bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Implementation of Situational Judgment Tests as an Evaluation Method for Training Oncology Physicians: Application in the KOKON-KTO Training
Authors: Rogge Alizé A. , Helmer Stefanie M. , Kiessling Claudia , Witt Claudia M. 
Published: March 2021

AbstractSituational judgment tests (SJTs) are often used in aptitude testing and present practice-specific challenges. Their implementation into online training programs provides the opportunity to assess learning progress and improve training quality. In this study, text-based SJTs for oncology physicians were developed, validated, and implemented into the KOKON-KTO training which uses a blended learning training format to teach oncology physicians how to consult cancer patients on complementary and integrative medicine (CIM). The SJT was implemented to measure the e-learning results. In the development and validation phase, a total of 15 SJTs (each SJT including 1 best choice answer based on training content and 4 distractors; 9 SJTs for oncologists and 6 SJTs for oncology gynecologists only) were developed by an interprofessional team (n=5) using real-case vignettes and applying an in-depth review process. Best answers were validated by experts (oncologists and oncology gynecologists) with experience in advising cancer patients on CIM. In the implementation and evaluation phase, SJTs were answered by KOKON-KTO training participants (n=19) pre- and post e-learning. Results were analyzed using descriptive measurements, item difficulties, and Cohen’s d for effect size pre- and post-training. The experts (n=12, 49.8% gynecologists) agreed with best choice answers (69.4% for oncology gynecology; 81.5% for oncology) in 12 out of 15 SJTs. Comparing pre- and post-training scores, KOKON-KTO training participants were able to improve knowledge substantially (effect sizes for oncologists d=1.7; oncology gynecologists d= .71). Future studies need to increase the number of experts and SJTs in order to apply further psychometric measurements. As part of the KOKON-KTO study, this project is registered as DRKS00012704 on the “German Clinical Trials Register” (Date of registration: 28.08.2017).
A power-quality monitoring and assessment system for high-speed railways based on train-network-data center integration
Authors: Zhu Jun , Hu Haitao , He Zhengyou , Guo Xiaomin , Pan Weiguo 
Published: March 2021

AbstractIn recent years, with the rapid development of high-speed railways (HSRs), power interruptions or disturbances in traction power supply systems have become increasingly dangerous. However, it is often impossible to detect these faults immediately through single-point monitoring or collecting data after accidents. To coordinate the power quality data of both traction power supply systems (TPSSs) and high-speed trains (HSTs), a monitoring and assessing system is proposed to access the power quality issues on HSRs. By integrating train monitoring, traction substation monitoring and data center, this monitoring system not only realizes the real-time monitoring of operational behaviors for both TPSSs and HSTs, but also conducts a comprehensive assessment of operational quality for train-network systems. Based on a large number of monitoring data, the field measurements show that this real-time monitoring system is effective for monitoring and evaluating a traction-network system.
Laboratory results of foam application testing for longwall shield dust control in a simulated environment
Authors: Reed W. R. , Shahan M. R. , Zheng Y. , Mazzella A. 
Published: March 2021

AbstractThere were 37 longwall faces operating in mines in the United States in 2019. The average panel width for these longwalls was approximately 368.5 m (1209 ft). This translates to a range of approximately 170–240 shields per longwall, depending upon the width of shield. The movement of longwall shields is a significant contributor to respirable dust overexposures to longwall operators. Foam is expected to have the potential to reduce this shield dust generation. The foam is applied to the area on the roof between the coal face and the shield tip after the shearer passes. In this study, the longwall shield dust simulator was used to test three foam agents for their ability to control dust from longwall shield movements. Results showed that at low-velocity ventilation (≈ 3.0 m/s (600 fpm)) all foam agents were able to produce dust reduction levels of at least 45%. At high-velocity ventilation (≈ 5.1 m/s (1000 fpm)), the reductions were lower and more variable, ranging from being undeterminable for one foam agent to having 46%–63% reductions for the other two foam agents, with one instance of an increase in dust concentration. Overall, the use of foam agents can provide longwall shield dust control. Important factors are roof coverage and the ability of foam to remain on the roof for extended time periods.
Presenting new approach for optimal placement of nuclear power plant connected to the grid after the trip
Authors: Kiomarsi Farshid , Shojaei Ali Asghar , Soltani Sepehr , Lotfi Hossein 
Published: March 2021

AbstractThis study presents a combination of optimal placement and power system development with the aim of supplying electricity for Nuclear Power Plant after the trip of power plant. Power supply to the internal loads of power plant by the off-site power system is one of the main fields of research in achieving the safety Nuclear Power Plant. One of the main purposes in this article is to introduce a suitable and safe place for the construction and connection of a Nuclear Power Plant to the power system. These locations are identified by the power plants on-site loads and the average of the lowest number of relay protection after the Nuclear Power Plant trip, based on electricity considerations. Along with the optimal placement in this paper, the power system development, including the generation and transmission development in order to provide electricity with higher reliability to the Nuclear Power Plant after the trip is also presented. Monte Carlo and Latin Hypercube Sampling probabilistic methods are proposed for locating the site of a Nuclear Power Plant and algorithms of Genetic and Particle Swarm Optimization for locating and developing power generation and transmission systems. The simulation results are implemented on the IEEE RTS 24-bus system, and finally suitable locations for the construction of the Nuclear Power Plant and the generation and transmission development with the aim of feeding the power plant from the off-site power system and sufficient assurance that the reactor core does not melt after the trip, are determined.
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning
Authors: Li Zhongxiao , Li Yisheng , Zhang Bin , Li Yu , Long Yongkang , Zhou Juexiao , Zou Xudong , Zhang Min , Hu Yuhui , Chen Wei , Gao Xin 
Published: March 2021

Abstract
Alternative polyadenylation (APA) is a crucial step in post-transcriptional regulation. Previous bioinformatic studies have mainly focused on the recognition of polyadenylation sites (PASs) in a given genomic sequence, which is a binary classification problem. Recently, computational methods for predicting the usage level of alternative PASs in the same gene have been proposed. However, all of them cast the problem as a non-quantitative pairwise comparison task and do not take the competition among multiple PASs into account. To address this, here we propose a deep learning architecture, Deep Regulatory Code and Tools for Alternative Polyadenylation (DeeReCT-APA), to quantitatively predict the usage of all alternative PASs of a given gene. To accommodate different genes with potentially different numbers of PASs, DeeReCT-APA treats the problem as a regression task with a variable-length target. Based on a convolutional neural network-long short-term memory (CNN-LSTM) architecture, DeeReCT-APA extracts sequence features with CNN layers, uses bidirectional LSTM to explicitly model the interactions among competing PASs, and outputs percentage scores representing the usage levels of all PASs of a gene. In addition to the fact that only our method can quantitatively predict the usage of all the PASs within a gene, we show that our method consistently outperforms other existing methods on three different tasks for which they are trained: pairwise comparison task, highest usage prediction task, and ranking task. Finally, we demonstrate that our method can be used to predict the effect of genetic variations on APA patterns and sheds light on future mechanistic understanding in APA regulation. Our code and data are available at https://github.com/lzx325/DeeReCT-APA-repo.
CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes
Authors: Shen Yin , Chen Ling-Ling , Gao Junxiang 
Published: March 2021

Abstract
Chromatin accessibility is a highly informative structural feature for understanding gene transcription regulation, because it indicates the degree to which nuclear macromolecules such as proteins and RNAs can access chromosomal DNA. Studies have shown that chromatin accessibility is highly dynamic during stress response, stimulus response, and developmental transition. Moreover, physical access to chromosomal DNA in eukaryotes is highly cell-specific. Therefore, current technologies such as DNase-seq, ATAC-seq, and FAIRE-seq reveal only a portion of the open chromatin regions (OCRs) present in a given species. Thus, the genome-wide distribution of OCRs remains unknown. In this study, we developed a bioinformatics tool called CharPlant for the de novo prediction of OCRs in plant genomes. To develop this tool, we constructed a three-layer convolutional neural network (CNN) and subsequently trained the CNN using DNase-seq and ATAC-seq datasets of four plant species. The model simultaneously learns the sequence motifs and regulatory logics, which are jointly used to determine DNA accessibility. All of these steps are integrated into CharPlant, which can be run using a simple command line. The results of data analysis using CharPlant in this study demonstrate its prediction power and computational efficiency. To our knowledge, CharPlant is the first de novo prediction tool that can identify potential OCRs in the whole genome. The source code of CharPlant and supporting files are freely available from https://github.com/Yin-Shen/CharPlant.
Postextraction infection and antibiotic prescribing among veterans receiving dental extractions
Authors: Caniff Kaylee E. , Young Lisa R. , Truong Shawna , Gibson Gretchen , Jurasic M. Marianne , Poggensee Linda , Fitzpatrick Margaret A. , Evans Charlesnika T. , Suda Katie J. 
Published: March 2021

AbstractObjective:To characterize postextraction antibiotic prescribing patterns, predictors for antibiotic prescribing and the incidence of and risk factors for postextraction oral infection.Design:Retrospective analysis of a random sample of veterans who received tooth extractions from January 1, 2017 through December 31, 2017.Setting:VA dental clinics.Patients:Overall, 69,610 patients met inclusion criteria, of whom 404 were randomly selected for inclusion. Adjunctive antibiotics were prescribed to 154 patients (38.1%).Intervention:Patients who received or did not receive an antibiotic were compared for the occurrence of postextraction infection as documented in the electronic health record. Multivariable logistic regression was performed to identify factors associated with antibiotic receipt.Results:There was no difference in the frequency of postextraction oral infection identified among patients who did and did not receive antibiotics (4.5% vs 3.2%; P = .59). Risk factors for postextraction infection could not be identified due to the low frequency of this outcome. Patients who received antibiotics were more likely to have a greater number of teeth extracted (aOR, 1.10; 95% CI, 1.03–1.18), documentation of acute infection at time of extraction (aOR, 3.02; 95% CI, 1.57–5.82), molar extraction (aOR, 1.78; 95% CI, 1.10–2.86) and extraction performed by an oral maxillofacial surgeon (aOR, 2.29; 95% CI, 1.44–3.58) or specialty dentist (aOR, 5.77; 95% CI, 2.05–16.19).Conclusion:Infectious complications occurred at a low incidence among veterans undergoing tooth extraction who did and did not receive postextraction antibiotics. These results suggest that antibiotics have a limited role in preventing postprocedural infection; however, future studies are necessary to more clearly define the role of antibiotics for this indication.
Is a reduction in viability enough to determine biofilm susceptibility to a biocide?
Authors: Ledwoch Katarzyna , Magoga Maddalena , Williams Dulcie , Fabbri Stefania , Walsh James , Maillard Jean-Yves 
Published: March 2021

AbstractObjective:The abundance and prevalence of dry-surface biofilms (DSBs) in hospitals constitute an emerging problem, yet studies rarely report the cleaning and disinfection efficacy against DSBs. Here, the combined impact of treatments on viability, transferability, and recovery of bacteria from DSBs has been investigated for the first time.Methods:Staphylococcus aureus DSBs were produced in alternating 48-hour wet–dry cycles for 12 days on AISI 430 stainless steel discs. The efficacy of 11 commercially available disinfectants, 4 detergents, and 2 contactless interventions were tested using a modified standardized product test. Reduction in viability, direct transferability, cross transmission (via glove intermediate), and DSB recovery after treatment were measured.Results:Of 11 disinfectants, 9 were effective in killing and removing bacteria from S. aureus DSBs with >4 log10 reduction. Only 2 disinfectants, sodium dichloroisocyanurate 1,000 ppm and peracetic acid 3,500 ppm, were able to lower both direct and cross transmission of bacteria (<2 compression contacts positive for bacterial growth). Of 11 disinfectants, 8 could not prevent DSB recovery for >2 days. Treatments not involving mechanical action (vaporized hydrogen peroxide and cold atmospheric plasma) were ineffective, producing <1 log10 reduction in viability, DSB regrowth within 1 day, and 100% transferability of DSB after treatment.Conclusions:Reduction in bacterial viability alone does not determine product performance against biofilm and might give a false sense of security to consumers, manufacturers and regulators. The ability to prevent bacterial transfer and biofilm recovery after treatment requires a better understanding of the effectiveness of biocidal products.
Future glacial lakes in High Mountain Asia: an inventory and assessment of hazard potential from surrounding slopes
Authors: Furian Wilhelm , Loibl David , Schneider Christoph 
Published: March 2021

AbstractBedrock overdeepenings exposed by continued glacial retreat can store precipitation and meltwater, potentially leading to the formation of new proglacial lakes. These lakes may pose threats of glacial lake outburst floods (GLOFs) in high mountain areas, particularly if new lakes form in geomorphological setups prone to triggering events such as landslides or moraine collapses. We present the first complete inventory for future glacial lakes in High Mountain Asia by computing the subglacial bedrock for ~100 000 glaciers and estimating overdeepening area, volume and impact hazard for the larger potential lakes. We detect 25 285 overdeepenings larger than 104m2with a volume of 99.1 ± 28.6 km3covering an area of 2683 ± 773.8 km2. For the 2700 overdeepenings larger than 105m2, we assess the lake predisposition for mass-movement impacts that could trigger a GLOF by estimating the hazard of material detaching from surrounding slopes. Our findings indicate a shift in lake area, volume and GLOF hazard from the southwestern Himalayan region toward the Karakoram. The results of this study can be used for anticipating emerging threats and potentials connected to glacial lakes and as a basis for further studies at suspected GLOF hazard hotspots.
Telephone triage of suspected head and neck cancer patients during the coronavirus disease 2019 pandemic using the Head and Neck Cancer Risk Calculator version 2
Authors: Banerjee S , Voliotidis D , Parvin L , Rama S P K 
Published: March 2021

AbstractObjectiveUtilisation of the Head and Neck Cancer Risk Calculator version 2 has been recommended during the coronavirus disease 2019 pandemic for the assessment of head and neck cancer referrals. As limited data were available, this study was conducted to analyse the use of the Head and Neck Cancer Risk Calculator version 2 in clinical practice.MethodPatients undergoing telephone triage in a two-week wait referral clinic were included. Data were collected and analysed using appropriate methods.ResultsSixty-four patients in the study were risk-stratified into low-risk (51.6 per cent, 33 of 64), moderate-risk (14.1 per cent, 9 of 64) and high-risk (34.4 per cent, 22 of 64) groups. Of the patients, 53.1 per cent (34 of 64) avoided an urgent hospital visit, and 96.9 per cent (62 of 64) were cancer free, while 3.1 per cent (2 of 64) were found to have a head and neck malignancy. The sensitivity, specificity, negative predictive value and accuracy were 50.00 per cent, 66.13 per cent, 99.92 per cent and 66.11 per cent, respectively.ConclusionIt is reasonable to use the calculator for triaging purposes, but it must always be accompanied by a meticulous clinical thought process.
Sexual reproductive strategies ofPuya nitida(Bromeliaceae) in a Colombian paramo, a tropical high-elevation ecosystem
Authors: Franco-Saldarriaga Alejandra , Bonilla-Gómez María Argenis 
Published: March 2021

AbstractThe low availability of pollinators in high-elevation ecosystems can lead to flowering plants showing different adaptive responses in order to assure their reproductive success. Shifts toward autogamy and asexual reproductive rates (the reproductive assurance hypothesis) and the compensatory measures to maintain outcrossing such as flower longevity and more prolonged pistil receptivity (the increased pollination probability hypothesis) are some of these responses. Several studies have tested both hypotheses, but investigations of plants of tropical alpine environments such as paramos that support these assumptions are still scarce.Puya nitida, an endemic Colombian plant species distributed in the paramo and subparamo in the Eastern Cordillera of Cundinamarca department, was used as a case study to test its reproductive characteristics that assure its sexual reproduction. We analysed the species’ floral morphology and development, its phenological patterns and its plant mating-system. We found thatPuya nitidashowed floral characteristics that promote pollination by birds, herkogamy and dichogamy, flowers and receptive stigmas with 9 and 12 days of longevity, respectively and an index of self-incompatibility that shows that it is mostly self-incompatible. We found a synchronic phenological pattern with an annual frequency and an intermediate duration with a peak in the period of lowest rainfall. Our results suggested that longer floral development, prolonged stigma receptivity, herkogamy and dichogamy and self-incompatibility might assure reproductive success, since the cross-pollination might be favoured when few pollinators are in attendance. Overall, these reproductive mechanisms add evidence to the increased pollination probability hypothesis, specifically for a plant species of a tropical high-elevation ecosystem where pollinators are scarce.
Impact of cardiovascular risk factors on myocardial work—insights from the STAAB cohort study
Authors: Sahiti Floran , Morbach Caroline , Cejka Vladimir , Tiffe Theresa , Wagner Martin , Eichner Felizitas A. , Gelbrich Götz , Heuschmann Peter U. , Störk Stefan 
Published: March 2021

AbstractMyocardial work is a new echocardiography-based diagnostic tool, which allows to quantify left ventricular performance based on pressure–strain loops, and has been validated against invasively derived pressure–volume measurements. Myocardial work is described by its components (global constructive work [GCW], global wasted work [GWW]) and indices (global work index [GWI], global work efficiency [GWE]). Applying this innovative concept, we characterized the prevalence and severity of subclinical left ventricular compromise in the general population and estimated its association with cardiovascular (CV) risk factors. Within the Characteristics and Course of Heart Failure STAges A/B and Determinants of Progression (STAAB) cohort study we comprehensively phenotyped a representative sample of the population of Würzburg, Germany, aged 30–79 years. Indices of myocardial work were determined in 1929 individuals (49.3% female, mean age 54 ± 12 years). In multivariable analysis, hypertension was associated with a mild increase in GCW, but a profound increase in GWW, resulting in higher GWI and lower GWE. All other CV risk factors were associated with lower GCW and GWI, but not with GWW. The association of hypertension and obesity with GWI was stronger in women. We conclude that traditional CV risk factors impact selectively and gender-specifically on left ventricular myocardial performance, independent of systolic blood pressure. Quantifying active systolic and diastolic compromise by derivation of myocardial work advances our understanding of pathophysiological processes in health and cardiac disease.
Regulation of mating genes during arbuscular mycorrhizal isolate co-existence—where is the evidence?
Authors: Malar C Mathu , Roux Christophe , Corradi Nicolas 
Published: March 2021

Abstract
A recent study published by Mateus et al. [1] claimed that 18 “mating-related” genes are differentially expressed in the model arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis when genetically distinct fungal strains co-colonize a host plant. To clarify the level of evidence for this interesting conclusion, we first aimed to validate the functional annotation of these 18 R. irregularis genes using orthology predictions. These analyses revealed that, although sequence relationship exists, only 2 of the claimed 18 R. irregularis mating genes are potential orthologues to validated fungal mating genes. We also investigated the RNA-seq data from Mateus et al. [1] using classical RNA-seq methods and statistics. This analysis found that the over-expression during strain co-existence was not significant at the typical cut-off of the R. irregularis strains DAOM197198 and B1 in plants. Overall, we do not find convincing evidence that the genes involved have functions in mating, or that they are reproducibly up or down regulated during co-existence in plants.
Inhomogeneous Kondo-lattice in geometrically frustrated Pr2Ir2O7
Authors: Kavai Mariam , Friedman Joel , Sherman Kyle , Gong Mingda , Giannakis Ioannis , Hajinazar Samad , Hu Haoyu , Grefe Sarah E. , Leshen Justin , Yang Qiu , Nakatsuji Satoru , Kolmogorov Aleksey N. , Si Qimiao , Lawler Michael , Aynajian Pegor 
Published: March 2021

AbstractMagnetic fluctuations induced by geometric frustration of local Ir-spins disturb the formation of long-range magnetic order in the family of pyrochlore iridates. As a consequence, Pr2Ir2O7 lies at a tuning-free antiferromagnetic-to-paramagnetic quantum critical point and exhibits an array of complex phenomena including the Kondo effect, biquadratic band structure, and metallic spin liquid. Using spectroscopic imaging with the scanning tunneling microscope, complemented with machine learning, density functional theory and theoretical modeling, we probe the local electronic states in Pr2Ir2O7 and find an electronic phase separation. Nanoscale regions with a well-defined Kondo resonance are interweaved with a non-magnetic metallic phase with Kondo-destruction. These spatial nanoscale patterns display a fractal geometry with power-law behavior extended over two decades, consistent with being in proximity to a critical point. Our discovery reveals a nanoscale tuning route, viz. using a spatial variation of the electronic potential as a means of adjusting the balance between Kondo entanglement and geometric frustration.