bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutational signature learning with supervised negative binomial non-negative matrix factorization
Authors: Lyu Xinrui , Garret Jean , Rätsch Gunnar , Lehmann Kjong-Van 
Published: May 2020

Abstract

Motivation
Understanding the underlying mutational processes of cancer patients has been a long-standing goal in the community and promises to provide new insights that could improve cancer diagnoses and treatments. Mutational signatures are summaries of the mutational processes, and improving the derivation of mutational signatures can yield new discoveries previously obscured by technical and biological confounders. Results from existing mutational signature extraction methods depend on the size of available patient cohort and solely focus on the analysis of mutation count data without considering the exploitation of metadata.

Results
Here we present a supervised method that utilizes cancer type as metadata to extract more distinctive signatures. More specifically, we use a negative binomial non-negative matrix factorization and add a support vector machine loss. We show that mutational signatures extracted by our proposed method have a lower reconstruction error and are designed to be more predictive of cancer type than those generated by unsupervised methods. This design reduces the need for elaborate post-processing strategies in order to recover most of the known signatures unlike the existing unsupervised signature extraction methods. Signatures extracted by a supervised model used in conjunction with cancer-type labels are also more robust, especially when using small and potentially cancer-type limited patient cohorts. Finally, we adapted our model such that molecular features can be utilized to derive an according mutational signature. We used APOBEC expression and MUTYH mutation status to demonstrate the possibilities that arise from this ability. We conclude that our method, which exploits available metadata, improves the quality of mutational signatures as well as helps derive more interpretable representations.

Availability and implementation
https://github.com/ratschlab/SNBNMF-mutsig-public.

Supplementary information
Supplementary data are available at Bioinformatics online.
Minimum Status, Matching and Domination of Graphs
Authors: Liang Caixia , Zhou Bo , Guo Haiyan 
Published: May 2020

Abstract
Given a graph, the status of a vertex is the sum of the distances between the vertex and all other vertices. The minimum status of a graph is the minimum of statuses of all vertices of this graph. We give a sharp upper bound for the minimum status of a connected graph with fixed order and matching number (domination number, respectively) and characterize the unique trees achieving the bound. We also determine the unique tree such that its minimum status is as small as possible when order and matching number (domination number, respectively) are fixed.
Shared decision-making in atrial fibrillation: patient-reported involvement in treatment decisions
Authors: Ali-Ahmed Fatima , Pieper Karen , North Rebecca , Allen Larry A , Chan Paul S , Ezekowitz Michael D , Fonarow Gregg C , Freeman James V , Go Alan S , Gersh Bernard J , Kowey Peter R , Mahaffey Kenneth W , Naccarelli Gerald V , Pokorney Sean D , Reiffel James A , Singer Daniel E , Steinberg Benjamin A , Peterson Eric D , Piccini Jonathan P , O’Brien Emily C 
Published: May 2020

Abstract

Aims
To determine the extent of shared decision-making (SDM), during selection of oral anticoagulant (OAC) and rhythm control treatments, in patients with newly diagnosed atrial fibrillation (AF).

Methods and results
We evaluated survey data from 1006 patients with new-onset AF enrolled at 56 US sites participating in the SATELLITE substudy of the Outcomes Registry for Better Informed Treatment of Atrial Fibrillation (ORBIT II). Patients completed surveys at enrolment and at 6-month follow-up. Patients were asked about who made their AF treatment decisions. Shared decision-making was classified as one that the patient felt was an autonomous decision or a shared decision with their healthcare provider (HCP). Approximately half of patients reported that their OAC treatment decisions were made entirely by their HCP. Compared with those reporting no SDM, patients reporting SDM for OAC were more often female (47.2% vs. 38.4%), while patients reporting SDM for rhythm control were more often male (62.2% vs. 57.6%). The most important factors cited by patients during decision-making for OAC were reducing stroke and bleeding risk, and their HCP’s recommendations. After adjustment, patients with self-reported understanding of OAC, and rhythm control options, had higher odds of having participated in SDM [odds ratio (OR) 2.54, confidence interval (CI): 1.75–3.68 and OR 2.36, CI: 1.50–3.71, both P ≤ 0.001, respectively].

Conclusion
Shared decision-making is not widely implemented in contemporary AF practice. Patient understanding about available therapeutic options is associated with a more than a two-fold higher likelihood of SDM, and may be a potential target for future interventions.
Percutaneous vs. surgical revascularization for patients with unprotected left main stenosis: a meta-analysis of 5-year follow-up randomized controlled trials
Authors: D’Ascenzo Fabrizio , De Filippo Ovidio , Elia Edoardo , Doronzo Mattia Paolo , Omedè Pierluigi , Montefusco Antonio , Pennone Mauro , Salizzoni Stefano , Conrotto Federico , Gallone Guglielmo , Angelini Filippo , Franchin Luca , Bruno Francesco , Boffini Massimo , Gaudino Mario , Rinaldi Mauro , De Ferrari Gaetano Maria 
Published: May 2020

Abstract

Aims
A 5-year survival of patients with unprotected left main (ULM) stenosis according to the choice of revascularization (percutaneous vs. surgical) remains to be defined.

Methods and results
Randomized controlled trials (RCTs) comparing percutaneous coronary intervention (PCI) vs. coronary artery bypass graft (CABG) with a follow-up of at least 5 years were included. All-cause death was the primary endpoint. MACCE [a composite endpoint of all-cause mortality, myocardial infarction (MI), stroke, and repeat revascularization] along with its single components and cardiovascular (CV) death were the secondary ones. Analyses were stratified according to the use of first- vs. last-generation coronary stents. Subgroup comparisons were performed according to SYNTAX score (below or above 33) and to age (using cut-offs of each trial’s subgroup analysis). Four RCTs with 4394 patients were identified: 2197 were treated with CABG, 657 with first generation, and 1540 with last-generation stents. At 5-year rates of all-cause death did not differ [odds ratio (OR) 0.93, 95% confidence interval (CI) 0.71–1.21], as those of CV death and stroke. Coronary artery bypass graft reduced rates of MACCE (OR 0.69, 95% CI 0.60–0.79), mainly driven by MI (OR 0.48, 95% CI 0.36–0.65) and revascularization (OR 0.53, 95% CI 0.45–0.64). Benefit of CABG for MACCE was consistent, although with different extent, across values of SYNTAX score (OR 0.76, 95% CI 0.59–0.97 for values &lt; 32 and OR 0.63, 95% CI 0.47–0.84 for values ≥ 33) while was not evident for ‘younger’ patients (OR 0.83, 95% CI 0.65–1.07 vs. OR 0.65, 95% CI 0.51–0.84 for ‘older’ patients).

Conclusion
For patients with ULM disease followed-up for 5 years, no significant difference was observed in all-cause and cardiovascular death between PCI and CABG. Coronary artery bypass graft reduced risk of MI, revascularization, and MACCE especially in older patients and in those with complex coronary disease and a high SYNTAX score.
Exploring Online Discussions Through an Academic Literacies Approach
Authors: Roose Tamara Mae , Newell George E 
Published: May 2020

AbstractThis preliminary study explores how international students bring their cultural knowledge and experiences into relationship with other writers’ ideas as they engage in an online discussion in response to a news text. This article focuses on a language excerpt from an online discussion group, including the assignment prompt, reading text, student responses, and comments to one another within a university ESL composition course. An intertextual analysis suggests that students’ engagement with multiple texts in this dialogic space and the integration of their own cultural resources led to socially constructed learning, relationship building, and a deepened understanding of the source text. This study extends the conversation in Academic Literacies research by illustrating how the construct can be used as a design frame for teaching an academic practice (writing about text) while also deliberately incorporating ways for students to draw upon their cultural identities and resources.
Advancing knowledge on social capital for young people’s mental health
Authors: Morgan Antony , Svedberg Petra , Nyholm Maria , Nygren Jens 
Published: May 2020

SummaryInequalities in young people’s mental health have been documented according to social class but less is known about determinants that can buffer or mediate the relationship. Social capital has the potential to contribute to alleviating observed health inequalities. However, clarity about how it can be understood and measured in relation to mental health among younger populations remains inconsistent. This scoping review examined published literature to investigate how social capital has been researched for young people’s mental health. An established framework was used to guide the methodology. Studies were included: on age (10–19 years); publication year (since 2000); language (English). Only studies using social capital as a central theme were included. No restriction was placed on mental health outcomes. Nine bibliographic databases were interrogated. Articles (1541) were screened, 793 retained for analysis and 73 articles were included. Most studies were conducted in North America and Europe. Twenty per cent provided insights into how social capital should be described in relation to young people. A majority of the studies provided links between varying social capital indicators and a range of mental health outcomes (70%), however such evidence was associational. Only few studies inferred the causal direction between social capital and health (10%) and there were no dedicated studies on measurement. Findings suggest that literature on social capital and young people’s mental health has grown but continues to be variously described and measured. It requires better utilization of existing knowledge and new research to improve its application in practice.
Self-management strategies to consider to combat endometriosis symptoms during the COVID-19 pandemic
Authors: Leonardi Mathew , Horne Andrew W , Vincent Katy , Sinclair Justin , Sherman Kerry A , Ciccia Donna , Condous George , Johnson Neil P , Armour Mike 
Published: May 2020

ABSTRACTThe care of patients with endometriosis has been complicated by the coronavirus disease 2019 (COVID-19) pandemic. Medical and allied healthcare appointments and surgeries are being temporarily postponed. Mandatory self-isolation has created new obstacles for individuals with endometriosis seeking pain relief and improvement in their quality of life. Anxieties may be heightened by concerns over whether endometriosis may be an underlying condition that could predispose to severe COVID-19 infection and what constitutes an appropriate indication for presentation for urgent treatment in the epidemic. Furthermore, the restrictions imposed due to COVID-19 can impose negative psychological effects, which patients with endometriosis may be more prone to already. In combination with medical therapies, or as an alternative, we encourage patients to consider self-management strategies to combat endometriosis symptoms during the COVID-19 pandemic. These self-management strategies are divided into problem-focused and emotion-focused strategies, with the former aiming to change the environment to alleviate pain, and the latter address the psychology of living with endometriosis. We put forward this guidance, which is based on evidence and expert opinion, for healthcare providers to utilize during their consultations with patients via telephone or video. Patients may also independently use this article as an educational resource. The strategies discussed are not exclusively restricted to consideration during the COVID-19 pandemic. Most have been researched before this period of time and all will continue to be a part of the biopsychological approach to endometriosis long after COVID-19 restrictions are lifted.
Clinical Characteristics of Patients With Coronavirus Disease 2019 in Japan: A Single-Center Case Series
Authors: Kobayashi Ken-ichiro , Kaki Takahiro , Mizuno Shinsuke , Kubo Kenji , Komiya Nobuhiro , Otsu Satoko 
Published: May 2020

Abstract
We report a case series of 6 patients with confirmed coronavirus disease 2019 (COVID-19) in Wakayama prefecture, Japan. All 6 of the patients tested positive via pharyngeal swab polymerase chain reaction (PCR) tests, and 2 of the 6 were still positive at 3 weeks after onset. All of the patients exhibited bilateral ground glass opacities on computed tomography (CT). This article also reports narrative information on the spectrum of symptoms collected directly from the patients. It would be difficult to triage patients with COVID-19 based on the typical symptoms of fever and/or cough, although PCR and CT are definitive in diagnosis.
Self-perceived competence and training needs analysis on antimicrobial stewardship among government ward pharmacists in Malaysia
Authors: Teoh Cherh Yun , Mhd. Ali Adliah , Mohamed Shah Noraida , Hassan Rohana , Lau Chee Lan 
Published: May 2020

Abstract

Background
There is a paucity of data on pharmacists’ competency and learning needs in antimicrobial stewardship (AMS).

Objectives
To identify and prioritize learning needs based on self-perceived competence of ward pharmacists in AMS, to identify predictors of self-perceived competence, learning methods in AMS and perceived barriers to learning.

Methods
A cross-sectional survey involving ward pharmacists from Hospital Canselor Tuanku Muhriz (HCTM) and hospitals under the Ministry of Health was conducted from May to July 2018.

Results
A total of 553 ward pharmacists from 67 hospitals responded to this survey (71.3% response rate). Knowledge of infections, antimicrobials and AMS systems, confidence to advise on various issues relating to antimicrobial therapy and participation in clinical audit and evaluation were among the learning needs identified (median score 3.00). Meanwhile, knowledge on the epidemiology of infections, off-label use of antimicrobials and pharmacoeconomics relating to antimicrobials had lower median scores (2.00) and were thus prioritized as high learning needs. Significant predictors of self-perceived competence in AMS were: gender (P &lt; 0.001); prior specific training in infections and AMS (P &lt; 0.001); postgraduate degree (P &lt; 0.001); practising in the area of infectious disease (P &lt; 0.05); and years of working experience as a ward pharmacist (P &lt; 0.005). Continuing medical education, seminars, courses and workshops were the most common (78.1%) and preferred (84.6%) learning methods in AMS. Lack of appropriate training (67.8%), time (44.5%) and funding (42.5%) topped the list of barriers to learning in AMS.

Conclusions
Findings in this study suggest the need to establish and intensify standardized training in AMS among government ward pharmacists.
Predicting the thickness of sand strata in a sand-shale interbed reservoir based on seismic facies analysis
Authors: Li Huilin , Gao Rui , Wang Yanghua 
Published: May 2020

Abstract
Seismic facies analysis is of great significance for the detection of residual oil in a sand-shale interbed reservoir. In this study, we propose to predict spatial distribution of sand thickness over a reservoir, based on seismic facies analysis. The target reservoir is a thin sand-shale interbed layer, and the layer thickness varies between 2 and 10 m. The thickness of sand strata within the reservoir layer appears to have a fragmentary distribution in lateral space. Thin thickness and fragmentary distribution are two factors that cause difficulty in sand thickness prediction. To tackle this problem, this study adopted a three-stage strategy. First, the reservoir over the entire study area was classified into five different lithofacies, following sedimentary microfacies analysis against the characteristics of gamma-ray logging data, and the corresponding seismic responses were meticulously depicted. Then, exploiting these seismic responses, or seismic facies, the spatial distribution of the gamma-ray values was evaluated within the thin sand-shale interbed reservoir. Finally, the spatial distribution of the sand thickness was predicted according to the spatial distribution of the gamma-ray values. The prediction was conducted independently for each seismic facies, rather than in a non-discriminatory manner. Comparing the prediction to the actual evaluation derived from well-logging data demonstrated that the thickness distribution resulting from seismic data has a high accuracy, because of the facies-based analysis.
Rebels and the Regime: The Politics of Civilian Victimization
Authors: Curtice Travis B 
Published: May 2020

AbstractRecent scholarship contends that during civil conflict rebels victimize civilians more when fighting democracies than authoritarian states. Yet to understand why rebels victimize civilians, it is important to consider when rebels target civilians and the severity of violence they use against civilians. Considering this distinction is critical to understanding the strategic calculus that rebels face while fighting states with varying regime types. By doing so, I argue that although civilian victimization by rebel groups is more likely in democracies, the count of civilians killed by rebels is higher when rebels fight autocracies. Employing a dataset of armed conflicts from 1989 to 2009 and a series of hurdle models, this study finds that rebel organizations fighting in authoritarian regimes are less likely to engage in civilian victimization; however, if they do use violence against civilians, the count of civilians targeted is higher.
Closed traumatic avulsion of both ring finger flexors with successful primary repair more than 4 weeks after injury and a review of the literature†
Authors: Johnson Miguel A , Colville James 
Published: May 2020

Abstract
Closed flexor digitorum profundus (FDP) tendon avulsions are a recognized injury in hand surgery. However, closed tendon avulsion of both flexor tendons in the same digit is rare, with the few cases reported in the literature and presented here. Management includes primary repair ideally within the first 2 weeks to achieve optimal outcome. While beyond 4 weeks a two-stage repair is the dictum, we present a case where both tendons were avulsed but primary repair of the FDP was possible more than 4 weeks after the injury, with a good outcome. This case highlights that primary tendon repair at 32 days, the longest noted in the literature in this group of patients, can result in a good outcome even if the injury is more than 4 weeks old. However, good intraoperative decision-making is key and the skillset must be present for conversion to a two-stage repair if necessary.
Urban coyotes are genetically distinct from coyotes in natural habitats
Authors: Adducci Anthony , Jasperse Jeremy , Riley Seth , Brown Justin , Honeycutt Rodney , Monzón Javier 
Published: May 2020

AbstractUrbanization is increasing throughout the world, transforming natural habitats. Coyotes (Canis latrans) are found in highly urban, suburban, rural and undeveloped mountainous habitats, making them an exemplary model organism to investigate the effects of urbanization on animals. We hypothesized that coyotes in natural habitats are more genetically related to distant coyotes in similar natural habitats and less related to coyotes in urban areas due to natal habitat-biased dispersal. We also hypothesized that increasing urbanization would result in decreased genetic diversity due to habitat fragmentation, dispersal barriers and genetic drift. We analyzed 10 microsatellite genetic markers from 125 individual coyotes sampled across a spectrum of highly urban to highly natural areas in southern California. Most coyotes clustered into four distinct genetic populations, whereas others appeared to have admixed ancestry. Three genetic populations were associated primarily with urban habitats in Los Angeles and Orange Counties. In contrast, the remaining population was associated with more naturally vegetated land near the surrounding mountains. Coyotes living in natural areas formed a genetically distinct cluster despite long geographic distances separating them. Genetic diversity was negatively associated with urban/suburban land cover and local road density, and positively associated with the relative amount of natural vegetation. These results indicate that genetic differentiation and loss of genetic diversity coincided with the extremely rapid expansion of Greater Los Angeles throughout the 1900s. Thus, urbanization reduces gene flow and erodes genetic diversity even in a habitat generalist thought to be minimally impacted by land development.
Leaving Hospital: A Step too Far for Risk-Based Regulation?
Authors: Moore Victoria L 
Published: May 2020

Abstract
Discharges from hospital are internationally recognised as a dangerous time in the care pathway of a patient, posing a risk to both their physical wellbeing and dignity. This article examines the effectiveness of risk-based regulation as a tool to address patient safety incidents linked to the hospital discharge process within the English National Health Service. It examines how the risk of this process is identified, conceptualised, and prioritised amongst the relevant statutory regulators, and argues that the risk is neither uniformly recognised by the statutory regulators within the English NHS, nor sufficiently addressed. Professional regulators in particular appear to have a poor awareness of the risk and their role in addressing it. Until these issues are resolved, patients leaving hospitals will continue to be exposed to patient safety incidents which should be avoidable.
What Would a Phenomenology of Logic Look Like?
Authors: Kinkaid James 
Published: May 2020

Abstract
The phenomenological movement begins in the Prolegomena to Husserl’s Logical Investigations as a philosophy of logic. Despite this, remarkably little attention has been paid to Husserl’s arguments in the Prolegomena in the contemporary philosophy of logic. In particular, the literature spawned by Gilbert Harman’s work on the normative status of logic is almost silent on Husserl’s contribution to this topic. I begin by raising a worry for Husserl’s conception of ‘pure logic’ similar to Harman’s challenge to explain the connection between logic and reasoning. If logic is the study of the forms of all possible theories, it will include the study of many logical consequence relations; by what criteria, then, should we select one (or a distinguished few) consequence relation(s) as correct? I consider how Husserl might respond to this worry by looking to his late account of the ‘genealogy of logic’ in connection with Gurwitsch’s claim that ‘[i]t is to prepredicative perceptual experience … that one must return for a radical clarification and for the definitive justification of logic’. Drawing also on Sartre and Heidegger, I consider how prepredicative experience might constrain or guide our selection of a logical consequence relation and our understanding of connectives like implication and negation.