bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pilot Educational Intervention to Promote Safe Pesticide Use Practices Among Farmworkers in Nepal
Authors: Koju Pramesh , Shakya Prabin R , Shrestha Archana , Karmacharya Biraj M , Shrestha Sudip , Jaacks Lindsay M 
Published: May 2020

Abstract

Objectives
The misuse of pesticides among farmworkers in Nepal is commonplace. To address this, we implemented a pilot educational intervention (three modules delivered over 3 days and lasting approximately 3 h each) in Kavre District of Nepal. Modules included: (i) health and environmental effects of pesticides, (ii) use of personal protective equipment, and (iii) label literacy and behavioral factors that influence pesticide exposure. In addition, 10 posters with key messages from each of the modules were hung throughout communities.

Methods
Surveys were administered to cross-sectional convenience samples of farmworkers at baseline (n = 106) and 1 year later (n = 98). Practices relating to pesticides at baseline and endline were compared using multivariable logistic regression to adjust for differences in demographic and socioeconomic characteristics between the samples.

Results
Compared with the baseline sample, farmworkers in the endline sample were significantly more likely to report: getting information regarding the amount of pesticides to use from experts or pesticide labels (versus personal judgment); wearing gloves while mixing pesticides; wearing boots while working in the field; using personal hygiene practices after handling pesticides such as bathing or washing hands and feet; changing clothes after handling pesticides; checking the wind direction before spraying; and delaying entry for a longer period of time after spraying.

Conclusions
These results suggest that a simple educational intervention can improve pesticide handling practices among farmworkers in Nepal. Future research should explore the impact of such interventions on pesticide exposure levels and health outcomes, and the potential to scale up these programs nationally.
DeepTE: a computational method for de novo classification of transposons with convolutional neural network
Authors: Yan Haidong , Bombarely Aureliano , Li Song 
Published: May 2020

Abstract

Motivation
Transposable elements (TEs) classification is an essential step to decode their roles in genome evolution. With a large number of genomes from non-model species becoming available, accurate and efficient TE classification has emerged as a new challenge in genomic sequence analysis.

Results
We developed a novel tool, DeepTE, which classifies unknown TEs using convolutional neural networks (CNNs). DeepTE transferred sequences into input vectors based on k-mer counts. A tree structured classification process was used where eight models were trained to classify TEs into super families and orders. DeepTE also detected domains inside TEs to correct false classification. An additional model was trained to distinguish between non-TEs and TEs in plants. Given unclassified TEs of different species, DeepTE can classify TEs into seven orders, which include 15, 24 and 16 super families in plants, metazoans and fungi, respectively. In several benchmarking tests, DeepTE outperformed other existing tools for TE classification. In conclusion, DeepTE successfully leverages CNN for TE classification, and can be used to precisely classify TEs in newly sequenced eukaryotic genomes.

Availability and implementation
DeepTE is accessible at https://github.com/LiLabAtVT/DeepTE.

Supplementary information
Supplementary data are available at Bioinformatics online.
Efficient toolkit implementing best practices for principal component analysis of population genetic data
Authors: Privé Florian , Luu Keurcien , Blum Michael G B , McGrath John J , Vilhjálmsson Bjarni J 
Published: May 2020

ABSTRACT

Motivation
Principal component analysis (PCA) of genetic data is routinely used to infer ancestry and control for population structure in various genetic analyses. However, conducting PCA analyses can be complicated and has several potential pitfalls. These pitfalls include (i) capturing linkage disequilibrium (LD) structure instead of population structure, (ii) projected PCs that suffer from shrinkage bias, (iii) detecting sample outliers and (iv) uneven population sizes. In this work, we explore these potential issues when using PCA, and present efficient solutions to these. Following applications to the UK Biobank and the 1000 Genomes project datasets, we make recommendations for best practices and provide efficient and user-friendly implementations of the proposed solutions in R packages bigsnpr and bigutilsr.

Results
For example, we find that PC19–PC40 in the UK Biobank capture complex LD structure rather than population structure. Using our automatic algorithm for removing long-range LD regions, we recover 16 PCs that capture population structure only. Therefore, we recommend using only 16–18 PCs from the UK Biobank to account for population structure confounding. We also show how to use PCA to restrict analyses to individuals of homogeneous ancestry. Finally, when projecting individual genotypes onto the PCA computed from the 1000 Genomes project data, we find a shrinkage bias that becomes large for PC5 and beyond. We then demonstrate how to obtain unbiased projections efficiently using bigsnpr. Overall, we believe this work would be of interest for anyone using PCA in their analyses of genetic data, as well as for other omics data.

Availability and implementation
R packages bigsnpr and bigutilsr can be installed from either CRAN or GitHub (see https://github.com/privefl/bigsnpr). A tutorial on the steps to perform PCA on 1000G data is available at https://privefl.github.io/bigsnpr/articles/bedpca.html. All code used for this paper is available at https://github.com/privefl/paper4-bedpca/tree/master/code.

Supplementary information
Supplementary data are available at Bioinformatics online.
Emotion Regulation Modulates Dietary Decision-Making via Activity in the Prefrontal–Striatal Valuation System
Authors: Morawetz Carmen , Steyrl David , Berboth Stella , Heekeren Hauke R , Bode Stefan 
Published: May 2020

AbstractThe consumption of indulgent, carbohydrate- and fat-rich foods is often used as a strategy to cope with negative affect because they provide immediate self-reward. Such dietary choices, however, can severely affect people’s health. One countermeasure could be to improve one’s emotion regulation ability. We used functional magnetic resonance imaging to examine the neural activity underlying the downregulation of incidental emotions and its effect on subsequent food choices. We investigated whether emotion regulation leads to healthier food choices and how emotion regulation interacts with the brain’s valuation and decision-making circuitry. We found that 1) the downregulation of incidental negative emotions was associated with a subsequent selective increase in decisions for tasty but also for healthy foods, 2) food preferences were predicted by palatability but also by the current emotional state, and 3) emotion regulation modulated decision-related activation in the ventromedial prefrontal cortex and ventral striatum. These results indicate that emotional states are indeed important for food choice and that the process of emotion regulation might boost the subsequent processing of health attributes, possibly via neural reward circuits. In consequence, our findings suggest that increasing emotion regulation ability could effectively modulate food choices by stimulating an incidental upvaluation of health attributes.
Social Media and the New World of Scientific Communication During the COVID-19 Pandemic
Authors: Pollett Simon , Rivers Caitlin 
Published: May 2020

Abstract
The human and social toll of the coronavirus disease 2019 (COVID-19) pandemic has already spurred several major public health “lessons learned,” and the theme of effective and responsible scientific communication is among them. We propose that Twitter has played a fundamental—but often precarious—role in permitting real-time global communication between scientists during the COVID-19 epidemic, on a scale not seen before. Here, we discuss 3 key facets to Twitter-enabled scientific exchange during public health emergencies, including some major drawbacks. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID-19 outbreak, as seen through the lens of a Twitter feed.
Clinical Features and Outcomes of Patients With Human Immunodeficiency Virus With COVID-19
Authors: Gervasoni Cristina , Meraviglia Paola , Riva Agostino , Giacomelli Andrea , Oreni Letizia , Minisci Davide , Atzori Chiara , Ridolfo Annalisa , Cattaneo Dario 
Published: May 2020

AbstractLittle is known about the clinical outcomes of patients with human immunodeficiency virus infected with SARS-CoV-2. We describe 47 patients referred to our hospital between 21 February and 16 April 2020 with proven/probable COVID-19, 45 (96%) of whom fully recovered and 2 who died.
Xpert Ultra Assay on Stool to Diagnose Pulmonary Tuberculosis in Children
Authors: Kabir Senjuti , Rahman S M Mazidur , Ahmed Shakil , Islam Md Shamiul , Banu Rupali Sisir , Shewade Hemant Deepak , Thekkur Pruthu , Anwar Sayeeda , Banu Nazneen Akhter , Nasrin Rumana , Uddin Mohammad Khaja Mafij , Choudhury Sabrina , Ahmed Shahriar , Paul Kishor Kumar , Khatun Razia , Chisti Mohammod Jobayer , Banu Sayera 
Published: May 2020

Abstract

Background
The World Health Organization recommends the Xpert MTB/RIF Ultra assay for diagnosing pulmonary tuberculosis (PTB) in children. Though stool is a potential alternative to respiratory specimens among children, the diagnostic performance of Xpert Ultra on stool is unknown. Thus, we assessed the diagnostic performance of Xpert Ultra on stool to diagnose PTB in children.

Methods
We conducted a cross-sectional study among consecutively recruited children (&lt; 15 years of age) with presumptive PTB admitted in 4 tertiary care hospitals in Dhaka, Bangladesh, between January 2018 and April 2019. Single induced sputum and stool specimens were subjected to culture, Xpert, and Xpert Ultra. We considered children as bacteriologically confirmed on induced sputum if any test performed on induced sputum was positive for Mycobacterium tuberculosis and bacteriologically confirmed if M. tuberculosis was detected on either induced sputum or stool.

Results
Of 447 children, 29 (6.5%) were bacteriologically confirmed on induced sputum and 72 (16.1%) were bacteriologically confirmed. With “bacteriologically confirmed on induced sputum” as a reference, the sensitivity and specificity of Xpert Ultra on stool were 58.6% and 88.1%, respectively. Xpert on stool had sensitivity and specificity of 37.9% and 100.0%, respectively. Among bacteriologically confirmed children, Xpert Ultra on stool was positive in 60 (83.3%), of whom 48 (80.0%) had “trace call.”

Conclusions
In children, Xpert Ultra on stool has better sensitivity but lesser specificity than Xpert. A high proportion of Xpert Ultra assays positive on stool had trace call. Future longitudinal studies on clinical evolution are required to provide insight on the management of children with trace call.
Impact of Community Treatment With Ivermectin for the Control of Scabies on the Prevalence of Antibodies to Strongyloides stercoralis in Children
Authors: Marks Michael , Gwyn Sarah , Toloka Hilary , Kositz Christian , Asugeni James , Asugeni Rowena , Diau Jason , Kaldor John M , Romani Lucia , Redman-MacLaren Michelle , MacLaren David , Solomon Anthony W , Mabey David C W , Steer Andrew C , Martin Diana 
Published: May 2020

Abstract
The prevalence of antibodies to Strongyloides stercoralis was measured in 0–12-year-olds using a bead-based immunoassay before and after ivermectin mass drug administration (MDA) for scabies in the Solomon Islands. Seroprevalence was 9.3% before and 5.1% after MDA (P = .019), demonstrating collateral benefits of ivermectin MDA in this setting.
Vascular access cannulation and haemostasis: a national observational study of French practices
Authors: Sallée Marion , Mercadal Lucile , Jean Guillaume , Guery Bruno , Borniche Didier , Charrel Jan-Marc , Hannedouche Thierry , Roy Frank Le , Brunet Philippe 
Published: May 2020

Abstract

Background
We report the results of an observational study of arteriovenous fistula (AVF) cannulation and haemostasis practices in France.

Methods
The study (sponsored by Brothier Pharmaceutical Inc.) was conducted in 150 dialysis units. Data obtained from 150 supervisory nurses, 1538 nurses and 3588 patients with an AVF were analysed.

Results
The nurses reported using rope-ladder, area or buttonhole cannulation techniques in 68, 26 and 6% of cases, respectively. Metal needles were used most frequently (64%), with mainly a diameter of 15 G or 16 G. The needle was introduced with the bevel up in 56% of cases. Compression applied using dressings (in particular, pure calcium alginate dressings) was the method of choice for haemostasis of the puncture sites and was assessed as being strong by most of the nurses and very strong in cases of prolonged bleeding. Most (82%) of the patients reported the use of local anaesthetic before cannulation and 23% reported an allergic skin reaction to the anaesthetic. Bleeding of the puncture sites lasted for &gt;10 min for 48% of the patients and it reappeared between two sessions for 29% of the patients. Whereas the nurses appeared to have a good understanding of AVF, more than half of the patients did not know how to care for it, with 55% requiring more information.

Conclusions
This study underlines the lack of national consensus concerning AVF cannulation practices. It suggests that haemostasis methods of the puncture sites can be improved and it highlights the need to improve patient knowledge.
The PrEscription of intraDialytic exercise to improve quAlity of Life in patients with chronic kidney disease trial: study design and baseline data for a multicentre randomized controlled trial
Authors: Greenwood Sharlene A , Koufaki Pelagia , Macdonald Jamie , Bhandari Sunil , Burton James , Dasgupta Indranil , Farrington Kenneth , Ford Ian , Kalra Philip A , Kean Sharon , Kumwenda Mick , Macdougall Iain C , Messow Claudia-Martina , Mitra Sandip , Reid Chante , Smith Alice C , Taal Maarten W , Thomson Peter C , Wheeler David C , White Claire , Yaqoob Magdi , Mercer Thomas H 
Published: May 2020

Abstract

Background
Exercise interventions designed to improve physical function and reduce sedentary behaviour in haemodialysis (HD) patients might improve exercise capacity, reduce fatigue and lead to improved quality of life (QOL). The PrEscription of intraDialytic exercise to improve quAlity of Life study aimed to evaluate the effectiveness of a 6-month intradialytic exercise programme on QOL and physical function, compared with usual care for patients on HD in the UK.

Methods
We conducted a prospective, pragmatic multicentre randomized controlled trial in 335 HD patients and randomly (1:1) assigned them to either (i) intradialytic exercise training plus usual care maintenance HD or (ii) usual care maintenance HD. The primary outcome of the study was the change in Kidney Disease Quality of Life Short Form (KDQOL-SF 1.3) Physical Component Score between baseline and 6 months. Additional secondary outcomes included changes in peak aerobic capacity, physical fitness, habitual physical activity levels and falls (International Physical Activity Questionnaire, Duke’s Activity Status Index and Tinetti Falls Efficacy Scale), QOL and symptom burden assessments (EQ5D), arterial stiffness (pulse wave velocity), anthropometric measures, resting blood pressure, clinical chemistry, safety and harms associated with the intervention, hospitalizations and cost-effectiveness. A nested qualitative study investigated the experience and acceptability of the intervention for both participants and members of the renal health care team.

Results
At baseline assessment, 62.4% of the randomized cohort were male, the median age was 59.3 years and 50.4% were white. Prior cerebrovascular events and myocardial infarction were present in 8 and 12% of the cohort, respectively, 77.9% of patients had hypertension and 39.4% had diabetes. Baseline clinical characteristics and laboratory data for the randomized cohort were generally concordant with data from the UK Renal Registry.

Conclusion
The results from this study will address a significant knowledge gap in the prescription of exercise interventions for patients receiving maintenance HD therapy and inform the development of intradialytic exercise programmes both nationally and internationally.

Trial Registration
ISRCTN N83508514; registered on 17 December 2014.
Coronavirus disease 2019: acute Fanconi syndrome precedes acute kidney injury
Authors: Kormann Raphaël , Jacquot Audrey , Alla Asma , Corbel Alice , Koszutski Matthieu , Voirin Paul , Garcia Parrilla Matthieu , Bevilacqua Sybille , Schvoerer Evelyne , Gueant Jean-Louis , Namour Farès , Levy Bruno , Frimat Luc , Oussalah Abderrahim 
Published: May 2020

Abstract

Background
Recent data have shown that severe acute respiratory syndrome coronavirus 2 can infect renal proximal tubular cells via Angiotensin Converting Enzyme 2 (ACE2) . Our objective was to determine whether Fanconi syndrome is a frequent clinical feature in coronavirus disease 2019 (COVID-19) patients.

Methods
A retrospective cohort of 42 laboratory-confirmed COVID-19 patients without history of kidney disease hospitalized in University Hospital of Nancy was investigated. Patients were admitted to the intensive care unit (ICU) (n = 28) or the Medical department (n = 14) and were screened at least once for four markers of proximal tubulopathy.

Results
The mean (standard deviation) follow-up was 19.7 (±12.2) days. Of the patients, 75% (30/40) showed at least two proximal tubule abnormalities (incomplete Fanconi syndrome). The main disorders were proteinuria (88%, n = 35), renal phosphate leak defined by renal phosphate threshold/glomerular filtration rate (TmPi/GFR) &lt;0.77 (55%, n = 22), hyperuricosuria (43%, n = 17) and normoglycaemic glycosuria (30%, n = 12). At the time of the first renal evaluation, ICU patients presented more frequent (96 versus 62%, P = 0.0095) and more severe (844 ± 343 versus 350 ± 221 mg/g, P = 0.0001) proteinuria, and a trend for an increased number of proximal tubule abnormalities (P = 0.038). During follow-up, they presented a lower nadir of serum phosphate [median (interquartile range) 0.68 (0.43–0.76) versus 0.77 (0.66–1.07) mmol/L, P = 0.044] and Acute kidney Injury (AKI) during the hospitalization (P = 0.045). Fanconi syndrome preceded severe AKI KDIGO Stages 2 and 3 in 88% (7/8) of patients. Proximal tubular abnormalities (such as proteinuria, TmPi/GFR and glycosuria in five, two and two patients, respectively) were not detected anymore in recovering patients before hospital discharge.

Conclusion
Incomplete Fanconi syndrome is highly frequent in COVID-19 patients and precedes AKI or disappears during the recovery phase.
Challenges in primary focal segmental glomerulosclerosis diagnosis: from the diagnostic algorithm to novel biomarkers
Authors: Jacobs-Cachá Conxita , Vergara Ander , García-Carro Clara , Agraz Irene , Toapanta-Gaibor Nestor , Ariceta Gema , Moreso Francesc , Serón Daniel , López-Hellín Joan , Soler Maria José 
Published: May 2020

AbstractPrimary or idiopathic focal segmental glomerulosclerosis (FSGS) is a kidney entity that involves the podocytes, leading to heavy proteinuria and in many cases progresses to end-stage renal disease. Idiopathic FSGS has a bad prognosis, as it involves young individuals who, in a considerably high proportion (∼15%), are resistant to corticosteroids and other immunosuppressive treatments as well. Moreover, the disease recurs in 30–50% of patients after kidney transplantation, leading to graft function impairment. It is suspected that this relapsing disease is caused by a circulating factor(s) that would permeabilize the glomerular filtration barrier. However, the exact pathologic mechanism is an unsettled issue. Besides its poor outcome, a major concern of primary FSGS is the complexity to confirm the diagnosis, as it can be confused with other variants or secondary forms of FSGS and also with other glomerular diseases, such as minimal change disease. New efforts to optimize the diagnostic approach are arising to improve knowledge in well-defined primary FSGS cohorts of patients. Follow-up of properly classified primary FSGS patients will allow risk stratification for predicting the response to different treatments. In this review we will focus on the diagnostic algorithm used in idiopathic FSGS both in native kidneys and in disease recurrence after kidney transplantation. We will emphasize those potential confusing factors as well as their detection and prevention. In addition, we will also provide an overview of ongoing studies that recruit large cohorts of glomerulopathy patients (Nephrotic Syndrome Study Network and Cure Glomerulonephropathy, among others) and the experimental studies performed to find novel reliable biomarkers to detect primary FSGS.
The integration of proportion and cell counts of stromal, not intratumoral, PD-1+ tumor-infiltrating lymphocytes has prognostic significance in esophageal squamous cell carcinoma
Authors: Song Qingkun , Shi Feng , Xiao Shuo , Li Yuchen , Zhao Yanjie , Chang Hong 
Published: May 2020

Summary
The present study aimed to investigate the prognostic effect of intratumoral and stromal exhausted tumor-infiltrating lymphocytes (TILs) on operable esophageal cancer patients. We performed a retrospective cohort study by consecutively recruiting 142 patients with esophageal cancer. The proportion and cell counts of intratumoral and stromal PD-1+ TILs in tumor microenvironment were independently evaluated by two pathologists. Neither proportion nor cell counts of intratumoral PD-1+ TILs was associated with prognosis (p &gt; 0.05). However, patients with the proportion of stromal PD1+ TILs &gt;20% had the median overall survival (OS) at 19 months, significantly longer than those with the proportion = 20%. The adjusted hazard ratio (HR) was 1.49 (95%CI 0.82, 2.69). Patients with cell counts of stromal PD1+ TILs = 18/ high-power field (HPF) had the median disease-free survival (DFS) at 10 months. However, patients with cell counts&gt;18/HPF had the median DFS at 48 months (p = 0.037), and the adjusted HR was 0.59 (95%CI 0.35, 1.01). Compared with patients with proportion = 20% and cell counts &gt;18/HPF of stromal PD1+ TILs, patients with proportion = 20% and cell counts = 18/HPF, proportion &gt;20% and cell counts &gt;18/HPF, and proportion &gt;20% and cell counts = 18/HPF, had the adjusted HRs increased to 3.73, 3.36 and 3.99 for DFS (p for trend being 0.030) and the adjusted HRs increased to 2.95, 3.64 and 3.82 (p for trend being 0.015) for OS, respectively. The integration of proportion and cell counts of PD-1+ stromal TILs has a significant association with the relapse and overall survival of esophageal cancer patients. Further prospective studies are warranted.