bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk Estimates of Agricultural Injuries and Fatalities in Central India
Authors: Khadatkar Abhijit , Kot Lokendra Singh 
Published: July 2021

Abstract
The purpose of the study was to describe the nature, magnitude, causes, and economic impact, and also to evaluate risk estimates of agricultural incidents occurring during 2012–2013 in Madhya Pradesh, India. The study was carried out in 360 villages in 9 districts of Madhya Pradesh namely Datia, Shivpuri, Balaghat, Barwani, Indore, Jhabua, Narshigpur, Satna, and Bhopal. A total of 92 793 agricultural workers participated in a survey of agricultural incidents. Of 21 agricultural incidents, 14% were fatal and 86% non-fatal in nature. The agricultural incident rates were 0.23/1000 agricultural worker per year and 0.2/1000 agricultural machines per year. The annual monetary loss due to deaths in agricultural incidents in Madhya Pradesh was estimated to be Rs. 16 935.4 lakhs. The economic loss due to agricultural incidents is more severe that resulted in significant loss to the workers due to absence from work. Hence, it is important to map down the cause and taking preventive measures to reduce the losses.
Contrasting processing tomato cultivars unlink yield and pollen viability under heat stress
Authors: Miller Golan , Beery Avital , Singh Prashant Kumar , Wang Fengde , Zelingher Rotem , Motenko Etel , Lieberman-Lazarovich Michal 
Published: July 2021

AbstractClimate change is causing temperature increment in crop production areas worldwide, generating conditions of heat stress that negatively affect crop productivity. Tomato (Solanum lycopersicum), a major vegetable crop, is highly susceptible to conditions of heat stress. When tomato plants are exposed to ambient day/night temperatures that exceed 32 °C/20 °C, respectively, during the reproductive phase, fruit set and fruit weight are reduced, leading to a significant decrease in yield. Processing tomato cultivars are cultivated in open fields, where environmental conditions are not controlled; therefore, plants are exposed to multiple abiotic stresses, including heat stress. Nonetheless, information on stress response in processing tomatoes is very limited. Understanding the physiological response of modern processing tomato cultivars to heat stress may facilitate the development of thermotolerant cultivars. Here, we compared two tomato processing cultivars, H4107 and H9780, that we found to be constantly differing in yield performance. Using field and temperature-controlled greenhouse experiments, we show that the observed difference in yield is attributed to the occurrence of heat stress conditions. In addition, fruit set and seed production were significantly higher in the thermotolerant cultivar H4107, compared with H9780. Despite the general acceptance of pollen viability as a measure of thermotolerance, there was no difference in the percentage of viable pollen between H4107 and H9780 under either of the conditions tested. In addition to observations of similar pollen germination and bud abscission rates, our results suggest that processing tomato cultivars may present a particular case, in which pollen performance is not determining reproductive thermotolerance. Our results also demonstrate the value of combining controlled and uncontrolled experimental settings, in order to validate and identify heat stress-related responses, thus facilitating the development of thermotolerant processing tomato cultivars.
DeepFeature: feature selection in nonimage data using convolutional neural network
Authors: Sharma Alok , Lysenko Artem , Boroevich Keith A , Vans Edwin , Tsunoda Tatsuhiko 
Published: July 2021

AbstractArtificial intelligence methods offer exciting new capabilities for the discovery of biological mechanisms from raw data because they are able to detect vastly more complex patterns of association that cannot be captured by classical statistical tests. Among these methods, deep neural networks are currently among the most advanced approaches and, in particular, convolutional neural networks (CNNs) have been shown to perform excellently for a variety of difficult tasks. Despite that applications of this type of networks to high-dimensional omics data and, most importantly, meaningful interpretation of the results returned from such models in a biomedical context remains an open problem. Here we present, an approach applying a CNN to nonimage data for feature selection. Our pipeline, DeepFeature, can both successfully transform omics data into a form that is optimal for fitting a CNN model and can also return sets of the most important genes used internally for computing predictions. Within the framework, the Snowfall compression algorithm is introduced to enable more elements in the fixed pixel framework, and region accumulation and element decoder is developed to find elements or genes from the class activation maps. In comparative tests for cancer type prediction task, DeepFeature simultaneously achieved superior predictive performance and better ability to discover key pathways and biological processes meaningful for this context. Capabilities offered by the proposed framework can enable the effective use of powerful deep learning methods to facilitate the discovery of causal mechanisms in high-dimensional biomedical data.
Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data
Authors: Popitsch Niko , Preuner Sandra , Lion Thomas 
Published: July 2021

Abstract

Motivation
Clinical decision making is increasingly guided by accurate and recurrent determination of presence and frequency of (somatic) variants and their haplotype through panel sequencing of disease-relevant genomic regions. Haplotype calling (phasing), however, is difficult and error prone unless variants are located on the same read which limits the ability of short-read sequencing to detect, e.g. co-occurrence of drug-resistance variants. Long-read panel sequencing enables direct phasing of amplicon variants besides having multiple other benefits, however, high error rates of current technologies prevented their applicability in the past.

Results
We have developed Nanopanel2, a variant caller for Nanopore panel sequencing data. Nanopanel2 works directly on base-called FAST5 files and uses allele probability distributions and several other filters to robustly separate true from false positive (FP) calls. It effectively calls SNVs and INDELs with variant allele frequencies as low as 1% and 5%, respectively, and produces only few low-frequency false-positive calls (∼1 FP call with VAF&lt;5% per kb amplicon). Haplotype compositions are then determined by direct phasing. Nanopanel2 is the first somatic variant caller for Nanopore data, enabling accurate, fast (turnaround &lt;48 h) and cheap (sequencing costs ∼10$/sample) diagnostic workflows.

Availabilityand implementation
The data for this study have been deposited at zenodo.org under DOIs accession numbers 4110691 and 4110698. Nanopanel2 is open source and available at https://github.com/popitsch/nanopanel2.

Supplementary information
Supplementary data are available at Bioinformatics online.
Coaching to enhance qualified surgeons’ non-technical skills: a systematic review
Authors: Granchi N , Ting Y Y , Foley K P , Reid J L , Vreugdenburg T D , Trochsler M I , Bruening M H , Maddern G J 
Published: July 2021

Abstract

Introduction
The lack of an effective continuing professional development programme for qualified surgeons, specifically one that enhances non-technical skills (NTS), is an issue receiving increased attention. Peer-based coaching, used in multiple professions, is a proposed method to deliver this. The aim of this study was to undertake a systematic review of the literature to summarize the quantity and quality of studies involving surgical coaching of NTS in qualified surgeons.

Methods
A systematic search of the literature was performed through MEDLINE, EMBASE, Cochrane Collaboration and PsychINFO. Studies were selected based on predefined inclusion and exclusion criteria. Data for the included studies was independently extracted by two reviewers and the quality of the studies evaluated using the Medical Education and Research Study Quality Instrument (MERSQI).

Results
Some 4319 articles were screened from which 19 met the inclusion criteria. Ten studies involved coaching of individual surgeons and nine looked at group coaching of surgeons as part of a team. Group coaching studies used non-surgeons as coaches, included objective assessment of NTS, and were of a higher quality (average MERSQI 13.58). Individual coaching studies focused on learner perception, used experienced surgeons as coaches and were of a lower quality (average MERSQI 11.58). Individual coaching did not show an objective improvement in NTS for qualified surgeons in any study.

Conclusion
Surgical coaching of qualified surgeons’ NTS in a group setting was found to be effective. Coaching of individual surgeons revealed an overall positive learner perception but did not show an objective improvement in NTS for qualified surgeons.
The UK ‘geography of discontent’: narratives, Brexit and inter-regional ‘levelling up’
Authors: McCann Philip , Ortega-Argilés Raquel 
Published: July 2021

Abstract
This paper explains the background to the notion of the ‘geography of discontent’ in the context of UK interregional inequalities and political shocks. The paper then examines how the geography of discontent has bound conflicting political and economic narratives together in ways, which makes the correcting for these regional imbalances all the more difficult, and results in ambiguity and a lack of clarity regarding the nature and form which Levelling Up processes should take.
Correlations, agreement and utility of frailty instruments in prevalent haemodialysis patients: baseline cohort data from the FITNESS study
Authors: Anderson Benjamin M , Qasim Muhammad , Correa Gonzalo , Evison Felicity , Gallier Suzy , Ferro Charles J , Jackson Thomas A , Sharif Adnan 
Published: July 2021

ABSTRACT

Background
Frailty is associated with poor outcomes for haemodialysis patients, but its prevalence is uncertain due to heterogeneous definitions. The aim of this study was to compare and contrast prevalence and features of commonly used frailty instruments in a British haemodialysis cohort.

Methods
The FITNESS (Frailty Intervention Trial iN End-Stage patientS on haemodialysis) study recruited adults aged ≥18 years after informed consent, with ≥3 months haemodialysis exposure and no hospital admission within 4 weeks unless for dialysis access. Study participants were clinically phenotyped with frailty instruments including the Frailty Index (FI), Frailty Phenotype (FP), Edmonton Frailty Scale (EFS) and Clinical Frailty Scale (CFS), alongside comprehensive baseline data collection of biochemical, clinical and social characteristics.

Results
Between 12 January 2018 and 18 April 2019, 485 haemodialysis patients were recruited. Baseline demographics were median age 63 years, male sex 58.6% and non-White ethnicity 42.1%. Prevalence of frailty was high; 41.9% of participants were frail by FP, 63.3% by FI, 50.2% by EFS and 53.8% by CFS. Female gender was associated with increased frailty, with no independent association observed with age or ethnicity. While correlation between frailty instruments was strong, intraclass correlation coefficient for frailty agreement was 0.628 (95% confidence interval 0.585–0.669) and only weak agreement between instrument pairs.

Conclusion
Frailty is highly prevalent among haemodialysis patients regardless of criteria used. However, our data suggest caution when interpreting heterogenous definitions of frailty for haemodialysis patients as they are not interchangeable. Consensus agreement on the optimal frailty definition for haemodialysis patients must balance ease of use with predictive ability for adverse outcomes before determining clinical application.
User compliance and remediation success after IoT malware notifications
Authors: Rodríguez Elsa , Verstegen Susanne , Noroozian Arman , Inoue Daisuke , Kasama Takahiro , van Eeten Michel , Gañán Carlos H 
Published: July 2021

Abstract
Internet Service Providers (ISPs) are getting involved in remediating Internet of Things (IoT) infections of end users. This endeavor runs into serious usability problems. Given that it is usually unknown what kind of device is infected, they can only provide users with very generic cleanup advice, trying to cover all device types and remediation paths. Does this advice work? To what extent do users comply with the instructions? And does more compliance lead to higher cleanup rates? This study is the first to shed light on these questions. In partnership with an ISP, we designed a randomized control experiment followed up by a user survey. We randomly assigned 177 consumers affected by malware from the Mirai family to three different groups: (i) notified via a walled garden (quarantine network), (ii) notified via email, and (iii) no immediate notification, i.e. a control group. The notification asks the user to take five steps to remediate the infection. We conducted a phone survey with 95 of these customers based on communication–human information processing theory. We model the impact of the treatment, comprehension, and motivation on the compliance rate of each customer, while controlling for differences in demographics and infected device types. We also estimate the extent to which compliance leads to successful cleanup of the infected IoT devices. While only 24% of notified users perform all five remediation steps, 92% of notified users perform at least one action. Compliance increases the probability of successful cleanup by 32%, while the presence of competing malware reduces it by 54%. We provide an empirical basis to shape ISP best practices in the fight against IoT malware.
Primary Hypogammaglobulinaemia with Inflammatory Bowel Disease-Like Features: An ECCO CONFER Multicentre Case Series
Authors: Albshesh Ahmad , Eder Piotr , Ribaldone Davide Giuseppe , Oldenburg Bas , de Boer Nanne K , Mantzaris Gerassimos J , Savarino Edoardo Vincenzo , Dragoni Gabriele , Weisshof Roni , Truyens Marie , Festa Stefano , Maillard Michel H , Capirchio Lena , Filip Rafal , Theodoraki Eirini , Kopylov Uri 
Published: July 2021

Abstract

Background
Hypogammaglobulinaemia is a disorder characterized by low serum immunoglobulin levels and a high prevalence of gastrointestinal manifestations. In some cases, clinical and endoscopic features are indistinguishable from those of inflammatory bowel disease [IBD].

Methods
This was a multicentre case series performed as a part of the European Crohn’s and Colitis Organisation [ECCO] Collaborative Network of Exceptionally Rare case reports [CONFER] project.

Results
This report includes 27 patients with primary hypogammaglobulinaemia and IBD-like features: 20 males and seven females, median age 45.6 years (interquartile range [IQR] 35.2–59). Crohn’s disease-like features were noted in 23 patients, and four patients had ulcerative colitis-like features. The diagnosis of hypogammaglobulinaemia preceded a diagnosis of IBD-like features in 20 patients [median of 7 years prior, IQR 2.6–20.6 years], and followed the appearance of IBD-like features in seven cases [median of 1 year after, IQR 0.45–5.6 years]. Hypogammaglobulinaemia aetiologies were common variable immunodeficiency [66.6%], agammaglobulinaemia [7.4%], selective IgA-deficiency [11.1%], Good’s syndrome [7.4%], IgG subclass deficiency with IgA deficiency [3.7%] and hyper-IgM [3.7%]. In addition to antibiotics and intravenous immunoglobulin [IVIG] for hypogammaglobulinaemia, 12 patients received IBD-related treatment including 5-aminosalicylate agents [two patients], corticosteroids [one patient], thiopurines [three patients], anti-tumour necrosis factor [four patients] and vedolizumab [two patients]. By the end of the follow-up (44.5 months [IQR 18–81]), 21/27 [77%] patients were in clinical remission.

Conclusion
This case series describes IBD-like features in patients with hypogammaglobulinaemia. The diagnosis of IBD-like features mainly occurred after that of hypogammaglobulinaemia, with successful recovery in the majority of cases after appropriate treatment.
Women leaders in Cardiology. Contemporary profile of the WHO European region
Authors: Borrelli Nunzia , Brida Margarita , Cader Aaysha , Sabatino Jolanda , Czerwińska-Jelonkiewicz Katarzyna , Shchendrygina Anastasia , Wood Alice , Allouche Emna , Avesani Martina , Gok Gulay , Marchenko Oksana , Calvieri Camilla , Baritussio Anna , Ilardi Federica , Caglar Nihan , Moscatelli Sara , Kotlar Irina , Trêpa Maria , Rubini Maria Gimenez , Chrysohoou Christina , Jovovic Ljiljana , Prokšelj Katja , Simkova Iveta , Babazade Nigar , Siller-Matula Jolanta , Chikhi Fatima , Kovačević-Preradović Tamara , Srbinovska Elizabeta , Johnson Victoria , Farrero Marta , Moharem-Elgamal Sarah , Gimelli Alessia 
Published: July 2021

AbstractAimsWomen’s participation is steadily growing in medical schools, but they are still not sufficiently represented in cardiology, particularly in cardiology leadership positions. We present the contemporary distribution of women leaders in cardiology departments in the World Health Organization European region.Methods and resultsBetween August and December 2020, we applied purposive sampling to collect data and analyse gender distribution of heads of cardiology department in university/third level hospitals in 23 countries: Austria, Azerbaijan, Belgium, Bosnia-Herzegovina, Croatia, France, Germany, Greece, Italy, North Macedonia, Morocco, Poland, Portugal, Russia, Serbia, Slovakia, Slovenia, Spain, Switzerland, Tunisia, Turkey, Ukraine, and the UK. Age, cardiology subspecialty, and number of scientific publications were recorded for a subgroup of cardiology leaders for whom data were available. A total of 849 cardiology departments were analysed. Women leaders were only 30% (254/849) and were younger than their men counterpart (♀ 52.2 ± 7.7 years old vs. ♂ 58.1 ± 7.6 years old, P = 0.00001). Most women leaders were non-interventional experts (♀ 82% vs. ♂ 46%, P &lt; 0.00001) and had significantly fewer scientific publications than men {♀ 16 [interquartile range (IQR) 2–41] publications vs. ♂ 44 (IQR 9–175) publications, P &lt; 0.00001}.ConclusionAcross the World Health Organization European region, there is a significant gender disparity in cardiology leadership positions. Fostering a diverse and inclusive workplace is a priority to achieve the full potential and leverage the full talents of both women and men.
Effects of canagliflozin on serum potassium in people with diabetes and chronic kidney disease: the CREDENCE trial
Authors: Neuen Brendon L , Oshima Megumi , Perkovic Vlado , Agarwal Rajiv , Arnott Clare , Bakris George , Cannon Christopher P , Charytan David M , Edwards Robert , Górriz Jose L , Jardine Meg J , Levin Adeera , Neal Bruce , De Nicola Luca , Pollock Carol , Rosenthal Norman , Wheeler David C , Mahaffey Kenneth W , Heerspink Hiddo J L 
Published: July 2021

Abstract

Aims
Hyperkalaemia is a common complication of type 2 diabetes mellitus (T2DM) and limits the optimal use of agents that block the renin–angiotensin–aldosterone system, particularly in patients with chronic kidney disease (CKD). In patients with CKD, sodium‒glucose cotransporter 2 (SGLT2) inhibitors provide cardiorenal protection, but whether they affect the risk of hyperkalaemia remains uncertain.

Methods and results
The CREDENCE trial randomized 4401 participants with T2DM and CKD to the SGLT2 inhibitor canagliflozin or matching placebo. In this post hoc analysis using an intention-to-treat approach, we assessed the effect of canagliflozin on a composite outcome of time to either investigator-reported hyperkalaemia or the initiation of potassium binders. We also analysed effects on central laboratory-determined hyper- and hypokalaemia (serum potassium ≥6.0 and &lt;3.5 mmol/L, respectively) and change in serum potassium. At baseline, the mean serum potassium in canagliflozin and placebo arms was 4.5 mmol/L; 4395 (99.9%) participants were receiving renin–angiotensin system blockade. The incidence of investigator-reported hyperkalaemia or initiation of potassium binders was lower with canagliflozin than with placebo [occurring in 32.7 vs. 41.9 participants per 1000 patient-years; hazard ratio (HR) 0.78, 95% confidence interval (CI) 0.64–0.95, P = 0.014]. Canagliflozin similarly reduced the incidence of laboratory-determined hyperkalaemia (HR 0.77, 95% CI 0.61–0.98, P = 0.031), with no effect on the risk of hypokalaemia (HR 0.92, 95% CI 0.71–1.20, P = 0.53). The mean serum potassium over time with canagliflozin was similar to that of placebo.

Conclusion
Among patients treated with renin–angiotensin–aldosterone system inhibitors, SGLT2 inhibition with canagliflozin may reduce the risk of hyperkalaemia in people with T2DM and CKD without increasing the risk of hypokalaemia.
3′ untranslated region of Ckip-1 inhibits cardiac hypertrophy independently of its cognate protein
Authors: Zhao Yinlong , Ling Shukuan , Li Jianwei , Zhong Guohui , Du Ruikai , Li Youyou , Wang Yanqing , Liu Caizhi , Jin Xiaoyan , Liu Wei , Liu Tong , Li Yuheng , Zhao Dingsheng , Sun Weijia , Liu Zizhong , Liu Zifan , Pan Junjie , Yuan Xinxin , Gao Xingcheng , Xing Wenjuan , Chang Yan-Zhong , Li Yingxian 
Published: July 2021

Abstract

Aims
3′ untranslated region (3′ UTR) of mRNA is more conserved than other non-coding sequences in vertebrate genomes, and its sequence space has substantially expanded during the evolution of higher organisms, which substantiates their significance in biological regulation. However, the independent role of 3′ UTR in cardiovascular disease was largely unknown.

Methods and results
Using bioinformatics, RNA fluorescent in situ hybridization and quantitative real-time polymerase chain reaction, we found that 3′ UTR and coding sequence regions of Ckip-1 mRNA exhibited diverse expression and localization in cardiomyocytes. We generated cardiac-specific Ckip-1 3′ UTR overexpression mice under wild type and casein kinase 2 interacting protein-1 (CKIP-1) knockout background. Cardiac remodelling was assessed by histological, echocardiography, and molecular analyses at 4 weeks after transverse aortic constriction (TAC) surgery. The results showed that cardiac Ckip-1 3′ UTR significantly inhibited TAC-induced cardiac hypertrophy independent of CKIP-1 protein. To determine the mechanism of Ckip-1 3′ UTR in cardiac hypertrophy, we performed transcriptome and metabolomics analyses, RNA immunoprecipitation, biotin-based RNA pull-down, and reporter gene assays. We found that Ckip-1 3′ UTR promoted fatty acid metabolism through AMPK–PPARα–CPT1b axis, leading to its protection against pathological cardiac hypertrophy. Moreover, Ckip-1 3′ UTR RNA therapy using adeno-associated virus obviously alleviates cardiac hypertrophy and improves heart function.

Conclusions
These findings disclose that Ckip-1 3′ UTR inhibits cardiac hypertrophy independently of its cognate protein. Ckip-1 3′ UTR is an effective RNA-based therapy tool for treating cardiac hypertrophy and heart failure.