bluuebunny/crossref_metadata_2025_split huggingface dataset:
TeraPCA: a fast and scalable software package to study genetic variation in tera-scale genotypes
Authors: Bose Aritra , Kalantzis Vassilis , Kontopoulou Eugenia-Maria , Elkady Mai , Paschou Peristera , Drineas Petros 
Published: April 2019

Abstract

Motivation
Principal Component Analysis is a key tool in the study of population structure in human genetics. As modern datasets become increasingly larger in size, traditional approaches based on loading the entire dataset in the system memory (Random Access Memory) become impractical and out-of-core implementations are the only viable alternative.

Results
We present TeraPCA, a C++ implementation of the Randomized Subspace Iteration method to perform Principal Component Analysis of large-scale datasets. TeraPCA can be applied both in-core and out-of-core and is able to successfully operate even on commodity hardware with a system memory of just a few gigabytes. Moreover, TeraPCA has minimal dependencies on external libraries and only requires a working installation of the BLAS and LAPACK libraries. When applied to a dataset containing a million individuals genotyped on a million markers, TeraPCA requires &lt;5 h (in multi-threaded mode) to accurately compute the 10 leading principal components. An extensive experimental analysis shows that TeraPCA is both fast and accurate and is competitive with current state-of-the-art software for the same task.

Availability and implementation
Source code and documentation are both available at https://github.com/aritra90/TeraPCA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Defining the Breakpoint Duration of Staphylococcus aureus Bacteremia Predictive of Poor Outcomes
Authors: Minejima Emi , Mai Nikki , Bui Nancy , Mert Melissa , Mack Wendy J , She Rosemary C , Nieberg Paul , Spellberg Brad , Wong-Beringer Annie 
Published: April 2019

Abstract

Background
Persistent Staphylococcus aureus bacteremia (SAB) is defined based on varying duration in literature. The primary objective was to determine the risk of poor outcomes in relation to bacteremia duration.

Methods
Multicenter, prospective, observational study of adult hospitalized patients with SAB. Medical records were reviewed for pertinent data. Patients were grouped by bacteremia duration: short (1–2 days), intermediate (3–6 days), and prolonged (≥7 days) and compared for risk factors and outcomes.

Results
Of 884 patients, 63% had short, 28% intermediate, and 9% prolonged bacteremia. Overall mean age was 57 years, and 70% were male. The prolonged group had the highest proportion of methicillin-resistant SAB (P &lt; .0001). Choice of antibiotic therapy did not significantly affect bacteremia duration; however, time to source-control procedure was delayed in the prolonged and intermediate groups compared with the short group (3.5 vs 3 vs 1 day, P &lt; .0001). Metastatic complications, length of stay, and 30-day mortality were progressively worse as bacteremia duration increased (P &lt; .0001). Every continued day of bacteremia was associated with a relative risk of death of 1.16 (95% confidence interval, 1.10–1.22; P &lt; .0001), with a significant increase in risk starting at 3 days as determined by receiver operating characteristic analysis.

Conclusions
Optimal management of SAB should target bacterial clearance as soon as possible to minimize incremental risk of mortality with each day of positive blood culture. Delay in source control but not type of antistaphylococcal therapy was significantly associated with prolonged bacteremia and worse outcomes.
Antiretroviral Drugs Associated With Subclinical Coronary Artery Disease in the Swiss Human Immunodeficiency Virus Cohort Study
Authors: Kovari Helen , Calmy Alexandra , Doco-Lecompte Thanh , Nkoulou René , Marzel Alex , Weber Rainer , Kaufmann Philipp A , Buechel Ronny R , Ledergerber Bruno , Tarr Philip E ,   Swiss Human Immunodeficiency Virus Cohort Study, Aubert V , Battegay M , Bernasconi E , Böni J , Braun D L , Bucher H C , Burton-Jeangros C , Calmy A , Cavassini M , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux C A , Gorgievski M , Günthard H , Haerry D , Hasse B , Hirsch H H , Hoffmann M , Hösli I , Kahlert C , Kaiser L , Keiser O , Klimkait T , Kouyos R , Kovari H , Ledergerber B , Martinetti G , Martinez de Tejada B , Marzolini C , Metzner K , Müller N , Nadal D , Nicca D , Pantaleo G , Rauch A , Rudin C , Schöni-Affolter F , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Vernazza P , Weber R , Yerly S 
Published: April 2019

Abstract

Background
Coronary artery disease (CAD) events have been associated with certain antiretroviral therapy (ART) agents. In contrast, the influence of ART on subclinical atherosclerosis is not clear. The study objective was to assess the association between individual ART agents and the prevalence and extent of subclinical CAD.

Methods
Coronary artery calcium (CAC) scoring and coronary computed tomography angiography (CCTA) were performed in ≥45-year-old Swiss Human Immunodeficiency Virus Cohort Study participants. The following subclinical CAD endpoints were analyzed separately: CAC score &gt;0, any plaque, calcified plaque, noncalcified/mixed plaque, segment involvement score (SIS), and segment severity score (SSS). Logistic regression models calculated by inverse probability of treatment weights (IPTW) were used to explore associations between subclinical CAD and cumulative exposure to the 10 most frequently used drugs.

Results
There were 403 patients who underwent CCTA. A CAC score &gt;0 was recorded in 188 (47%), any plaque in 214 (53%), calcified plaque in 151 (38%), and noncalcified/mixed plaque in 150 (37%) participants. A CAC score &gt;0 was negatively associated with efavirenz (IPTW adjusted odds ratio per 5 years 0.73, 95% confidence interval [CI] 0.56–0.96), tenofovir disoproxil fumarate (0.68, 95% CI 0.49–0.95), and lopinavir (0.64, 95% CI 0.43–0.96). Any plaque was negatively associated with tenofovir disoproxil fumarate (0.71, 95% CI 0.51–0.99). Calcified plaque was negatively associated with efavirenz (0.7, 95% CI 0.57–0.97). Noncalcified/mixed plaque was positively associated with abacavir (1.46, 95% CI 1.08–1.98) and negatively associated with emtricitabine (0.67, 95% CI 0.46–0.99). For SSS and SIS, we found no association with any drug.

Conclusions
An increased risk of noncalcified/mixed plaque was only found in patients exposed to abacavir. Emtricitabine was negatively associated with noncalcified/mixed plaque, while tenofovir disoproxil fumarate and efavirenz were negatively associated with any plaque and calcified plaque, respectively.
A Retrospective Cohort Study to Assess the Impact of an Inpatient Infectious Disease Telemedicine Consultation Service on Hospital and Patient Outcomes
Authors: Monkowski Daniel , Rhodes Luther V , Templer Suzanne , Kromer Sharon , Hartner Jessica , Pianucci Kimberly , Kincaid Hope 
Published: April 2019

Abstract

Background
Here, we review our experience of providing inpatient infectious disease (ID) consultations using real-time interactive telemedicine assessments. We sought to obtain a baseline and document trends regarding the use of telemedicine ID (teleID) consults as an adjunct to the standard of care through the time period in which teleID consultations were introduced.

Methods
Data were pulled via manual, retrospective chart reviews of the electronic medical record. Primary outcomes included lengths of stay (LOS), antibiotic usage, and relapse incidences.

Results
There were a total of 244 patients at 1 remote hospital site who were provided with ID consultations, either in person, via teleID, or both. Before the availability of teleID (pre-teleID), there were 73 patients transferred for ID consults, while 171 patients were seen via teleID once available. While all 73 patients in the pre-teleID group were transferred from the remote hospital to the hub hospital, only 14 (8.2%) of all remote hospital patients assessed by teleID were transferred. Patient LOS across both facilities decreased when patients were seen via teleID, compared to pre-teleID (P = .0001). The median number of days that patients received antibiotics decreased in the teleID group (median 15, interquartile range [IQR] 9–25), compared to the pre-teleID group (median 19, IQR 11–28), but this decrease was not statistically significant (P = .0770). There was no statistically significant difference in relapse rates, although data were lacking because of patients being lost to follow-up.

Conclusions
ID telemedicine practice directed at inpatients appears to be a promising route of care.
Celiprolol but not losartan improves the biomechanical integrity of the aorta in a mouse model of vascular Ehlers–Danlos syndrome
Authors: Dubacher Nicolo , Münger Justyna , Gorosabel Maria C , Crabb Jessica , Ksiazek Agnieszka A , Caspar Sylvan M , Bakker Erik N T P , van Bavel Ed , Ziegler Urs , Carrel Thierry , Steinmann Beat , Zeisberger Steffen , Meienberg Janine , Matyas Gabor 
Published: April 2019

AbstractAimsAntihypertensive drugs are included in the medical therapy of vascular Ehlers–Danlos syndrome (vEDS). The β-blocker celiprolol has been suggested to prevent arterial damage in vEDS, but the underlying mechanism remains unclear. It is also unknown whether the widely used angiotensin II receptor type 1 antagonist losartan has a therapeutic effect in vEDS. Here, we evaluated the impact of celiprolol and losartan on the biomechanical integrity of the vEDS thoracic aorta.Methods and resultsWe established a new approach to measure the maximum tensile force at rupture of uniaxially stretched murine thoracic aortic rings. In a vEDS model, which we (re-)characterized here at molecular level, heterozygous mice showed a significant reduction in the rupture force compared to wild-type mice, reflecting the increased mortality due to aortic rupture. For the assessment of treatment effects, heterozygous mice at 4 weeks of age underwent a 4-week treatment with celiprolol, losartan, and, as a proof-of-concept drug, the matrix metalloproteinase inhibitor doxycycline. Compared to age- and sex-matched untreated heterozygous mice, treatment with doxycycline or celiprolol resulted in a significant increase of rupture force, whereas no significant change was detected upon losartan treatment.ConclusionsIn a vEDS model, celiprolol or doxycycline, but not losartan, can improve the biomechanical integrity of the aortic wall, thereby potentially reducing the risk of dissection and rupture. As doxycycline is a broad-spectrum antibiotic with considerable side effects, celiprolol may be more suitable for a long-term therapy and thus rather indicated for the medication of patients with vEDS.
Prevalence of type III arch configuration in patients with type B aortic dissection
Authors: Marrocco-Trischitta Massimiliano M , Rylski Bartosz , Schofer Florian , Secchi Francesco , Piffaretti Gabriele , de Beaufort Hector , Belvroy Viony , Bismuth Jean , Czerny Martin , Trimarchi Santi 
Published: April 2019

Abstract

OBJECTIVES
Type III aortic arch configuration consistently presents anatomical and biomechanical characteristics which have been associated with an increased risk of type B aortic dissection (TBD). Our aim was to investigate the prevalence of type III arch in patients with TBD and type B intramural haematoma (IMH-B).

METHODS
A multicentre retrospective analysis was performed on patients with TBD and IMH-B observed between 2002 and 2017. The computed tomographic images were reviewed to identify the type of aortic arch. Exclusion criteria included previous arch surgery, presence of aortic dissection or aneurysm proximal to the left subclavian artery and bovine arches. An ad hoc systematic literature review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines to assess the prevalence of type III arch in non-TBD and non-aneurysmal patients.

RESULTS
Two hundred and sixty-one patients with TBD/IMH-B were found to be suitable for the study and were stratified according to aortic arch classification. The ad hoc literature search provided 10 relevant articles, from which a total of 7983 control cases were retrieved. TBD/IMH-B patients were significantly younger than controls [64.3, standard error: 0.74 (62.84–65.76) vs mean pooled age 70.5, standard error: 0.40 (69.71–71.28)]. Patients with TBD/IMH-B presented with a significantly higher prevalence of type III arch [41.0% (107/261) (35.2–47.1)] than controls [16% (1241/7983) (10–22)].

CONCLUSIONS
Our data indicate an association between type III arch configuration and the occurrence of TBD/IMH-B. These findings warrant further studies to disclose the potential role of type III arch configuration as an anatomical risk factor for TBD/IMH-B.
In situ skeletonized bilateral thoracic artery for left coronary circulation: a 20-year experience
Authors: Bonacchi Massimo , Prifti Edvin , Bugetti Marco , Cabrucci Francesco , Cresci Michael , Lucá Fabiana , Parise Orlando , Matteucci Francesco , Sani Guido , Johnson Daniel M , Gelsomino Sandro 
Published: April 2019

Abstract

OBJECTIVES
Our goal was to analyse the outcomes in a patient population using a standardized technique for coronary artery bypass grafting (CABG) consisting of total arterial myocardial revascularization utilizing the in situ skeletonized bilateral thoracic artery for left coronary circulation. We also explored potential predictors of long-time unfavourable outcomes.

METHODS
Patients undergoing total arterial myocardial revascularization using in situ skeletonized bilateral thoracic artery for left coronary circulation between January 1997 and May 2017 were included prospectively in this study. The median follow-up (100% complete) was 103 months (interquartile range 61–189 months) and ranged from 1 to 245 months.

RESULTS
A total of 1325 consecutive patients were recruited. During the follow-up period, there were 131 deaths (9.8%), 146 repeat revascularizations (11.0%) and 229 major adverse cardiac events (17.2%). The 18-year freedom from major adverse cardiac events was 62.6 ± 9.3%, 62.5 ± 6.3% and 53.9 ± 11.0%, respectively. Multivariable models showed that a left ventricular ejection fraction ≤35%, chronic obstructive pulmonary disease, peripheral vascular disease (P &lt; 0.001), chronic kidney disease and age ≥80 years (P = 0.002) were independent predictors of diminished long-term survival. Moreover, peripheral vascular disease and off-pump coronary artery bypass (both, P &lt; 0.001) predicted repeat revascularization. Finally, age ≥80 years, peripheral vascular disease, left ventricular ejection fraction ≤35%, off-pump coronary artery bypass and chronic pulmonary obstructive disease were independent predictors of major adverse cardiac events during the long-term follow-up period (all, P &lt; 0.001).

CONCLUSIONS
Coronary artery bypass using the in situ skeletonized bilateral thoracic artery for left coronary circulation configuration for total arterial myocardial revascularization resulted in satisfactory long-term results with a low incidence of death and late events and may represent a technique of choice in selected patients having CABG. Larger and long-term prospective studies are, however, warranted.
Does volunteer community health work empower women? Evidence from Ethiopia’s Women’s Development Army
Authors: Closser Svea , Napier Harriet , Maes Kenneth , Abesha Roza , Gebremariam Hana , Backe Grace , Fossett Sarah , Tesfaye Yihenew 
Published: April 2019

AbstractOf the millions of Community Health Workers (CHWs) serving their communities across the world, there are approximately twice as many female CHWs as there are male. Hiring women has in many cases become an ethical expectation, in part because working as a CHW is often seen as empowering the CHW herself to enact positive change in her community. This article draws on interviews, participant observation, document review and a survey carried out in rural Amhara, Ethiopia from 2013 to 2016 to explore discourses and experiences of empowerment among unpaid female CHWs in Ethiopia’s Women’s Development Army (WDA). This programme was designed to encourage women to leave the house and gain decision-making power vis-à-vis their husbands—and to use this power to achieve specific, state-mandated, domestically centred goals. Some women discovered new opportunities for mobility and self-actualization through this work, and some made positive contributions to the health system. At the same time, by design, women in the WDA had limited ability to exercise political power or gain authority within the structures that employed them, and they were taken away from tending to their individual work demands without compensation. The official rhetoric of the WDA—that women’s empowerment can happen by rearranging village-level social relations, without offering poor women opportunities like paid employment, job advancement or the ability to shape government policy—allowed the Ethiopian government and its donors to pursue ‘empowerment’ without investments in pay for lower-level health workers, or fundamental freedoms introduced into state-society relations.
Genome-wide analysis revealed sex-specific gene expression in asthmatics
Authors: Gautam Yadu , Afanador Yashira , Abebe Tilahun , López Javier E , Mersha Tesfaye B 
Published: April 2019

Abstract
Global gene-expression analysis has shown remarkable difference between males and females in response to exposure to many diseases. Nevertheless, gene expression studies in asthmatics have so far focused on sex-combined analysis, ignoring inherent variabilities between the sexes, which potentially drive disparities in asthma prevalence. The objectives of this study were to identify (1) sex-specific differentially expressed genes (DEGs), (2) genes that show sex-interaction effects and (3) sex-specific pathways and networks enriched in asthma risk. We analyzed 711 males and 689 females and more than 2.8 million transcripts covering 20 000 genes leveraged from five different tissues and cell types (i.e. epithelial, blood, induced sputum, T cells and lymphoblastoids). Using tissue-specific meta-analysis, we identified 439 male- and 297 female-specific DEGs in all cell types, with 32 genes in common. By linking DEGs to the genome-wide association study (GWAS) catalog and the lung and blood eQTL annotation data from GTEx, we identified four male-specific genes (FBXL7, ITPR3 and RAD51B from epithelial tissue and ALOX15 from blood) and one female-specific gene (HLA-DQA1 from epithelial tissue) that are disregulated during asthma. The hypoxia-inducible factor 1 signaling pathway was enriched only in males, and IL-17 and chemokine signaling pathways were enriched in females. The cytokine–cytokine signaling pathway was enriched in both sexes. The presence of sex-specific genes and pathways demonstrates that sex-combined analysis does not identify genes preferentially expressed in each sex in response to diseases. Linking DEG and molecular eQTLs to GWAS catalog represents an important avenue for identifying biologically and clinically relevant genes.
Minimizing the risk for left ventricular rupture during transcatheter aortic valve implantation by reducing the presence of stiff guidewires in the ventricle
Authors: Nielsen Niels Erik , Baranowska Julia , Bramlage Peter , Baranowski Jacek 
Published: April 2019

Abstract

OBJECTIVES
The presence of a stiff guidewire in the apex of the left ventricle (LV) is a known risk factor for LV perforation. Our goal was to minimize the risk of LV rupture during transcatheter aortic valve implantation (TAVI) by omitting the interaction between the stiff guidewire and the LV apex using a modified procedure.

METHODS
A TAVI protocol designed to allow minimal interaction between a stiff guidewire and the LV was developed in Linköping University Hospital in Sweden. A total of 316 patients were treated exclusively by this approach between March 2014 and May 2018.

RESULTS
All procedures were completed successfully. There were no cases (0%) of ventricular perforation. Only 1 patient (0.3%) had a pericardial effusion, and it was due to annulus rupture. There was 1 case of acute kidney injury (0.3%). Five patients (1.6%) required a new permanent pacemaker. Stroke occurred in 3 patients (0.9%). No patient had valve embolization. Vascular complications were experienced by 6 patients (1.9%). A mild paravalvular leak occurred in 27 (8.5%) patients. At 30 days post-TAVI, 6 patients (2%) had died. The mortality rate at 1 year was 8.6% (n = 20/232).

CONCLUSIONS
Our series shows that TAVI without the prolonged use of a stiff guidewire in the LV apex is feasible. The risk of LV perforation is eliminated by this approach, and other procedural complications are limited.
The Presidential Pardon of Fujimori: Political Struggles in Peru and the Subsidiary Role of the Inter-American Court of Human Rights
Authors: Cornejo Chavez Leiry , Pérez-León-Acevedo Juan-Pablo , García-Godos Jemima 
Published: April 2019

Abstract∞
In 2017, former Peruvian president Alberto Fujimori was pardoned after serving less than half of a 25-year sentence for human rights violations. The measure was taken amidst political turmoil and an impeachment process led by the Fujimorista party against former president Pedro Pablo Kuczynski. Fujimori’s victims in the Barrios Altos and La Cantuta cases requested the Inter-American Court of Human Rights (IACtHR) to annul the pardon due to its incompatibility with Peru’s human rights obligations. The IACtHR decided that it was for the Peruvian courts to exercise jurisdictional control over the pardon, thus affirming its subsidiary role. Through an examination of the political situation, the underlying principles of the IACtHR’s jurisprudence on amnesties, and rule of law and international standards, this article argues that the IACtHR had sufficient grounds to overturn the pardon. The court’s resolution to refer the matter to the Peruvian jurisdiction may be explained by an increasing awareness of its subsidiary role, particularly regarding sensitive political issues.
Inviolability Not Immunity
Authors: Weatherall Thomas 
Published: April 2019

Abstract
Recent proceedings involving former Sudanese President Omar Al-Bashir have highlighted a novel intersection of international and domestic law: the domestic execution of international arrest warrants for an incumbent high state official. While the overwhelming trend over the past decade has been for international and domestic courts to analyse this issue from the perspective of immunity, that approach is not sufficient. The domestic execution of an international arrest warrant presents a question of inviolability, not immunity. Although the immunity and inviolability enjoyed by incumbent high state officials under customary international law often apply coextensively, the two doctrines are distinct in function and scope. While immunity precludes the exercise of jurisdiction by a foreign court, it is inviolability that operates as a privilege from physical interference by domestic authorities. The arrest and surrender of incumbent high state officials is likely to persist as both an objective and a challenge for international courts. If they are to succeed in this regard, international courts must account for why the privilege of inviolability does not bar the execution of international arrest warrants.