bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations of Genetic Factors, Educational Attainment, and Their Interaction With Kidney Function Outcomes
Authors: Thio Chris H L , van Zon Sander K R , van der Most Peter J , Snieder Harold , Bültmann Ute , Gansevoort Ron T 
Published: October 2020

Abstract
Both genetic predisposition and low educational attainment (EA) are associated with higher risk of chronic kidney disease. We examined the interaction of EA and genetic risk in kidney function outcomes. We included 3,597 participants from the Prevention of Renal and Vascular End-Stage Disease Cohort Study, a longitudinal study in a community-based sample from Groningen, the Netherlands (median follow-up, 11 years; 1997–2012). Kidney function was approximated by obtaining estimated glomerular filtration rate (eGFR) from serum creatinine and cystatin C. Individual longitudinal linear eGFR trajectories were derived from linear mixed models. Genotype data on 63 single-nucleotide polymorphisms, with known associations with eGFR, were used to calculate an allele-weighted genetic score (WGS). EA was categorized into high, medium, and low. In ordinary least squares analysis, higher WGS and lower EA showed additive effects on reduced baseline eGFR; the interaction term was nonsignificant. In analysis of eGFR decline, the significant interaction term suggested amplification of genetic risk by low EA. Adjustment for known renal risk factors did not affect our results. This study presents the first evidence of gene-environment interaction between EA and a WGS for eGFR decline and provides population-level insights into the mechanisms underlying socioeconomic disparities in chronic kidney disease.
Dormancy and germination of the trimorphic achenes of a cold desert annual: spreading the risk over time
Authors: Lu Juanjuan , Dong Wenjing , Tan Dunyan , Baskin Carol C , Baskin Jerry M 
Published: October 2020

Abstract
Many studies have been done on the relationship between variation in morphology, dispersal ability and degree of dormancy of heterocarpic species with dimorphic diaspores. However, there are far fewer such studies on species that produce trimorphic diaspores. Our aim was to compare dormancy and germination of achenes from peripheral, intermediate and central positions in the capitulum of the diaspore-trimorphic cold desert annual Asteraceae species Heteracia szovitsii, an important component of plant communities in the cold deserts of NW China. Dormancy breaking/germination responses of the three achene morphs and of seeds isolated from the pericarp were tested in the laboratory using standard procedures, and seedling emergence phenology of the achene morphs was monitored under natural cold desert temperature conditions in an experimental garden with and without supplemental watering. Depth of dormancy of the three achene morphs was peripheral &gt; intermediate &gt; central. Seedlings from the three morphs emerged in spring and in autumn. Cumulative seedling emergence percentage from achenes during 47 months of burial was central &gt; intermediate &gt; peripheral. Central achene morphs emerged over a period of ~12 months after sowing, while intermediate and peripheral achene morphs did so for ~40 and 47 months, respectively. Thus, H. szovitsii exhibits a temporal dispersal strategy. No viable central or intermediate achene morphs were present after 16 and 40 months, respectively, but ~60 % of the non-emerged peripheral achenes morphs were viable after 47 months. Based on our results on diaspore dormancy and those of a previous study of diaspore spatial dispersal of H. szovitsii, we conclude that this species has a high–intermediate–low risk diaspore dispersal/dormancy strategy that likely increases the chances for population persistence over time and space.
Conditional out-of-distribution generation for unpaired data using transfer VAE
Authors: Lotfollahi Mohammad , Naghipourfar Mohsen , Theis Fabian J , Wolf F Alexander 
Published: October 2020

Abstract

Motivation
While generative models have shown great success in sampling high-dimensional samples conditional on low-dimensional descriptors (stroke thickness in MNIST, hair color in CelebA, speaker identity in WaveNet), their generation out-of-distribution poses fundamental problems due to the difficulty of learning compact joint distribution across conditions. The canonical example of the conditional variational autoencoder (CVAE), for instance, does not explicitly relate conditions during training and, hence, has no explicit incentive of learning such a compact representation.

Results
We overcome the limitation of the CVAE by matching distributions across conditions using maximum mean discrepancy in the decoder layer that follows the bottleneck. This introduces a strong regularization both for reconstructing samples within the same condition and for transforming samples across conditions, resulting in much improved generalization. As this amount to solving a style-transfer problem, we refer to the model as transfer VAE (trVAE). Benchmarking trVAE on high-dimensional image and single-cell RNA-seq, we demonstrate higher robustness and higher accuracy than existing approaches. We also show qualitatively improved predictions by tackling previously problematic minority classes and multiple conditions in the context of cellular perturbation response to treatment and disease based on high-dimensional single-cell gene expression data. For generic tasks, we improve Pearson correlations of high-dimensional estimated means and variances with their ground truths from 0.89 to 0.97 and 0.75 to 0.87, respectively. We further demonstrate that trVAE learns cell-type-specific responses after perturbation and improves the prediction of most cell-type-specific genes by 65%.

Availability and implementation
The trVAE implementation is available via github.com/theislab/trvae. The results of this article can be reproduced via github.com/theislab/trvae_reproducibility.
ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq data
Authors: Smolander Johannes , Junttila Sini , Venäläinen Mikko S , Elo Laura L 
Published: October 2020

Abstract

Motivation
Single-cell RNA-seq allows researchers to identify cell populations based on unsupervised clustering of the transcriptome. However, subpopulations can have only subtle transcriptomic differences and the high dimensionality of the data makes their identification challenging.

Results
We introduce ILoReg, an R package implementing a new cell population identification method that improves identification of cell populations with subtle differences through a probabilistic feature extraction step that is applied before clustering and visualization. The feature extraction is performed using a novel machine learning algorithm, called iterative clustering projection (ICP), that uses logistic regression and clustering similarity comparison to iteratively cluster data. Remarkably, ICP also manages to integrate feature selection with the clustering through L1-regularization, enabling the identification of genes that are differentially expressed between cell populations. By combining solutions of multiple ICP runs into a single consensus solution, ILoReg creates a representation that enables investigating cell populations with a high resolution. In particular, we show that the visualization of ILoReg allows segregation of immune and pancreatic cell populations in a more pronounced manner compared with current state-of-the-art methods.

Availability and implementation
ILoReg is available as an R package at https://bioconductor.org/packages/ILoReg.

Supplementary information
Supplementary data are available at Bioinformatics online.
The political economy of and practical policies for inclusive growth—a case study of Scotland
Authors: Houston Donald , Varna Georgiana , Docherty Iain 
Published: October 2020

AbstractThe concept of ‘inclusive growth’ (IG) is discussed in a political economy framework. The article reports comparative analysis of economic and planning policy documents from Scotland, England and the UK and findings from expert workshops held in Scotland, which identify four key policy areas for ‘inclusive growth’: skills, transport and housing for young people; city-regional governance; childcare; and place-making. These policies share with the ‘Foundational Economy’ an emphasis on everyday infrastructure and services, but add an emphasis on inter-generational justice and stress the importance of community empowerment as much as re-municipalisation. Factors enabling IG policy development include: the necessary political powers; a unifying political discourse and civic institutions; and inclusive governance and participatory democracy.
An Efficient Algorithm to Extract Control Flow-Based Features for IoT Malware Detection
Authors: Nghi Phu Tran , Dai Tho Nguyen , Huy Hoang Le , Ngoc Toan Nguyen , Ngoc Binh Nguyen 
Published: October 2020

Abstract
Control flow-based feature extraction method has the ability to detect malicious code with higher accuracy than traditional text-based methods. Unfortunately, this method has been encountered with the NP-hard problem, which is infeasible for the large-sized and high-complexity programs. To tackle this, we propose a control flow-based feature extraction dynamic programming algorithm for fast extraction of control flow-based features with polynomial time O($N^{2}$), where N is the number of basic blocks in decompiled executable codes. From the experimental results, it is demonstrated that the proposed algorithm is more efficient and effective in detecting malware than the existing ones. Applying our algorithm to an Internet of Things dataset gives better results on three measures: Accuracy = 99.05%, False Positive Rate = 1.31% and False Negative Rate = 0.66%.
Kawasaki disease: case report of a diagnostic dilemma and often a missed diagnosis
Authors: Bin Jawaid Zaib , Du Jin Ling , Iqbal Sohail , Zhang Lei 
Published: October 2020

Abstract

Background
Management of cardiovascular sequelae to Kawasaki disease (KD) is challenging to adult cardiologists. Vasculitis of medium-sized arteries especially coronary arteries often leads to focal intimal thickening and aneurysmal dilatation of one or more coronary arteries. It needs special attention to recognize coronary artery involvement because of potential long-term morbidity and mortality. We present a case of diagnostic dilemma in young adult Chinese male with KD.

Case summary
This asymptomatic patient was found to have deep Q waves in anterior leads on screening electrocardiography and was thought to have myocarditis after depiction of wall motion abnormality on echocardiography, later to be confirmed to have left anterior descending artery (LAD) territory infarct on cardiac magnetic resonance imaging. Coronary computed tomography angiogram depicted proximal LAD aneurysm with calcified plaque/thrombus. Additionally, there was an 18 mm giant right coronary artery (RCA) aneurysm with braid-like appearance and soft plaque (mural thrombus). His previous medical history included fever and cervical lymphadenopathy. Because of the high risk he was commenced on long-term low-dose aspirin and β-adrenergic-blocking agent to reduce myocardial oxygen consumption; however, 3 years later, he presented to the emergency department with acute inferior myocardial infarction. He was noted to have total occlusion of the proximal RCA and was treated aggressively with thrombectomy and percutaneous balloon angioplasty followed by medical management with β-blockers, sacubitril/valsartan, clopidogrel, and rivaroxaban without subsequent adverse cardiovascular events.

Discussion
Kawasaki disease is one of the main causes of coronary artery disease in young adults and can be easily overlooked.
Thoracic endovascular aortic repair for aortobronchial fistula: a case series
Authors: Vijayvergiya Rajesh , Kasinadhuni Ganesh , Revaiah Pruthvi C , Lal Anupam , Sharma Ashish , Kumar Rupesh 
Published: October 2020

Abstract

Background
Aortobronchial fistula (ABF) formation following the rupture of thoracic pseudoaneurysm is a rare clinical entity. Its aetiology includes atherosclerosis, infections, trauma, post-surgery, and post-endovascular aortic repair. The clinical presentation of ABF includes intermittent or massive haemoptysis, acute respiratory distress, hypotension, and even death. These patients require an emergency aortic intervention to stop active haemorrhage. Thoracic endovascular aortic repair (TEVAR) is a less invasive, safe, and effective treatment compared to conventional open surgical repair

Case summary
We hereby report three cases of ruptured descending thoracic aortic pseudoaneurysms resulting in a fistula formation. The first two cases had tuberculosis as their underlying aetiology, while the third case was the result of previous open post-aortic surgery. All patients presented with massive haemoptysis and were successfully treated by emergency TEVAR and had favourable outcomes.

Discussion
Thoracic endovascular aortic repair is a rapid, less invasive, and effective treatment for emergency management of ABF. It has more than 85% technical success rates in the reported literature. We had procedural success in all three cases. The short and midterm outcome of ABF following TEVAR is favourable and encouraging.
COVID-19 and ST elevations–keep an open mind: a case report
Authors: Kendall Michael R , Reddy Sridhar M , Meinke Laura E , Acharya* Deepak 
Published: October 2020

Abstract

Background
Coronavirus disease 2019 (COVID-19) has been associated with a range of cardiovascular manifestations, including myocardial injury and thrombo-embolism. Pulmonary embolism (PE) causing anteroseptal/anterior ST elevations that mimic myocardial infarction have previously been described. This phenomenon is thought to be related to right ventricular injury from large emboli.

Case summary
A 48-year-old woman with history of type 2 diabetes mellitus and hypertension presented to her local hospital with fever, cough, nausea, and dyspnoea. A test for SARS-CoV-2 was taken, and she was discharged with instructions to self-quarantine. She was subsequently notified of a positive SARS-CoV-2 result. Three days later, she re-presented with worsening dyspnoea and respiratory failure requiring intubation. On hospital Day 6, she became acutely hypoxic and hypotensive. Telemetry was noted to have ST changes, prompting ECG that revealed sinus tachycardia with prominent new ST elevations in her precordial leads. Transthoracic echocardiogram showed normal left ventricular function; however, the right ventricle was moderately dilated with positive McConnell’s sign. Due to her unstable clinical state and high suspicion for PE, she was treated with tenecteplase 50 mg i.v. with complete resolution of her ST elevations and improved oxygenation.

Discussion
Given the high rates of thrombo-embolic events in COVID-19 patients, PE should be in the differential diagnosis of ST elevation, particularly in younger patients with few risk factors for coronary artery disease.
Frailty of Māori, Pasifika, and Non-Māori/Non-Pasifika Older People in New Zealand: A National Population Study of Older People Referred for Home Care Services
Authors: Abey-Nesbit Rebecca , Peel Nancye M , Matthews Hector , Hubbard Ruth E , Nishtala Prasad S , Bergler Ulrich , Deely Joanne M , Pickering John W , Schluter Philip J , Jamieson Hamish A 
Published: October 2020

Abstract

Background
Little is known about the prevalence of frailty in indigenous populations. We developed a frailty index (FI) for older New Zealand Māori and Pasifika who require publicly funded support services.

Methods
An FI was developed for New Zealand adults aged 65 and older who had an interRAI Home Care assessment between June 1, 2012 and October 30, 2015. A frailty score for each participant was calculated by summing the number of deficits recorded and dividing by the total number of possible deficits. This created a FI with a potential range from 0 to 1. Linear regression models for FIs with ethnicity were adjusted for age and sex. Cox proportional hazards models were used to assess the association between the FI and mortality for Māori, Pasifika, and non-Māori/non-Pasifika.

Results
Of 54 345 participants, 3096 (5.7%) identified as Māori, 1846 (3.4%) were Pasifika, and 49 415 (86.7%) identified as neither Māori nor Pasifika. New Zealand Europeans (48 178, 97.5%) constituted most of the latter group. Within each sex, the mean FIs for Māori and Pasifika were greater than the mean FIs for non-Māori and non-Pasifika, with the difference being more pronounced in women. The FI was associated with mortality (Māori subhazard ratio [SHR] 2.53, 95% CI 1.63–3.95; Pasifika SHR 6.03, 95% CI 3.06–11.90; non-Māori and non-Pasifika SHR 2.86, 95% CI 2.53–3.25).

Conclusions
This study demonstrated differences in FI between the ethnicities in this select cohort. After adjustment for age and sex, increases in FI were associated with increased mortality. This suggests that FI is predictive of poor outcomes in these ethnic groups.
Recovery From Mobility Limitation in Middle-Aged African Americans: The Jackson Heart Study
Authors: Odden Michelle C , Sims Kendra D , Thorpe Roland J , Sims Mario , Dhamoon Mandip , Min Yuan-I , Correa Adolfo 
Published: October 2020

Abstract

Background
Despite evidence that African Americans shoulder a high burden of mobility limitation, little is known about factors associated with recovery.

Method
Participants from the Jackson Heart Study underwent 3 in-person exams from 2000 to 2013. Mobility limitations were assessed over this period by self-reported limitations in walking half a mile or climbing stairs during annual phone calls. The outcome of interest, recovery from mobility limitation, was defined as no mobility limitation the year following an incident event. Candidate predictor variables were assessed in logistic regression models, including sociodemographic, psychosocial, and health measures. Inverse probability weights were used to address missing data in the outcome.

Results
Among 4526 participants (mean [SD] age = 54.5 (12.8) years) without a mobility limitation at baseline, 1445 (32%) had an incident mobility limitation over 12 years of follow-up, and 709 (49%) reported recovery from mobility limitation by 1 year later. Low income and daily discrimination were associated with a lower likelihood of recovery even after adjustment for covariates. In adjusted models, greater comorbidity was associated with a lower likelihood of recovering (p-value for trend = .05). History of heart failure and cancer were associated with a lower likelihood of recovering from mobility limitation (OR: 0.52, 95% CI: 0.29, 0.94 and OR: 0.74, 95% CI: 0.55, 1.00). Adiposity, smoking status, and physical activity were not associated with recovery from mobility limitation.

Conclusion
Half of incident mobility limitations in this population of middle-aged African Americans were transient. Adverse sociodemographic factors and comorbidities were associated with lower likelihood of recovery.
Retooling the Health Care Workforce for an Aging America: A Current Perspective
Authors: Foley Kevin T , Luz Clare C 
Published: October 2020

Abstract
A 2008 Institute of Medicine (IoM) report outlined a vision for health care and a workforce capable of addressing health and extended care needs of our aging population. It highlighted dramatic shortages necessitating bold action and outlined recommendations aimed at building a sizable and qualified workforce. This study updates report findings and progress made on its recommendations. Through review of publicly accessible, internet-based literature and government and professional organization websites, current workforce data and recent policy changes are compared to the report’s statistics and recommendations. Direct comparisons are limited by changing definitions, context, and data collection and analyses methods. Future workforce-need projections are estimated using reports from various sources. Inability to forecast medical advances, socioeconomic changes, and world events affects the accuracy of these projections. Nonetheless, clear conclusions emerge despite such limitations. Progress toward fulfilling the IoM goals is variable and insufficient. The current and projected numbers for all geriatric health providers remain inadequate compared to estimated 2030 demand. Challenges in meeting estimated needs persist essentially unchanged. The 2008 IoM framework and recommendations remain relevant and constitute an important roadmap to complete unfinished goals. Initial findings from this update provide a platform for developing practice and policy reforms.
Reforming WTO Conflict Management: Why and How to Improve the Use of ‘Specific Trade Concerns’
Authors: Wolfe Robert 
Published: October 2020

ABSTRACT
With its dispute settlement system in peril, the role of the World Trade Organization in mitigating commercial conflict is more important than ever, but its working practices need reform. The Sanitary and Phytosanitary Measures and Technical Barriers to Trade committees have developed a mechanism for members to raise ‘specific trade concerns’ about the laws, regulations, and practices of their trading partners, both proposed and already implemented. These specific trade concerns can mitigate sources of friction and help avoid recourse to formal dispute settlement. This article assesses experience with specific trade concerns and analyzes suggestions for reform of the process and its extension to all World Trade Organization committees. The important World Trade Organization reform question is whether procedural changes in Geneva can make specific trade concerns more effective for all members while facilitating enhanced participation by members who do not now make full use of the possibilities that such procedures offer.
In a flash of time: knowledge resources that enable professional cross-boundary work
Authors: Cross David , Swart Juani 
Published: October 2020

Abstract
In this paper, we highlight the networked context of the professions. In particular, we indicate that neo-classical professionals tend to work across organizational boundaries in project teams, often to meet the needs of clients and the wider society. However, little is known about the resources that professionals draw on to meet immediate, fast paced, client demands in project network organizations (PNOs). We pinpoint how knowledge resources, human, social and organizational capital enable professionals to produce outputs at a fast pace/tempo. Temporality emerged as an unexpected but key issue in our empirical research and we explore this further here. First, we put forward how professional work organization(s) has changed by focusing on the boundaries of organizations, and how this is often temporary and project-driven. Second, we use the specific lens of knowledge resources which are drawn upon to enable networked working and ask the question: which knowledge resources enable professionals to work at a fast pace within networks? Third, appreciative of the vast literature on temporary and networked organizations in professional work, our focus is beyond a single profession or organization, and hence, we build upon the prior research on PNOs. We do this by drawing on empirical data of a humanitarian aid project networked organization (HN) that upscales across its network at high speed, often within days, to generate funds for humanitarian disasters in order to save lives.