bluuebunny/crossref_metadata_2025_split huggingface dataset:
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing
Authors: Rozhoňová Hana , Danciu Daniel , Stark Stefan , Rätsch Gunnar , Kahles André , Lehmann Kjong-Van 
Published: July 2022

AbstractMotivationSeveral recently developed single-cell DNA sequencing technologies enable whole-genome sequencing of thousands of cells. However, the ultra-low coverage of the sequenced data (&lt;0.05× per cell) mostly limits their usage to the identification of copy number alterations in multi-megabase segments. Many tumors are not copy number-driven, and thus single-nucleotide variant (SNV)-based subclone detection may contribute to a more comprehensive view on intra-tumor heterogeneity. Due to the low coverage of the data, the identification of SNVs is only possible when superimposing the sequenced genomes of hundreds of genetically similar cells. Thus, we have developed a new approach to efficiently cluster tumor cells based on a Bayesian filtering approach of relevant loci and exploiting read overlap and phasing.ResultsWe developed Single Cell Data Tumor Clusterer (SECEDO, lat. ‘to separate’), a new method to cluster tumor cells based solely on SNVs, inferred on ultra-low coverage single-cell DNA sequencing data. We applied SECEDO to a synthetic dataset simulating 7250 cells and eight tumor subclones from a single patient and were able to accurately reconstruct the clonal composition, detecting 92.11% of the somatic SNVs, with the smallest clusters representing only 6.9% of the total population. When applied to five real single-cell sequencing datasets from a breast cancer patient, each consisting of ≈2000 cells, SECEDO was able to recover the major clonal composition in each dataset at the original coverage of 0.03×, achieving an Adjusted Rand Index (ARI) score of ≈0.6. The current state-of-the-art SNV-based clustering method achieved an ARI score of ≈0, even after merging cells to create higher coverage data (factor 10 increase), and was only able to match SECEDOs performance when pooling data from all five datasets, in addition to artificially increasing the sequencing coverage by a factor of 7. Variant calling on the resulting clusters recovered more than twice as many SNVs as would have been detected if calling on all cells together. Further, the allelic ratio of the called SNVs on each subcluster was more than double relative to the allelic ratio of the SNVs called without clustering, thus demonstrating that calling variants on subclones, in addition to both increasing sensitivity of SNV detection and attaching SNVs to subclones, significantly increases the confidence of the called variants.Availability and implementationSECEDO is implemented in C++ and is publicly available at https://github.com/ratschlab/secedo. Instructions to download the data and the evaluation code to reproduce the findings in this paper are available at: https://github.com/ratschlab/secedo-evaluation. The code and data of the submitted version are archived at: https://doi.org/10.5281/zenodo.6516955.Supplementary informationSupplementary data are available at Bioinformatics online.
PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project
Authors: Ruan Eric , Nemeth Erika , Moffitt Richard , Sandoval Lorena , Machiela Mitchell J , Freedman Neal D , Huang Wen-Yi , Wong Wendy , Chen Kai-Ling , Park Brian , Jiang Kevin , Hicks Belynda , Liu Jia , Russ Daniel , Minasian Lori , Pinsky Paul , Chanock Stephen J , Garcia-Closas Montserrat , Almeida Jonas S 
Published: July 2022

AbstractMotivationThe Division of Cancer Epidemiology and Genetics (DCEG) and the Division of Cancer Prevention (DCP) at the National Cancer Institute (NCI) have recently generated genome-wide association study (GWAS) data for multiple traits in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Genomic Atlas project. The GWAS included 110 000 participants. The dissemination of the genetic association data through a data portal called GWAS Explorer, in a manner that addresses the modern expectations of FAIR reusability by data scientists and engineers, is the main motivation for the development of the open-source JavaScript software development kit (SDK) reported here.ResultsThe PLCO GWAS Explorer resource relies on a public stateless HTTP application programming interface (API) deployed as the sole backend service for both the landing page’s web application and third-party analytical workflows. The core PLCOjs SDK is mapped to each of the API methods, and also to each of the reference graphic visualizations in the GWAS Explorer. A few additional visualization methods extend it. As is the norm with web SDKs, no download or installation is needed and modularization supports targeted code injection for web applications, reactive notebooks (Observable) and node-based web services.Availability and implementationcode at https://github.com/episphere/plco; project page at https://episphere.github.io/plco
Introduction: Centering Women on Post-2010 Chinese TV
Authors: Zhao Jamie J , Ng Eve 
Published: July 2022

Abstract
This introduction to the special issue on the topic of “Centering Women on Post-2010 Chinese TV” presents a brief review of major topics in the scholarship on televisual representations of women in contemporary China. The issue includes five research articles that, collectively, address research gaps in studies of post-2010 Chinese televisual-cultural discourses to do with ethnic minority women, women’s media authorship, women’s extramarital romance, and national heroines of the COVID-19 pandemic. We propose novel focuses for examining women’s plural roles and subjectivities on and off the TV screen. We thus call for complex understandings that move beyond the predominant attention of existing scholarship on conventional depictions of women as (virtuous) wives, (good) mothers, (inspirational) female professionals or heroines, and masculine feminist girls. Instead, this special issue sheds light on the polyvalent and contested positionality of Chinese women as gendered, ethnicized, (trans)nationalized, and romanticized subjects during a (post-)globalization and (post-)pandemic age.
Statin Use May Be Associated With a Lower Risk of Invasive Aspergillosis in Lung Transplant Recipients
Authors: Villalobos Armelle Pérez-Cortés , Foroutan Farid , Davoudi Setareh , Kothari Sagar , Martinu Tereza , Singer Lianne G , Keshavjee Shaf , Husain Shahid 
Published: July 2022

Abstract

Background
Statins are competitive inhibitors of 3-hydroxy-3methylglutaryl coenzyme A reductase (HMG-CoA reductase) that catalyses HMG-CoA conversion to mevalonate, a process involved in synthesizing cholesterol in humans and ergosterol in fungi. The effect of statin use on the risk of development of invasive aspergillosis (IA) in lung transplant recipients (LTRs) is not well documented.

Methods
This retrospective study included LTRs from 2010 to 2017 who were followed for one-year post-transplant. Proven or probable IA was diagnosed as per ISHLT criteria. We performed a multivariable Cox proportional hazards model of the association between IA and statin use (minimum of 2 weeks duration prior to IA), adjusting for other known IA risk factors.

Results
We identified 785 LTRs, 44% female, mean age 53 years old, the most common underlying disease being pulmonary fibrosis (23.8%). In total, 451 LTRs (57%) received statins post-transplant, atorvastatin was the most commonly used statin (68%). The mean duration of statins post-transplant was 347 days (interquartile range [IQR]: 305 to 346). And 55 (7%) LTRs developed IA in the first-year post-transplant. Out of these 55 LTRs, 9 (16.3%) had received statin before developing IA. In multivariable analysis, statin use was independently associated with a lower risk of IA (P = .002, SHR 0.30, 95% confidence interval [CI] 95% .14–.64). Statin use was also associated with a lower incidence of post-transplant Aspergillus colonization, 114 (34%) in the no statin group vs 123 (27%) in the statin group (P = .038).

Conclusions
The use of statin for a minimum of two weeks during the first-year post-transplant was associated with a 70% risk reduction of IA in LTRs.
The Status Dilemma in World Politics: An Anatomy of the China–India Asymmetrical Rivalry
Authors: Pu Xiaoyu 
Published: July 2022

Abstract
The role of status in world politics has become an important research topic. This article examines China–India relations through a new framework for status dilemmas. This article, through a careful comparison of the status dilemma with other models of conflict, clarifies the logic and mechanism of status dilemmas in world politics. In particular, it differentiates between the status competition model and the status dilemma model. The status dilemma entails overestimation of the competitive nature of the status relationship and underestimation of the potential compatibility of the status goal. The article demonstrates that the China–India relationship is not always a zero-sum game, even though its competitive nature is real. Asymmetrical power and motivated reasoning contribute to misunderstanding and misperception. The power asymmetry makes India oversensitive to Chinese actions, and it makes China less sensitive to India’s concerns. Motivated reasoning, based on historical memory and domestic politics, moreover, makes India’s perception of China more negative and competitive than China’s apprehension of India. The status dilemma has broad implications for power politics in the new era which suggest that policymakers should realistically evaluate the challenges of status competition while avoiding deterministic zero-sum thinking.
Treatment with sotrovimab for SARS-CoV-2 infection in a cohort of high-risk kidney transplant recipients
Authors: Villanego Florentino , Mazuecos Auxiliadora , Cubillo Beatriz , Merino M José , Poveda Inmaculada , Saura Isabel M , Segurado Óscar , Cruzado Leónidas , Eady Myriam , Zárraga Sofía , Aladrén M José , Cabello Sheila , López Verónica , González Esther , Lorenzo Inmaculada , Espí-Reig Jordi , Fernández Constantino , Osma July , Ruiz-Fuentes M Carmen , Toapanta Néstor , Franco Antonio , Burballa Carla C , Muñoz Miguel A , Crespo Marta , Pascual Julio 
Published: July 2022

ABSTRACT

Background
Sotrovimab is a neutralizing monoclonal antibody (mAb) that seems to remain active against recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. The evidence on its use in kidney transplant (KT) recipients, however, is limited.

Methods
We performed a multicenter, retrospective cohort study of 82 KT patients with SARS-CoV-2 infection {coronavirus disease 2019 [COVID-19]} treated with sotrovimab.

Results
Median age was 63 years. Diabetes was present in 43.9% of patients, and obesity in 32.9% of patients; 48.8% of patients had an estimated glomerular filtration rate under 30 mL/minute/1.73 m2. Additional anti–COVID-19 therapies were administered to 56 patients, especially intravenous steroids (65.9%). Sotrovimab was administered early (&lt;5 days from the onset of the symptoms) in 46 patients (56%). Early-treated patients showed less likely progression to severe COVID-19 than those treated later, represented as a lower need for ventilator support (2.2% vs 36.1%; P &lt; .001) or intensive care admission (2.2% vs 25%; P = .002) and COVID-19–related mortality (2.2% vs 16.7%; P = .020). In the multivariable analysis, controlling for baseline risk factors to severe COVID-19 in KT recipients, early use of sotrovimab remained as a protective factor for a composite outcome, including need for ventilator support, intensive care, and COVID-19–related mortality. No anaphylactic reactions, acute rejection episodes, impaired kidney function events, or non-kidney side effects related to sotrovimab were observed.

Conclusions
Sotrovimab had an excellent safety profile, even in high-comorbidity patients and advanced chronic kidney disease stages. Earlier administration could prevent progression to severe disease, while clinical outcomes were poor in patients treated later. Larger controlled studies enrolling KT recipients are warranted to elucidate the true efficacy of monoclonal antibody therapies.
A Clothoid Curve-Based Intersection Collision Warning Scheme in Internet of Vehicles
Authors: Luo Xuanhao , Feng Yong , Wang Chengdong 
Published: July 2022

Abstract
One of the most important problems in traffic safety is providing effective collision warnings in intersection areas. In this paper, we propose a Clothoid Curve-based Intersection Collision Warning scheme (CICW) in the Internet of Vehicles. In CICW, we first present a clothoid curve-based vehicle trajectory prediction model. In this model, vehicles can establish the trajectory prediction equations by themselves. Each vehicle solves the equations based on its internal state information, electronic map, GPS data and neighbour vehicles’ state information derived from periodical beacons. The vehicle then predicates the crossing points of the predicted trajectory between itself and the neighbour vehicles. Based on the reference points, it further obtains the earliest possible collision location and then issues a warning. Extensive simulation results show that the performance of the proposed scheme achieves higher collision warning accuracy and a lower error warning ratio compared to existing schemes.
The Ability of Bumblebees Bombus terrestris (Hymenoptera: Apidae) to Detect Floral Humidity is Dependent Upon Environmental Humidity
Authors: Harrison Amy S , Rands Sean A 
Published: July 2022

Abstract
Flowers produce local humidity that is often greater than that of the surrounding environment, and studies have shown that insect pollinators may be able to use this humidity difference to locate and identify suitable flowers. However, environmental humidity is highly heterogeneous, and is likely to affect the detectability of floral humidity, potentially constraining the contexts in which it can be used as a salient communication pathway between plants and their pollinators. In this study, we use differential conditioning techniques on bumblebees Bombus terrestris audax (Harris) to explore the detectability of an elevated floral humidity signal when presented against different levels of environmental noise. Artificial flowers were constructed that could be either dry or humid, and individual bumblebees were presented with consistent rewards in either the humid or dry flowers presented in an environment with four levels of constant humidity, ranging from low (~20% RH) to highly saturated (~95% RH). Ability to learn was dependent upon both the rewarding flower type and the environment: the bumblebees were able to learn rewarding dry flowers in all environments, but their ability to learn humid rewarding flowers was dependent on the environmental humidity, and they were unable to learn humid rewarding flowers when the environment was highly saturated. This suggests that floral humidity might be masked from bumblebees in humid environments, suggesting that it may be a more useful signal to insect pollinators in arid environments.
Subclinical left ventricular systolic dysfunction and incident stroke in the elderly: long-term findings from Cardiovascular Abnormalities and Brain Lesions
Authors: Yoshida Yuriko , Jin Zhezhen , Russo Cesare , Homma Shunichi , Nakanishi Koki , Ito Kazato , Mannina Carlo , Elkind Mitchell S V , Rundek Tatjana , Yoshita Mitsuhiro , DeCarli Charles , Wright Clinton B , Sacco Ralph L , Di Tullio Marco R 
Published: July 2022

Abstract

Aims
Heart disease is associated with an increased risk for ischaemic stroke. However, the predictive value of reduced left ventricular ejection fraction (LVEF) for stroke is controversial and only observed in patients with severe reduction. LV global longitudinal strain (LV GLS) can detect subclinical LV systolic impairment when LVEF is normal. We investigated the prognostic role of LV GLS for incident stroke in a predominantly elderly cohort.

Methods and results
Two-dimensional echocardiography with speckle tracking was performed in the Cardiac Abnormalities and Brain Lesions (CABL) study. Among 708 stroke-free participants (mean age 71.4 ± 9.4 years, 60.9% women), abnormal LV GLS (&gt;−14.7%: 95% percentile of the subgroup without risk factors) was detected in 133 (18.8%). During a mean follow-up of 10.8 ± 3.9 years, 47 participants (6.6%) experienced an ischaemic stroke (26 cardioembolic or cryptogenic, 21 other subtypes). The cumulative incidence of ischaemic stroke was significantly higher in participants with abnormal LV GLS than with normal LV GLS (P &lt; 0.001). In multivariate stepwise logistic regression analysis, abnormal LV GLS was associated with ischaemic stroke independently of cardiovascular risk factors including LVEF, LV mass, left atrial volume, subclinical cerebrovascular disease at baseline, and incident atrial fibrillation [hazard ratio (HR): 2.69, 95% confidence interval (CI): 1.47–4.92; P = 0.001]. Abnormal LV GLS independently predicted cardioembolic or cryptogenic stroke (adjusted HR: 3.57, 95% CI: 1.51–8.43; P = 0.004) but not other subtypes.

Conclusion
LV GLS was a strong independent predictor of ischaemic stroke in a predominantly elderly stroke-free cohort. Our findings provide insights into the brain–heart interaction and may help improve stroke primary prevention strategies.
A framework of deep learning networks provides expert-level accuracy for the detection and prognostication of pulmonary arterial hypertension
Authors: Diller Gerhard-Paul , Benesch Vidal Maria Luisa , Kempny Aleksander , Kubota Kana , Li Wei , Dimopoulos Konstantinos , Arvanitaki Alexandra , Lammers Astrid E , Wort Stephen J , Baumgartner Helmut , Orwat Stefan , Gatzoulis Michael A 
Published: July 2022

Abstract

Aims
To test the hypothesis that deep learning (DL) networks reliably detect pulmonary arterial hypertension (PAH) and provide prognostic information.

Methods and results
Consecutive patients with PAH, right ventricular (RV) dilation (without PAH), and normal controls were included. An ensemble of deep convolutional networks incorporating echocardiographic views and estimated RV systolic pressure (RVSP) was trained to detect (invasively confirmed) PAH. In addition, DL-networks were trained to segment cardiac chambers and extracted geometric information throughout the cardiac cycle. The ability of DL parameters to predict all-cause mortality was assessed using Cox-proportional hazard analyses. Overall, 450 PAH patients, 308 patients with RV dilatation (201 with tetralogy of Fallot and 107 with atrial septal defects) and 67 normal controls were included. The DL algorithm achieved an accuracy and sensitivity of detecting PAH on a per patient basis of 97.6 and 100%, respectively. On univariable analysis, automatically determined right atrial area, RV area, RV fractional area change, RV inflow diameter and left ventricular eccentricity index (P &lt; 0.001 for all) were significantly related to mortality. On multivariable analysis DL-based RV fractional area change (P &lt; 0.001) and right atrial area (P = 0.003) emerged as independent predictors of outcome. Statistically, DL parameters were non-inferior to measures obtained manually by expert echocardiographers in predicting prognosis.

Conclusion
The study highlights the utility of DL algorithms in detecting PAH on routine echocardiograms irrespective of RV dilatation. The algorithms outperform conventional echocardiographic evaluation and provide prognostic information at expert-level. Therefore, DL methods may allow for improved screening and optimized management of PAH.
Comparative analysis of right ventricular strain in Fabry cardiomyopathy and sarcomeric hypertrophic cardiomyopathy
Authors: Meucci Maria Chiara , Lillo Rosa , Lombardo Antonella , Lanza Gaetano A , Bootsma Marianne , Butcher Steele C , Massetti Massimo , Manna Raffaele , Bax Jeroen J , Crea Filippo , Ajmone Marsan Nina , Graziani Francesca 
Published: July 2022

AbstractAimsTo perform a comparative analysis of right ventricle (RV) myocardial mechanics, assessed by 2D speckle-tracking echocardiography (2D-STE), between patients with Fabry disease and patients with sarcomeric disease.Methods and resultsPatients with Fabry cardiomyopathy (FC) (n = 28) were compared with patients with sarcomeric hypertrophic cardiomyopathy (HCM), matched for degree of left ventricle hypertrophy (LVH) and demographic characteristics (n = 112). In addition, patients with Fabry disease and no LVH [phenotype-negative carriers of pathogenic α-galactosidase gene mutations (GLA LVH-)] (n = 28) were compared with age and sex-matched carriers of sarcomeric gene mutations without LVH [Phenotype-negative carriers of pathogenic sarcomeric gene mutations (Sarc LVH-)] (n = 56). Standard echocardiography and 2D-STE were performed in all participants. Despite a subtle impairment of RV global longitudinal strain (RV-GLS) was common in both groups, patients with FC showed a more prominent reduction of RV free wall longitudinal strain (RV-FWS) and lower values of difference between RV-FWS and RV-GLS (ΔRV strain), in comparison to individuals with HCM (P &lt; 0.001 and P = 0.002, respectively). RV-FWS and ΔRV strain demonstrated an independent and additive value in discriminating FC from HCM, over the presence of symmetric LVH, systolic anterior motion of the mitral valve and RV hypertrophy. Similar results were found in GLA LVH- patients: they had worse RV-FWS and lower values of ΔRV strain as compared to Sarc LVH- patients (both P &lt; 0.001).ConclusionPatients with FC show a specific pattern of RV myocardial mechanics, characterized by a larger impairment of RV-FWS and lower ΔRV strain in comparison to patients with HCM, which may be helpful in the differential diagnosis between these two diseases.
Scuttle for shelter: flight-to-safety and political uncertainty during the Spanish Second Republic
Authors: Battilossi Stefano , Houpt Stefan O , Verdickt Gertjan 
Published: July 2022

Abstract
The Spanish Second Republic was a unique experiment of democratization in interwar Europe, which was characterized by extreme levels of political uncertainty. We find that investors responded to shifts in uncertainty by selling stocks in favor of government bonds—a behavior known as flight-to-safety. Additionally, we find that political uncertainty caused stock market stress and induced significant differences in the cross-section of expected stock returns, consistent with the exposures to political uncertainty. The fact that investors recurrently scuttled to shelter into government bonds suggests that they did not perceive a radical change in the political regime as an immediate and credible threat.
Role Change and Russia's Responses to Upheavals in Ukraine
Authors: Strycharz Damian 
Published: July 2022

AbstractRussia reacted in markedly different ways to comparable upheavals in Ukraine: the Orange Revolution in 2004 and the Euromaidan Revolution in 2013/2014. This paper argues that a combination of important external and internal factors led to a change in Russia's dominant national role conceptions, which contributed to Moscow's more assertive foreign policy, exemplified by divergent reactions to these two upheavals. Consequently, the paper aims to contribute to the existing scholarship on role change, demonstrating mechanisms behind such changes and examining the necessary scope conditions. The analysis reveals two types of role change: long-term, comprehensive ones that may lead to shifts in foreign policy behavior and swift changes motivated by contemporary events that result from role conflict.