bluuebunny/crossref_metadata_2025 huggingface dataset:
Associations Between Community Social Capital and Preservation of Functional Capacity in the Aftermath of a Major Disaster
Authors: Gero Krisztina , Hikichi Hiroyuki , Aida Jun , Kondo Katsunori , Kawachi Ichiro
Published: May 2020

The strength of social connections in the community (“social capital”) is hypothesized to be a crucial ingredient in disaster resilience. We examined whether community-level social capital is correlated with the ability to maintain functional capacity among older residents who experienced the 2011 Great East Japan Earthquake and Tsunami. The baseline of our cohort (mean age, 74 years) was established in 2010, 7 months before the disaster in Iwanuma, a Japanese city located 80 km from the epicenter. Disaster-related personal experiences (e.g., housing damage or relocation) were assessed through a follow-up survey (n = 3,594; follow-up rate, 82.1%) conducted in 2013, 2.5 years after the earthquake. Multiple membership multilevel models were used to evaluate the associations between functional capacity, measured by the Instrumental Activities of Daily Living scale, and 3 subscales of community-level social capital: social cohesion, social participation, and reciprocity. Community-level social participation was associated with a lower risk of functional decline after disaster exposure. The average level of social participation in the community also mitigated the adverse impact of housing damage on functional status, suggesting a buffering mechanism.
Hidden Imputations and the Kaplan-Meier Estimator
Authors: Cole Stephen R , Edwards Jessie K , Naimi Ashley I , Muñoz Alvaro
Published: May 2020

The Kaplan-Meier (KM) estimator of the survival function imputes event times for right-censored and left-truncated observations, but these imputations are hidden and therefore sometimes unrecognized by applied health scientists. Using a simple example data set and the redistribution algorithm, we illustrate how imputations are made by the KM estimator. We also discuss the assumptions necessary for valid analyses of survival data. Illustrating imputations hidden by the KM estimator helps to clarify these assumptions and therefore may reduce inappropriate inferences.
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

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

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

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

The 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

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

Little 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

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 (< 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

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

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 >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

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

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) <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

Primary 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

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 > 0.05). However, patients with the proportion of stromal PD1+ TILs >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>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 >18/HPF of stromal PD1+ TILs, patients with proportion = 20% and cell counts = 18/HPF, proportion >20% and cell counts >18/HPF, and proportion >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.
Using Data to Advance Educational Research, Policy, and Practice: Design, Content, and Research Potential of the Netherlands Cohort Study on Education
Authors: Haelermans Carla , Huijgen Timo , Jacobs Madelon , Levels Mark , van der Velden Rolf , van Vugt Lynn , van Wetten Sanne
Published: May 2020

In many countries, the quality of (large-scale quantitative) educational research is threatened by data challenges. In this article, we present an innovative data research project from the Netherlands in which many of the challenges that come forward in previous literature are addressed. The Netherlands Cohort Study on Education [in Dutch abbreviated as NCO (Nationaal Cohortonderzoek Onderwijs)] uses longitudinal register data on track placement of cohorts of pupils in primary and secondary education from Statistics Netherlands, which will be combined with school admin data on pupils’ performance and data from the major (inter)national surveys. NCO maps pupils’ pathways and performances through primary and secondary education and their trajectory into tertiary education. NCO so far covers more than 10 complete cohorts and is complemented with the newest data every year. These registers are made available at Statistics Netherlands. A major contribution of NCO is that data from school administrative systems and additional research projects are linked with administrative register data, thereby creating a unique data set that enriches not only research, but also policy and practice. This data brief elaborates on the possibilities of this database by exploring and following one of the cohorts over time.
Factors affecting the utilization of antenatal care services among women in Guinea: a population-based study
Authors: Shibre Gebretsadik , Zegeye Betregiorgis , Idriss-Wheeler Dina , Yaya Sanni
Published: May 2020

Introduction

Evidence suggests that a better understanding of determinants of antenatal care (ANC) utilization is crucial to reducing maternal and child deaths. Little is known about the utilization of ANC services in Guinea.

Objective

The aim of this study was to explore factors determining utilization of skilled ANC in Guinea.

Methods

This study focused on a sample of 7812 ever married women. Using multivariate logistic regression, factors associated with the utilization of ANC were identified. The output of the multivariate logistic regression was presented using adjusted odds ratio and the corresponding 95% confidence interval (CI).

Results

Several factors had significant association with utilization of skilled ANC service in Guinea: having decision-making power (2.21, 95% CI: 1.63, 3.00), employment status (1.86, 95% CI: 1.39, 2.48), media exposure (1.60, 95% CI: 1.26, 2.02), maternal education (2.68, 95% CI: 1.36, 5.28), husband/partner education status (1.66, 95% CI: 1.08, 2.55), household economic status (2.19, 95% CI: 1.40, 3.44), place of residence (0.29, 95% CI: 0.16, 0.50) and ethnicity (0.40, 95% CI: 0.23, 0.69).

Conclusions

These findings suggest a variety of socio-demographic and economic factors as well as media exposure are associated with women’s use of ANC. Policymakers should implement appropriate measures to address the existing variations and gaps in ANC services utilization among different subgroups of women in Guinea.
Genome-wide identification, characterization and expression analysis of lineage-specific genes within Hanseniaspora yeasts
Authors: Chen Kai , Tian Zhonghuan , Chen Ping , He Hua , Jiang Fatang , Long Chao-an
Published: May 2020

Lineage-specific genes (LSGs) are defined as genes with sequences that are not significantly similar to those in any other lineage. LSGs have been proposed, and sometimes shown, to have significant effects in the evolution of biological function. In this study, two sets of Hanseniaspora spp. LSGs were identified by comparing the sequences of the Kloeckera apiculata genome and of 80 other yeast genomes. This study identified 344 Hanseniaspora-specific genes (HSGs) and 109 genes (‘orphan genes’) specific to K. apiculata. Three thousand three hundred thirty-one K. apiculata genes that showed significant similarity to at least one sequence outside the Hanseniaspora were classified into evolutionarily conserved genes. We analyzed their sequence features, functional categories, gene origin, gene structure and gene expression. We also investigated the predicted cellular roles and Gene Ontology categories of the LSGs using functional inference. The patterns of the functions of LSGs do not deviate significantly from genome-wide average. The results showed that a few LSGs were formed by gene duplication, followed by rapid sequence divergence. Many of the HSGs and orphan genes exhibited altered expression in response to abiotic stress. Studying these LSGs might be helpful for understanding the molecular mechanism of yeast adaption.
Rapid prediction of earthquake ground shaking intensity using raw waveform data and a convolutional neural network
Authors: Jozinović Dario , Lomax Anthony , Štajduhar Ivan , Michelini Alberto
Published: May 2020

This study describes a deep convolutional neural network (CNN) based technique to predict intensity measurements (IMs) of earthquake ground shaking. The input data to the CNN model consists of multistation, 3C acceleration waveforms recorded during the 2016 Central Italy earthquake sequence for M ≥ 3.0 events. Using a 10 s window starting at the earthquake origin time, we find that the CNN is capable of accurately predicting IMs at stations far from the epicentre which have not yet recorded the maximum ground shaking. The CNN IM predictions do not require previous knowledge of the earthquake source (location and magnitude). Comparison between the CNN model predictions and those obtained with the Bindi et al. GMPE (which requires location and magnitude) shows that the CNN model features similar error variance but smaller bias. Although the technique is not strictly designed for earthquake early warning, we find that it can provide useful estimates of ground motions within 15–20 s after earthquake origin time depending on various setup elements (e.g. times for data transmission, computation, latencies). The technique has been tested on raw data without any initial data pre-selection in order to closely replicate real-time data streaming. When noise examples were included with the earthquake data the CNN was found to be stable, accurately predicting the ground shaking intensity corresponding to the noise amplitude.
Structure of the Ecuadorian forearc from the joint inversion of receiver functions and ambient noise surface waves
Authors: Koch Clinton D , Lynner Colton , Delph Jonathan , Beck Susan L , Meltzer Anne , Font Yvonne , Soto-Cordero Lillian , Hoskins Mariah , Stachnik Josh C , Ruiz Mario , Alvarado Alexandra , Agurto-Detzel Hans , Charvis Philippe , Regnier Marc , Rietbrock Andreas
Published: May 2020

The Ecuadorian forearc is a complex region of accreted terranes with a history of large megathrust earthquakes. Most recently, a Mw 7.8 megathrust earthquake ruptured the plate boundary offshore of Pedernales, Ecuador on 16 April 2016. Following this event, an international collaboration arranged by the Instituto Geofisico at the Escuela Politécnica Nacional mobilized a rapid deployment of 65 seismic instruments along the Ecuadorian forearc. We combine this new seismic data set with 14 permanent stations from the Ecuadorian national network to better understand how variations in crustal structure relate to regional seismic hazards along the margin. Here, we present receiver function adaptive common conversion point stacks and a shear velocity model derived from the joint inversion of receiver functions and surface wave dispersion data obtained through ambient noise cross-correlations for the upper 50 km of the forearc. Beneath the forearc crust, we observe an eastward dipping slow velocity anomaly we interpret as subducting oceanic crust, which shallows near the projected centre of the subducting Carnegie Ridge. We also observe a strong shallow positive conversion in the Ecuadorian forearc near the Borbon Basin indicating a major discontinuity at a depth of ∼7 km. This conversion is not ubiquitous and may be the top of the accreted terranes. We also observe significant north–south changes in shear wave velocity. The velocity changes indicate variations in the accreted terranes and may indicate an increased amount of hydration beneath the Manabí Basin. This change in structure also correlates geographically with the southern rupture limit of multiple high magnitude megathrust earthquakes. The earthquake record along the Ecuadorian trench shows that no event with a Mw >7.4 has ruptured south of ∼0.5°S in southern Ecuador or northern Peru. Our observations, along with previous studies, suggest that variations in the forearc crustal structure and subducting oceanic crust may influance the occurrence and spatial distribution of high magnitude seismicity in the region.
Genome editing strategies for fetal hemoglobin induction in beta-hemoglobinopathies
Authors: Demirci Selami , Leonard Alexis , Tisdale John F
Published: May 2020

Genome editing to correct a defective β-globin gene or induce fetal globin (HbF) for patients with beta-hemoglobinopathies has the potential to be a curative strategy available to all. HbF reactivation has long been an area of intense interest given the HbF inhibition of sickle hemoglobin (HbS) polymerization. Patients with HbS who also have high HbF tend to have less severe or even minimal clinical manifestations. Approaches to genetically engineer high HbF include de novo generation of naturally occurring hereditary persistence of fetal hemoglobin (HPFH) mutations, editing of transcriptional HbF repressors or their binding sites and/or regulating epigenetic intermediates controlling HbF expression. Recent preclinical and early clinical trial data show encouraging results; however, long-term follow-up is lacking, and the safety and efficacy concerns of genome editing remain.
Recent advances in Wilms’ tumor predisposition
Authors: Maciaszek Jamie L , Oak Ninad , Nichols Kim E
Published: May 2020

Wilms’ tumor (WT), the most common childhood kidney cancer, develops in association with an underlying germline predisposition in up to 15% of cases. Germline alterations affecting the WT1 gene and epigenetic alterations affecting the 11p15 locus are associated with a selective increase in WT risk. Nevertheless, WT also occurs in the context of more pleiotropic cancer predispositions, such as DICER1, Li-Fraumeni and Bloom syndrome, as well as Fanconi anemia. Recent germline genomic investigations have increased our understanding of the host genetic factors that influence WT risk, with sequencing of rare familial cases and large WT cohorts revealing an expanding array of predisposition genes and associated genetic conditions. Here, we describe evidence implicating WT1, the 11p15 locus, and the recently identified genes CTR9, REST and TRIM28 in WT predisposition. We discuss the clinical features, mode of inheritance and biological aspects of tumorigenesis, when known. Despite these described associations, many cases of familial WT remain unexplained. Continued investigations are needed to fully elucidate the landscape of germline genetic alterations in children with WT. Establishing a genetic diagnosis is imperative for WT families so that individuals harboring a predisposing germline variant can undergo surveillance, which should enable the early detection of tumors and use of less intensive treatments, thereby leading to improved overall outcomes.
Pharmacological Augmentation in Unipolar Depression: A Guide to the Guidelines
Authors: Taylor Rachael W , Marwood Lindsey , Oprea Emanuella , DeAngel Valeria , Mather Sarah , Valentini Beatrice , Zahn Roland , Young Allan H , Cleare Anthony J
Published: May 2020

Background

Pharmacological augmentation is a recommended strategy for patients with treatment-resistant depression. A range of guidelines provide advice on treatment selection, prescription, monitoring and discontinuation, but variation in the content and quality of guidelines may limit the provision of objective, evidence-based care. This is of importance given the side effect burden and poorer long-term outcomes associated with polypharmacy and treatment-resistant depression. This review provides a definitive overview of pharmacological augmentation recommendations by assessing the quality of guidelines for depression and comparing the recommendations made.

Methods

A systematic literature search identified current treatment guidelines for depression published in English. Guidelines were quality assessed using the Appraisal of Guidelines for Research and Evaluation II tool. Data relating to the prescription of pharmacological augmenters were extracted from those developed with sufficient rigor, and the included recommendations compared.

Results

Total of 1696 records were identified, 19 guidelines were assessed for quality, and 10 were included. Guidelines differed in their quality, the stage at which augmentation was recommended, the agents included, and the evidence base cited. Lithium and atypical antipsychotics were recommended by all 10, though the specific advice was not consistent. Of the 15 augmenters identified, no others were universally recommended.

Conclusions

This review provides a comprehensive overview of current pharmacological augmentation recommendations for major depression and will support clinicians in selecting appropriate treatment guidance. Although some variation can be accounted for by date of guideline publication, and limited evidence from clinical trials, there is a clear need for greater consistency across guidelines to ensure patients receive consistent evidence-based care.
Quasi-Affineness and the 1-Resolution Property
Authors: Deshmukh Neeraj , Hogadi Amit , Mathur Siddharth
Published: May 2020

We prove that, under mild hypothesis, every normal algebraic space that satisfies the $1$-resolution property is quasi-affine. More generally, we show that for algebraic stacks satisfying similar hypotheses, the 1-resolution property guarantees the existence of a finite flat cover by a quasi-affine scheme.
Chikungunya-Induced Arthritis in Reunion Island: A Long-Term Observational Follow-Up Study Showing Frequently Persistent Joint Symptoms, Some Cases of Persistent Chikungunya Immunoglobulin M Positivity, and No Anticyclic Citrullinated Peptide Seroconversion After 13 Years
Authors: Guillot Xavier , Ribera Anne , Gasque Philippe
Published: May 2020

Background

Reunion Island was struck by a massive Chikungunya outbreak in 2005–2006. Chikungunya infection is characterized by inflammatory joint symptoms, which may evolve into chronic arthritis.

Methods

In this long-term longitudinal observational monocentric study, after the 2005–2006 outbreak in Reunion Island, 159 patients were first referred to a rheumatologist for post-Chikungunya chronic musculoskeletal pain, 73 of them were diagnosed with classifiable Chikungunya-related chronic inflammatory rheumatic diseases (>3 month symptom duration from the initial viral infection). Thirty of these 73 patients were clinically evaluated by a second rheumatologist in 2018–2019. The main objective of this second examination was to estimate the proportion of patients with persistent Chikungunya-related inflammatory joint symptoms after 13 years.

Results

Inflammatory joint symptoms persisted in 17/30 patients after 13 years (therefore in at least 23.3% of the 73 patients initially diagnosed with Chikungunya-related inflammatory joint symptoms and 10.7% of the 159 patients referred for post-Chikungunya chronic musculoskeletal pain). In the symptom persistence subgroup, the prevalence of positive autoantibodies (antinuclear or ACPA) was significantly higher – without any seroconversion, Chikungunya IgG and IgM levels were higher, long-term IgM positivity and radiographic damage were more frequent. Overall, after 13 years, pain and fatigue levels remained significant, 5 patients were still treated by methotrexate, 3 by TNF-blockers, highlighting long-term Chikungunya-related patient burden.

Conclusions

Such a long-term persistence of Chikungunya-related chronic inflammatory rheumatic diseases had not been reported so far. Furthermore, the long-term Chikungunya IgM positivity we observed in some cases might corroborate the hypothesis of residual viral antigen-driven chronic arthritis.
Pivotal role of the carbohydrate recognition domain in self-interaction of CLEC4A to elicit the ITIM-mediated inhibitory function in murine conventional dendritic cellsin vitro
Authors: Nasu Junta , Uto Tomofumi , Fukaya Tomohiro , Takagi Hideaki , Fukui Takehito , Miyanaga Noriaki , Nishikawa Yotaro , Yamasaki Sho , Yamashita Yoshihiro , Sato Katsuaki
Published: May 2020

C-type lectin receptors (CLRs), pattern recognition receptors (PRRs) with a characteristic carbohydrate recognition domain (CRD) in the extracellular portion, mediate crucial cellular functions upon recognition of glycosylated pathogens and self-glycoproteins. CLEC4A is the only classical CLR that possesses an intracellular immunoreceptor tyrosine-based inhibitory motif (ITIM), which possibly transduces negative signals. However, how CLEC4A exerts cellular inhibition remains unclear. Here, we report that the self-interaction of CLEC4A through the CRD is required for the ITIM-mediated suppressive function in conventional dendritic cells (cDCs). Human type 2 cDCs (cDC2) and monocytes display a higher expression of CLEC4A than cDC1 and plasmacytoid DCs (pDCs) as well as B cells. The extracellular portion of CLEC4A specifically binds to a murine cDC cell line expressing CLEC4A, while its extracellular portion lacking the N-glycosylation site or the EPS motif within the CRD reduces their association. Furthermore, the deletion of the EPS motif within the CRD or ITIM in CLEC4A almost completely impairs its suppressive effect on the activation of the murine cDC cell line, whereas the absence of the N-glycosylation site within the CRD exhibits partial inhibition on their activation. On the other hand, antagonistic monoclonal antibody (mAb) to CLEC4A, which inhibits the self-interaction of CLEC4A and its downstream signaling in murine transfectants, enhances the activation of monocytes and monocyte-derived immature DCs upon stimulation with a Toll-like receptor (TLR) ligand. Thus, our findings suggest a pivotal role of the CRD in self-interaction of CLEC4A to elicit the ITIM-mediated inhibitory signal for the control of the function of cDCs.
Revision of EUCAST breakpoints: consequences for susceptibility of contemporary Danish mould isolates to isavuconazole and comparators
Authors: Jørgensen Karin Meinike , Guinea Jesus , Meletiadis Joseph , Hare Rasmus Krøger , Arendrup Maiken Cavling
Published: May 2020

Background

EUCAST recently revised the definition of the ‘I’ category from ‘intermediate’ to ‘susceptible, increased exposure’. Consequently, all current antifungal breakpoints have been reviewed and revised breakpoints (v 10.0) have been released.

Objectives

We investigated isavuconazole and comparator MICs (mg/L) against contemporary moulds and the consequences of the breakpoint revision for susceptibility classification.

Methods

Six hundred and ninety-six Aspergillus and 46 other moulds were included. EUCAST E.Def 10.1 azole resistance screening was performed for Aspergillus fumigatus and E.Def 9.3.1 testing of non-susceptible A. fumigatus and other moulds. Most non-wildtype/resistant isolates underwent cyp51A sequencing.

Results

Isavuconazole MIC50/MIC90s were ≤1/≤2 mg/L for Aspergillus flavus, A. fumigatus and Aspergillus nidulans versus 2/4 mg/L for Aspergillus niger and 2/16 mg/L for Aspergillus terreus. For the remaining moulds, MICs were highest for Fusarium (16 to >16 mg/L), lowest for dermatophytes (0.06–0.5 mg/L) and in between for Mucorales and others (1 to >16 mg/L). A very strong isavuconazole–voriconazole MIC correlation was found for A. fumigatus (Pearson r = 0.888) and itraconazole–posaconazole correlation for A. fumigatus (r = 0.905) and A. terreus (r = 0.848). For A. fumigatus, the revised breakpoints lowered isavuconazole resistance (22.6% to 7.7%, P < 0.0001) and increased voriconazole resistance (3.8% to 6.7%, P = 0.025), resulting in similar resistance rates across the four azoles (range: 6.7%–7.7%). For A. terreus, isavuconazole resistance remained unchanged (81.3%) and higher than itraconazole (43.8%, P = 0.004) and posaconazole (53.1%, P = 0.03) resistance. Azole cross-resistance was found in 24/24, 13/20 and 4/90 isolates, and Cyp51A alterations in 16/18, 1/7 and 2/4 sequenced isolates with isavuconazole MICs of >4, 4 and 2 mg/L, respectively.

Conclusions

Isavuconazole displays broad anti-mould activity. The revised breakpoints result in fewer misclassifications of wildtype isolates without compromising detection of resistant mutants.
PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records
Authors: Zheng Neil S , Feng QiPing , Kerchberger V Eric , Zhao Juan , Edwards Todd L , Cox Nancy J , Stein C Michael , Roden Dan M , Denny Joshua C , Wei Wei-Qi
Published: May 2020

Objective

Developing algorithms to extract phenotypes from electronic health records (EHRs) can be challenging and time-consuming. We developed PheMap, a high-throughput phenotyping approach that leverages multiple independent, online resources to streamline the phenotyping process within EHRs.

Materials and Methods

PheMap is a knowledge base of medical concepts with quantified relationships to phenotypes that have been extracted by natural language processing from publicly available resources. PheMap searches EHRs for each phenotype’s quantified concepts and uses them to calculate an individual’s probability of having this phenotype. We compared PheMap to clinician-validated phenotyping algorithms from the Electronic Medical Records and Genomics (eMERGE) network for type 2 diabetes mellitus (T2DM), dementia, and hypothyroidism using 84 821 individuals from Vanderbilt Univeresity Medical Center's BioVU DNA Biobank. We implemented PheMap-based phenotypes for genome-wide association studies (GWAS) for T2DM, dementia, and hypothyroidism, and phenome-wide association studies (PheWAS) for variants in FTO, HLA-DRB1, and TCF7L2.

Results

In this initial iteration, the PheMap knowledge base contains quantified concepts for 841 disease phenotypes. For T2DM, dementia, and hypothyroidism, the accuracy of the PheMap phenotypes were >97% using a 50% threshold and eMERGE case-control status as a reference standard. In the GWAS analyses, PheMap-derived phenotype probabilities replicated 43 of 51 previously reported disease-associated variants for the 3 phenotypes. For 9 of the 11 top associations, PheMap provided an equivalent or more significant P value than eMERGE-based phenotypes. The PheMap-based PheWAS showed comparable or better performance to a traditional phecode-based PheWAS. PheMap is publicly available online.

Conclusions

PheMap significantly streamlines the process of extracting research-quality phenotype information from EHRs, with comparable or better performance to current phenotyping approaches.