from PubMed and other databases and will include the reference list of studies included in the systematic review. The primary outcome will be to assess the efficacy of palliative care on chronic illness. Secondary outcomes will include health-related quality of life, care giver burden, quality of care and cost-effectiveness of interventions. The study population will consist of patients aged 18 years or over. ETHICS AND DISSEMINATION: For purposes of privacy and confidentiality, the systematic review will be limited to studies with de-identified data. The systematic review will be published in a peer-reviewed journal. It will also be disseminated electronically and in print. Brief reports of review findings will be disseminated directly to appropriate audiences via email and other modes of communication. Updates of the review will be conducted to inform and guide healthcare practice and policy. TRIAL REGISTRATION NUMBER: PROSPEROCRD42011001794.
Variation in Performance of Neonatal Intensive Care Units in the United States.

Importance: Hospitals use rates from the best quartile or decile as benchmarks for quality improvement aims, but to what extent these aims are achievable is uncertain. Objective: To determine the proportion of neonatal intensive care units (NICUs) in 2014 that achieved rates for death and major morbidities as low as the shrunken adjusted rates from the best quartile and decile in 2005 and the time it took to achieve those rates. Design, Setting, and Participants: A total of 408 164 infants with a birth weight of 501 to 1500 g born from January 1, 2005, to December 31, 2014, and cared for at 756 Vermont Oxford Network member NICUs in the United States were evaluated. Logistic regression models with empirical Bayes factors were used to estimate standardized morbidity ratios for each NICU. Each ratio was multiplied by the overall network rate to calculate the 10th, 25th, 50th, 75th, and 90th percentiles of the shrunken adjusted rates for each year. The proportion in 2014 that achieved the 10th and 25th percentile rates from 2005 and the number of years it took for 75% of NICUs to achieve the 2005 rates from the best quartile were estimated. Main Outcomes and Measures: Death prior to hospital discharge, infection more than 3 days after birth, severe retinopathy of prematurity, severe intraventricular hemorrhage, necrotizing enterocolitis, and chronic lung disease among infants less than 33 weeks' gestational age at birth. Results: Of the 756 hospitals, 695 provided data for 2014. The mean unadjusted infant-level rate of death before hospital discharge decreased from 14.0% in 2005 to 10.9% in 2014. In 2014, 689 of 695 NICUs (99.1%; 95% CI, 97.4%-100.0%) achieved the 2005 shrunken adjusted rates from the best quartile for death prior to discharge, 678 of 695 (97.6%; 95% CI, 95.8%-99.6%) for late-onset infection, 558 of 681 (81.9%; 95% CI, 77.2%-86.6%) for severe retinopathy of prematurity, 611 of 693 (88.2%; 95% CI, 81.7%-97.0%) for severe intraventricular hemorrhage, 529 of 696 (76.0%; 95% CI, 71.8%-81.2%) for necrotizing enterocolitis, and 286 of 693 (41.3%; 95% CI, 36.1%-45.6%) for chronic lung disease. It took 3 years before 445 NICUs (75.0%) achieved the 2005 shrunken adjusted rate from the best quartile for death prior to discharge, 5 years to achieve the rate from the best quartile for late-onset infection, 6 years to achieve the rate from the best quartile for severe retinopathy of prematurity and severe intraventricular hemorrhage, and 8 years to achieve the rate from the best quartile for necrotizing enterocolitis. Conclusions and Relevance: From 2005 to 2014, rates of death prior to discharge and serious morbidities decreased among the NICUs in this study. Within 8 years, 75% of NICUs achieved rates of performance from the best quartile of the 2005 benchmark for all outcomes except chronic lung disease. These findings provide a novel way to quantify the magnitude and pace of improvement in neonatology.
Vietnamese medical students and binge drinking: a qualitative study of perceptions, attitudes, beliefs and experience.

OBJECTIVES: To explore the perceptions, attitudes, beliefs, and experiences related to Vietnamese medical students' binge drinking. DESIGN: A qualitative study comprising semi-structured focus groups/interviews with medical students and semi-structured interviews with key informants. Thematic analysis of data. SETTING: Participants were a convenience sample of usual volunteers from a medical university in Viet Nam. PARTICIPANTS: 19 medical students from year 1 to 6 and 4 key informants agreed to participate in the study. RESULTS: The study found participants believe medical students drink less than other students and are not binge drinkers yet they experience and/or witness many binge drinking occasions among medical students. Participants consider alcohol use as culturally acceptable in Vietnamese society and a way for medical students to create and improve relationships with their friends, teachers, or work colleagues. Group affiliation and peer pressure to drink excessive alcohol are identified among medical students, especially male students. CONCLUSION: The culture of drinking behaviour was explored among medical students in Viet Nam. This study reveals a dichotomy between the belief of not being binge drinkers and the experience of many binge drinking occasions among medical students. This tension suggests future research about binge drinking behaviour of Vietnamese medical students is required.
Déjà vu--a study of duplicate citations in Medline.

MOTIVATION: Duplicate publication impacts the quality of the scientific corpus, has been difficult to detect, and studies this far have been limited in scope and size. Using text similarity searches, we were able to identify signatures of duplicate citations among a body of abstracts. RESULTS: A sample of 62,213 Medline citations was examined and a database of manually verified duplicate citations was created to study author publication behavior. We found that 0.04% of the citations with no shared authors were highly similar and are thus potential cases of plagiarism. 1.35% with shared authors were sufficiently similar to be considered a duplicate. Extrapolating, this would correspond to 3500 and 117,500 duplicate citations in total, respectively. AVAILABILITY: eTBLAST, an automated citation matching tool, and Déjà vu, the duplicate citation database, are freely available at http://invention.swmed.edu/ and http://spore.swmed.edu/dejavu
Genetic Diversity and Population Structure of the Rare and Endangered Plant Species Pulsatilla patens (L.) Mill in East Central Europe.

Pulsatilla patens s.s. is a one of the most endangered plant species in Europe. The present range of this species in Europe is highly fragmented and the size of the populations has been dramatically reduced in the past 50 years. The rapid disappearance of P. patens localities in Europe has prompted the European Commission to initiate active protection of this critically endangered species. The aim of this study was to estimate the degree and distribution of genetic diversity within European populations of this endangered species. We screened 29 populations of P. patens using a set of six microsatellite primers. The results of our study indicate that the analyzed populations are characterized by low levels of genetic diversity (Ho = 0.005) and very high levels of inbreeding (FIS = 0.90). These results suggest that genetic erosion could be partially responsible for the lower fitness in smaller populations of this species. Private allelic richness was very low, being as low as 0.00 for most populations. Average genetic diversity over loci and mean number of alleles in P. patens populations were significantly correlated with population size, suggesting severe genetic drift. The results of AMOVA point to higher levels of variation within populations than between populations. The results of Structure and PCoA analyses suggest that the genetic structure of the studied P. patens populations fall into three clusters corresponding to geographical regions. The most isolated populations (mostly from Romania) formed a separate group with a homogeneous gene pool located at the southern, steppic part of the distribution range. Baltic, mostly Polish, populations fall into two genetic groups which were not fully compatible with their geographic distribution. Our results indicate the serious genetic depauperation of P. patens in the western part of its range, even hinting at an ongoing extinction vortex. Therefore, special conservation attention is required to maintain the populations of this highly endangered species of European Community interest.
Genetic diversity and differentiation of core vs. peripheral populations of eastern white cedar, Thuja occidentalis (Cupressaceae).

PREMISE OF THE STUDY: Geographically peripheral (marginal) populations are expected to have lower genetic diversity and higher genetic differentiation than geographically core (central) populations as a result of supposedly lower effective population size (N(e)) and higher genetic drift, founder effect, fragmentation, and isolation in peripheral than in core populations. Here we address this issue for a long-lived plant species, eastern white cedar (Thuja occidentalis). METHODS: Genetic diversity and population structure of 13 natural populations of eastern white cedar from its Canadian eastern peripheral and core natural ranges in New Brunswick, Nova Scotia, and Prince Edward Island were studied using six nuclear microsatellite DNA markers. KEY RESULTS: The core populations of eastern white cedar had significantly higher allelic diversity (mean A = 8.83, A(r) = 8.13, A(e) = 4.03) and N(e) (428) than the peripheral populations (A = 6.64, A(r) = 6.15, A(e) = 3.12, N(e) = 198). However, expected heterozygosity was similar in the core (H(e) = 0.64) and peripheral (H(e) = 0.60) populations. Genetic differentiation was significantly higher among the peripheral (F(ST) = 0.089) than among the core (F(ST) = 0.032) populations. No genetic differentiation (F(ST)/Φ(RT) = 0.000) was detected between core and peripheral regions. CONCLUSIONS: Peripheral populations have significantly lower N(e) and genetic diversity in terms of allelic diversity (richness) and significantly higher genetic differentiation than the core populations of eastern white cedar in its Canadian eastern range. However, core and peripheral populations have similar levels of expected heterozygosity. Implications for conservation of eastern white cedar genetic resources are discussed.
PubMed related articles: a probabilistic topic-based model for content similarity.

BACKGROUND: We present a probabilistic topic-based model for content similarity called pmra that underlies the related article search feature in PubMed. Whether or not a document is about a particular topic is computed from term frequencies, modeled as Poisson distributions. Unlike previous probabilistic retrieval models, we do not attempt to estimate relevance-but rather our focus is "relatedness", the probability that a user would want to examine a particular document given known interest in another. We also describe a novel technique for estimating parameters that does not require human relevance judgments; instead, the process is based on the existence of MeSH in MEDLINE. RESULTS: The pmra retrieval model was compared against bm25, a competitive probabilistic model that shares theoretical similarities. Experiments using the test collection from the TREC 2005 genomics track shows a small but statistically significant improvement of pmra over bm25 in terms of precision. CONCLUSION: Our experiments suggest that the pmra model provides an effective ranking algorithm for related article search.
Combined neutrophil/platelet/lymphocyte/differentiation score predicts chemosensitivity in advanced gastric cancer.

BACKGROUND: Gastric cancer is common in developing regions, and we hope to find out an economical but practical prognostic indicator. It was reported that pre-treatment peripheral neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR), as well as differentiation status, were associated with cancer progression. Hence, we introduced a novel combined Neutrophil/platelet/lymphocyte/differentiation Score (cNPLDS) to improve the prediction value of palliative chemotherapeutic response in advanced gastric cancer. METHODS: According to statistical sample size estimation, 136 primary diagnosed unresectable advanced ptaients were included for a retrospective study. The follow-up end-point was progression free survival (PFS) during the first-line palliative chemotherapy. Differentiation stratified patients into well, medium and poor groups by score 1 to 3, while patients with neither elevated NLR and PLR, only one elevated, or both elevated were of the combined NLR-PLR score (cNPS) 1 to 3, respectively. The cNPLDS was calculated by multiplying the tumor differentiation score and cNPS. RESULTS: Determined by the receiver operating characteristic (ROC) curve, the optimal cut-off points for NLR and PLR were 3.04 and 223. Through univariate analysis and survival analysis, poor differentiation, high NLR, high PLR, high cNPS, and high cNPLDS respectively indicated inferior PFS during the first-line palliative chemotherapy. Patients were furhter classified into low to high risk groups by cNPLDS. Groups of elevated NLR, PLR, cNPS, and cNPLDS showed lower disease control rate. Compared to other parameters, cNPLDS significantly improved the accuracy in predicing the first-progression. CONCLUSIONS: This study indicates that the novel parameter cNPLDS is superior to NLR or PLR alone, or even cNPS, in predicting the first-line chemosensitivity in advanced gastric cancer.
Identification of residue pairing in interacting β-strands from a predicted residue contact map.

BACKGROUND: Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a noisy contact map, due to the presence of characteristic contact patterns in β-β interactions. This information may benefit the tertiary structure prediction of mainly β proteins. In this work, we propose a novel ridge-detection-based β-β contact predictor to identify residue pairing in β strands from any predicted residue contact map. RESULTS: Our algorithm RDb2C adopts ridge detection, a well-developed technique in computer image processing, to capture consecutive residue contacts, and then utilizes a novel multi-stage random forest framework to integrate the ridge information and additional features for prediction. Starting from the predicted contact map of CCMpred, RDb2C remarkably outperforms all state-of-the-art methods on two conventional test sets of β proteins (BetaSheet916 and BetaSheet1452), and achieves F1-scores of ~ 62% and ~ 76% at the residue level and strand level, respectively. Taking the prediction of the more advanced RaptorX-Contact as input, RDb2C achieves impressively higher performance, with F1-scores reaching ~ 76% and ~ 86% at the residue level and strand level, respectively. In a test of structural modeling using the top 1 L predicted contacts as constraints, for 61 mainly β proteins, the average TM-score achieves 0.442 when using the raw RaptorX-Contact prediction, but increases to 0.506 when using the improved prediction by RDb2C. CONCLUSION: Our method can significantly improve the prediction of β-β contacts from any predicted residue contact maps. Prediction results of our algorithm could be directly applied to effectively facilitate the practical structure prediction of mainly β proteins. AVAILABILITY: All source data and codes are available at http://166.111.152.91/Downloads.html or the GitHub address of https://github.com/wzmao/RDb2C .
Deciphering functional diversification within the lichen microbiota by meta-omics.

BACKGROUND: Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system. RESULTS: The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach. Five highly abundant bacterial orders-Sphingomonadales, Rhodospirillales, Myxococcales, Chthoniobacterales, and Sphingobacteriales-harbor functions that are of substantial importance for the holobiome. Identified functions range from the provision of vitamins and cofactors to the degradation of phenolic compounds like phenylpropanoid, xylenols, and cresols. CONCLUSIONS: Functions that facilitate the persistence of Lobaria pulmonaria under unfavorable conditions were present in previously overlooked fractions of the microbiota. So far, unrecognized groups like Chthoniobacterales (Verrucomicrobia) emerged as functional protectors in the lichen microbiome. By combining multi-omics and imaging techniques, we highlight previously overlooked participants in the complex microenvironment of the lichens.
Health outcomes of patients with chronic disease managed with a healthcare kiosk in primary care: protocol for a pilot randomised controlled trial.

INTRODUCTION: The rising prevalence of chronic disease is leading to an increase in the demand for primary care services and a shortage of primary care physicians globally. Addressing these challenges calls for innovations in the healthcare delivery model with greater use of healthcare technology tools. We previously examined the feasibility of using an automated healthcare kiosk for the management of patients with stable chronic disease in the primary care setting. The aim of this follow-up study is to evaluate the health outcomes of patients with chronic disease who are on kiosk management compared with patients who are on routine management by nurse clinicians. METHODS AND ANALYSIS: The pilot study will be a two-armed randomised controlled trial of 120 patients with well-controlled chronic disease on 4-monthly follow-up visits over a 12-month period. Patients with prior diagnoses of hypertension, hyperlipidaemia and/or diabetes will be included in the study and will be randomly assigned to intervention or control groups to receive kiosk or nurse management, respectively. The main primary outcome measure is the overall chronic disease control of the patients. Other primary outcome measures are the blood pressure and low-density lipoprotein cholesterol levels for patients without diabetes, and blood pressure, low-density lipoprotein cholesterol and haemoglobin A1c levels for patients with diabetes. Secondary outcome measures are visit duration, patient satisfaction with the management process, health-related quality of life and the occurrence of any adverse event. Data will be captured longitudinally at baseline, 4 months, 8 months and 12 months, and will be analysed using multiple regression models. ETHICS AND DISSEMINATION: The study has been approved by the Singapore Health Services (SingHealth) Centralised Institutional Review Board (2017/2715). Findings of the study will be submitted for publication in peer-reviewed journals and presented at national and international conferences. TRIAL REGISTRATION NUMBER: NCT03274089; Pre-results.