bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybrid Arch Repair with Supra-Aortic Debranching and Using Castor Stent-Graft
Authors: Gao Xijie , Liu Guohong , Lu Jun , Zhao Jianbo 
Published: June 2022

Abstract
Background The management of aortic lesions involving the aortic arch in patients who cannot tolerate thoracotomy is a challenge.
Case Description A 32-year-old woman who underwent a giant aneurysm at the proximal end of the descending aorta with significant vascular wall calcification. The patient underwent Castor single-branched stent-grafting in the brachiocephalic trunk combined with surgical supra-aortic debranching, which avoided surgical aortic arch replacement and stent fenestration.reopening. The patient was followed up for 9 months, and surgery-related complications were not observed.
Conclusion Hybrid arch repair with supra-aortic debranching and using Castor single-branched stent can be used to treat aortic lesions involving the aortic arch.
Intercultural discussion of conceptual universals in discourse: joint online methodology to bring about social change through novel conceptualizations of Covid-19
Authors: Schnell Zsuzsanna , Ervas Francesca 
Published: June 2022

AbstractThe present article addresses the professional conclusions of an international platform of education in intercultural discourse in the European Union’s EDUC Project. In flagging social issues and concerns,cross-cultural academic collaborationis a powerful tool to bring aboutsocial change. In our educational project participants encounter different cultures, so the discussed topics, and especially the metaphors for the Covid-19 pandemic, receive instant reflections fromdifferent cultural perspectives, multiplying the potential sphere of validinterpretations, yielding novel perspectives inintercultural pragmaticsand communication. This gives birth to anovel methodologythat builds on the open-minded integration of different points of view, understanding universal traits of human cognition and differences in culture in the linguistics of discourse.
A novel methodology of international discourse: online joint course across cultures
Authors: Schnell Zsuzsanna , Podeschi Christopher 
Published: June 2022

AbstractThis article explores a novel methodology in the globalized classroom to face and tackle new challenges across cultures. The new online educational form of international discourse has the potential to make a difference in and outside Academia as it encompasses interpersonal communication across cultures and thus offers a novel framework for interpretation of different sociocultural perspectives to bring about social change. It transcends geographical and physical boundaries as it brings people together for discussion in the online joint event. Our study guides the reader through a collaborative educational framework and offers a methodology that transcends boundaries, exemplifying a tool for 21st century education. It offers techniques that bring on social change and enhances open-mindedness in tackling social problems with valuable methods from the fields of humanities and intercultural, collaborative communication.
Equal but different! Improving care for older LGBT+ adults
Authors: Bailey Dan , Calasanti Toni , Crowe Andrew , di Lorito Claudio , Hogan Patrick , de Vries Brian 
Published: June 2022

Abstract
International human rights movements have improved the visibility and equality of lesbian, gay, bisexual and transgender+ (LGBT+) communities and their members. Health outcomes for LGBT+ people remain, however, worse than for their non-LGBT+ peers. Older LGBT+ people have experienced fewer positive changes, in part due to their lived experience of discrimination and their ongoing, unintentional invisibility in medical and social care. This article highlights the impacts of societal structure, health and social care on the lives of older LGBT+ people including physical and mental health, End of Life, Dementia, Housing and Care Settings, and a focus on the experiences of trans-people. We look at the existing improvements developed by LGBT+ communities (and their allies) and propose refreshing Person-Centred Care to improve inclusivity. Finally, we provide a framework for looking at the areas in which service challenges arise and suggest ways to address these to make health and social care services more ready to meet the needs of older LGBT+ people.
‘Normative Facts as Reasons’
Authors: Molina Yohan 
Published: June 2022

Abstract
In ‘Normative Facts and Reasons’, Fabienne Peter proposes that there are two different types of practical warrant, which she terms ‘entitlement warrant’ and ‘reason-based justification’. This thesis relies fundamentally on her distinction between normative facts and normative reasons. I will raise two general critical observations. First, I will claim that Peter advocates a representation-dependent conception of reasons that is at odds with an intuitive and accepted understanding of them. Second, I will contend that reasons need not be the entities we directly handle in our deliberations, which undermines the idea that reasons are propositions. In this way, her distinction fails: normative reasons are just normative facts. This implies that the existence of two types of practical warrant, based either on normative facts or reasons, is unfounded.
ggtranscript: an R package for the visualization and interpretation of transcript isoforms usingggplot2
Authors: Gustavsson Emil K , Zhang David , Reynolds Regina H , Garcia-Ruiz Sonia , Ryten Mina 
Published: June 2022

AbstractMotivationThe advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use.Availability and implementationggtranscript is an R package available at https://github.com/dzhang32/ggtranscript (DOI: https://doi.org/10.5281/zenodo.6374061) via an open-source MIT licence. Further documentation is available at https://dzhang32.github.io/ggtranscript/.
CancerCellTracker: a brightfield time-lapse microscopy framework for cancer drug sensitivity estimation
Authors: Jiang Qibing , Sudalagunta Praneeth , Silva Maria C , Canevarolo Rafael R , Zhao Xiaohong , Ahmed Khandakar Tanvir , Alugubelli Raghunandan Reddy , DeAvila Gabriel , Tungesvik Alexandre , Perez Lia , Gatenby Robert A , Gillies Robert J , Baz Rachid , Meads Mark B , Shain Kenneth H , Silva Ariosto S , Zhang Wei 
Published: June 2022

AbstractMotivationTime-lapse microscopy is a powerful technique that relies on images of live cells cultured ex vivo that are captured at regular intervals of time to describe and quantify their behavior under certain experimental conditions. This imaging method has great potential in advancing the field of precision oncology by quantifying the response of cancer cells to various therapies and identifying the most efficacious treatment for a given patient. Digital image processing algorithms developed so far require high-resolution images involving very few cells originating from homogeneous cell line populations. We propose a novel framework that tracks cancer cells to capture their behavior and quantify cell viability to inform clinical decisions in a high-throughput manner.ResultsThe brightfield microscopy images a large number of patient-derived cells in an ex vivo reconstruction of the tumor microenvironment treated with 31 drugs for up to 6 days. We developed a robust and user-friendly pipeline CancerCellTracker that detects cells in co-culture, tracks these cells across time and identifies cell death events using changes in cell attributes. We validated our computational pipeline by comparing the timing of cell death estimates by CancerCellTracker from brightfield images and a fluorescent channel featuring ethidium homodimer. We benchmarked our results using a state-of-the-art algorithm implemented in ImageJ and previously published in the literature. We highlighted CancerCellTracker’s efficiency in estimating the percentage of live cells in the presence of bone marrow stromal cells.Availability and implementationhttps://github.com/compbiolabucf/CancerCellTracker.Supplementary informationSupplementary data are available at Bioinformatics online.
ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise
Authors: May Vinzenz , Koch Leonard , Fischer-Zirnsak Björn , Horn Denise , Gehle Petra , Kornak Uwe , Beule Dieter , Holtgrewe Manuel 
Published: June 2022

AbstractMotivationWhile the identification of small variants in panel sequencing data can be considered a solved problem, the identification of larger, multi-exon copy number variants (CNVs) still poses a considerable challenge. Thus, CNV calling has not been established in all laboratories performing panel sequencing. At the same time, such laboratories have accumulated large datasets and thus have the need to identify CNVs on their data to close the diagnostic gap.ResultsIn this article, we present our method clearCNV that addresses this need in two ways. First, it helps laboratories to properly assign datasets to enrichment kits. Based on homogeneous subsets of data, clearCNV identifies CNVs affecting the targeted regions. Using real-world datasets and validation, we show that our method is highly competitive with previous methods and preferable in terms of specificity.Availability and implementationThe software is available for free under a permissible license at https://github.com/bihealth/clear-cnv.Supplementary informationSupplementary data are available at Bioinformatics online.
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling
Authors: Singh Jaswinder , Paliwal Kuldip , Litfin Thomas , Singh Jaspreet , Zhou Yaoqi 
Published: June 2022

AbstractMotivationRecently, AlphaFold2 achieved high experimental accuracy for the majority of proteins in Critical Assessment of Structure Prediction (CASP 14). This raises the hope that one day, we may achieve the same feat for RNA structure prediction for those structured RNAs, which is as fundamentally and practically important similar to protein structure prediction. One major factor in the recent advancement of protein structure prediction is the highly accurate prediction of distance-based contact maps of proteins.ResultsHere, we showed that by integrated deep learning with physics-inferred secondary structures, co-evolutionary information and multiple sequence-alignment sampling, we can achieve RNA contact-map prediction at a level of accuracy similar to that in protein contact-map prediction. More importantly, highly accurate prediction for top L long-range contacts can be assured for those RNAs with a high effective number of homologous sequences (Neff &gt; 50). The initial use of the predicted contact map as distance-based restraints confirmed its usefulness in 3D structure prediction.Availability and implementationSPOT-RNA-2D is available as a web server at https://sparks-lab.org/server/spot-rna-2d/ and as a standalone program at https://github.com/jaswindersingh2/SPOT-RNA-2D.Supplementary informationSupplementary data are available at Bioinformatics online.
Clinical value of the expression levels of protein tyrosine phosphatase non-receptor type 22.6 mRNA in peripheral blood mononuclear cells in Crohn’s disease
Authors: Hu Mei , Chen Zhitao , Liao Yusheng , Wu Jie , Zheng Dan , Zhang Heng 
Published: June 2022

Abstract

Objective
To explore the relationship between the expression levels of protein tyrosine phosphatase non-receptor type (PTPN) 22.6 mRNA in peripheral blood mononuclear cells (PBMCs) and the disease activity as well as clinical characteristics in Crohn’s disease (CD) patients.

Methods
A total of 480 subjects were enrolled. Data were collected including baseline information, expression levels of PTPN22.6 mRNA in PBMCs for all subjects, C-reactive protein (CRP) levels in serum, clinical characteristics, and disease activity for all patients. Expression levels of PTPN22.6 mRNA in PBMCs, CRP levels in serum, clinical characteristics according to Montreal Classification [8], and Crohn’s disease activity index (CDAI) were the primary observation outcomes.

Results
The expression levels of PTPN22.6 mRNA (P = 0.032) in PBMCs and serum CRP levels (P &lt; 0.001) were significantly higher in active CD patients than in inactive CD patients (P = 0.032). Correlation analysis showed that there was a positive correlation between expression levels of PTPN22.6 mRNA and CDAI value (r = 0.512, P = 0.003), as well as expression levels of PTPN22.6 mRNA and CRP levels in the CD group (r = 0.456, P = 0.006). There were significantly higher expression levels of PTPN22.6 mRNA in PBMCs in patients with structuring behavior than that in patients with non-stricturing and non-penetrating (NSNP) behaviors (P = 0.018) and penetrating behaviors (P = 0.024).

Conclusions
The expression levels of PTPN22.6 mRNA can be used as an indicator to help predict CD diagnosis, disease activity, serum CRP level, and behavior type of CD disease.
The genome of Prunus humilis provides new insights to drought adaption and population diversity
Authors: Wang Yi , Xie Jun , Zhang HongNa , Li Weidong , Wang Zhanjun , Li Huayang , Tong Qian , Qiao Gaixia , Liu Yujuan , Tian Ying , Wei Yong Zan , Li Ping , Wang Rong , Cheng Weiping , Liang Zhengchang , Xu Meilong 
Published: June 2022

Abstract
Prunus humilis (2n = 2x = 16) is a dwarf shrub fruit tree native to China and distributed widely in the cold and arid northern region. In this study, we obtained the whole genome sequences of P. humilis by combining Illumina, PacBio and HiC sequencing technologies. This genome was 254.38 Mb long and encodes 28,301 putative proteins. Phylogenetic analysis indicated that P. humilis shares the same ancestor with Prunus mume and Prunus armeniaca at ∼ 29.03 Mya. Gene expansion analysis implied that the expansion of WAX-related and LEA genes might be associated with high drought tolerance of P. humilis and LTR maybe one of the driver factors for the drought adaption by increase the copy number of LEAs. Population diversity analysis among 20 P. humilis accessions found that the genetic diversity of P. humilis populations was limited, only 1.40% base pairs were different with each other, and more wild resources need to be collected and utilized in the breeding and improvement. This study provides new insights to the drought adaption and population diversity of P. humilis that could be used as a potential model plant for horticultural research.
Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness
Authors: Yang Jing-Shan , Qian Zhi-Hao , Shi Tao , Li Zhi-Zhong , Chen Jin-Ming 
Published: June 2022

Abstract
Nymphoides indica, an aquatic plant, is an invasive species that causes both ecological and economic damage in North America and elsewhere. However, the lack of genomic data of N. indica limits the in-depth analysis of this invasive species. Here, we report a chromosome-level genome assembly of nine pseudochromosomes of N. indica with a total size of ∼ 520 Mb. More than half of the N. indica genome consists of transposable elements (TEs), and a higher density of TEs around genes may play a significant role in response to an ever-changing environment by regulating the nearby gene. Additionally, our analysis revealed that N. indica only experienced a gamma (γ) whole-genome triplication event. Functional enrichment of the N. indica-specific and expanded gene families highlighted genes involved in the responses to hypoxia and plant–pathogen interactions, which may strengthen the ability to adapt to external challenges and improve ecological fitness. Furthermore, we identified 160 members of the nucleotide-binding site and leucine-rich repeat gene family, which may be linked to the defence response. Collectively, the high-quality N. indica genome reported here opens a novel avenue to understand the evolution and rapid invasion of Nymphoides spp.
Environmental Inequality in Four European Cities: A Study Combining Household Survey and Geo-Referenced Data
Authors: Diekmann Andreas , Bruderer Enzler Heidi , Hartmann Jörg , Kurz Karin , Liebe Ulf , Preisendörfer Peter 
Published: June 2022

AbstractCombining individual-level survey data and geo-referenced administrative noise data for four European cities (Bern, Zurich, Hanover, and Mainz; n = 7,450), we test the social gradient hypothesis, which states that exposure to residential noise is higher for households in a lower socioeconomic position (measured by income and migration background). In addition, we introduce and test the ‘environmental shielding hypothesis’, which states that, given environmental ‘bads’ in the neighbourhood, privileged social groups have better opportunities to shield themselves against them. Our results show that, for many residents of the four cities, observed road traffic and aircraft noise levels are above World Health Organization limits. Estimates of spatial error regression models only partly support the social gradient hypothesis. While we find significant but relatively small income effects and somewhat stronger effects of having a (non-Western) migration background, these effects are not significant in all cities. However, especially high-income households are more capable of avoiding exposure to indoor noise. Due to their residence characteristics and having the resources to maintain high standards of noise protection, these households have more capabilities to shield themselves against environmental bads in their neighbourhood. This supports the environmental shielding hypothesis.
Rivaroxaban and aspirin vs. aspirin alone in Asian compared with non-Asian patients with chronic coronary artery disease or peripheral arterial disease: the COMPASS trial
Authors: Hori Masatsugu , Zhu Jun , Liang Yan , Bhatt Deepak L , Bosch Jackie , Connolly Stuart J , Fox Keith A A , Maggioni Aldo , Yusuf Salim , Eikelboom John W 
Published: June 2022

Abstract

Aims
It is unknown whether Asian and non-Asian patients with atherosclerotic vascular disease derive similar benefits from long-term antithrombotic therapy.

Methods and results
In patients with chronic coronary artery disease (CAD) and/or peripheral artery disease (PAD) enrolled in The Cardiovascular Outcomes for People Using Anticoagulation Strategies trial, the effects of rivaroxaban 2.5 mg b.i.d. plus aspirin 100 mg o.d. were compared with those of aspirin 100 mg o.d. in Asian vs. non-Asian patients (race was self-identified). Asians (n = 4269) vs. non-Asians (n = 23 126) had similar rates of major adverse cardiovascular events (MACEs) (4.85% vs. 4.83%, P = 0.30) and modified International Society on Thrombosis and Haemostasis (ISTH) major bleeding (2.72% vs. 2.58%, P = 0.22), but higher rates of intracranial haemorrhage (ICH) (0.63% vs. 0.29%, P = 0.01) and minor bleeding (13.61% vs. 6.49%, P &lt; 0.001). In Asians vs. non-Asians, the combination of rivaroxaban and aspirin compared with aspirin alone produced consistent reductions in MACE [Asians: hazard ratio (HR): 0.64, 95% confidence interval (CI): 0.45–0.90; non-Asians: HR: 0.78, 95% CI: 0.67–0.90; P(heterogeneity) = 0.29], increases in modified ISTH major bleeding (Asians: HR 2.24, 95% CI: 1.40–3.58; non-Asians: HR: 1.60, 95% CI: 1.30–1.97; P = 0.20), and net clinical outcome (Asians: HR: 0.77, 95% CI: 0.56–1.05; non-Asians: HR: 0.81, 95% CI: 0.70–0.93, P = 0.78), but borderline higher rates of ICH (Asians: HR: 3.50, 95% CI: 0.98–12.56; non-Asians: HR: 0.81, 95% CI: 0.43, 1.53; P = 0.04).

Conclusion
Asian compared with non-Asian patients with chronic CAD and/or PAD have higher rates of ICH and minor bleeding. The combination of rivaroxaban and aspirin vs. aspirin alone produces similar effects for MACE, modified ISTH major bleeding, and net clinical outcome but may be associated with higher rates of ICH in Asian patients.
Polygenic risk score for ACE-inhibitor-associated cough based on the discovery of new genetic loci
Authors: Ghouse Jonas , Tragante Vinicius , Muhammad Ayesha , Ahlberg Gustav , Skov Morten W , Roden Dan M , Jonsdottir Ingileif , Andreasen Laura , Lundegaard Pia Rengtved , Trudsø Linea C , Banasik Karina , Brunak Søren , Ostrowski Sisse R ,   eMERGE consortium, Torp-Pedersen Christian , Pedersen Ole V , Sørensen Erik , Køber Lars , Iversen Kasper , Thorsteinsdottir Unnur , Thorgeirsson Gudmundur , Ullum Henrik , Gudbjartsson Daniel F , Mosley Jonathan D , Holm Hilma , Stefansson Kari , Bundgaard Henning , Olesen Morten Salling 
Published: June 2022

Abstract

Aims
To search for sequence variants associated with ACEi discontinuation and to test their association with ACEi-associated adverse drug reactions (ADRs).

Methods and results
A genome-wide association study (GWAS) on ACEi discontinuation was conducted, including 33 959 ACEi-discontinuers and 44 041 controls. Cases were defined as persons who switched from an ACEi treatment to an angiotensin receptor blocker. Controls were defined as persons who continued ACEi treatment for at least 1 year. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were computed for ACEi discontinuation risk by mixed model regression analysis. Summary statistics from the individual cohorts were meta-analyzed with a fixed-effects model. To test for association with specific ACEi-associated ADRs, any genome-wide significant (P &lt; 5 × 10-8) ACEi discontinuation variants was tested for association with ACEi-associated cough and angioedema. A polygenetic risk score (PRS) based on ACEi discontinuation GWAS data was constructed and tested for association with ACEi-associated cough and angioedema in two population-based samples. In total, seven genetic genome-wide loci were identified, of which six were previously unreported. The strongest association with ACEi discontinuation was at 20q13.3 (NTSR1; OR: 1.21; 95% CI: 1.17–1.24; P = 2.1 × 10–34). Five of seven lead variants were associated with ACEi-associated cough, whereas none were associated with ACEi-associated angioedema. The ACEi discontinuation PRS was associated with ACEi-associated cough in a dose–response manner but not with ACEi-associated angioedema. ACEi discontinuation was genetically correlated with important causes for cough, including gastro-esophageal reflux disease, allergic rhinitis, hay fever, and asthma, which indicates partly shared genetic underpinning between these traits.

Conclusion
This study showed the advantage of using prescription patterns to discover genetic links with ADRs. In total, seven genetic loci that associated with ACEi discontinuation were identified. There was evidence of a strong association between our ADR phenotype and ACEi-associated cough. Taken together, these findings increase insight into the pathophysiological processes that underlie ACEi-associated ADRs.