bluuebunny/crossref_metadata_2025_split huggingface dataset:
Political Judging and Judicial Restraint: The Case of Learned and Augustus Hand
Authors: Allen Jak 
Published: March 2020

Abstract
In recent decades, accusations of partisanship by the U.S. judiciary have intensified. A consequence has been the erroneous framing of judges within the conventional, and sometimes epithetical, political binary of liberalism and conservatism. This article argues that the application of such labels has distorted the full thrust of the complex individuals who have constituted the American judiciary and proposes reframing our perception of judges, both past and present, by seeking more viable standards for measuring judicial performance. To do so, it draws on the early twentieth-century examples of Learned and Augustus Hand of the Second Circuit Court of Appeals. Despite being praised as symbols of judicial independence, scholars have often framed the judges in political terms. This article draws on the Hands’ public speeches, publications, and private correspondence to argue that they adopted a non-partisan view of judging that transcended political affiliations and displayed a much deeper consideration about their roles as judges than conventional political labels suggest. By inserting greater nuance into our historical understanding of the delicate relationship between politics and law, we can yet save courts from the threat that politically charged language poses to their legitimacy.
Dual-dropout graph convolutional network for predicting synthetic lethality in human cancers
Authors: Cai Ruichu , Chen Xuexin , Fang Yuan , Wu Min , Hao Yuexing 
Published: March 2020

Abstract

Motivation
Synthetic lethality (SL) is a promising form of gene interaction for cancer therapy, as it is able to identify specific genes to target at cancer cells without disrupting normal cells. As high-throughput wet-lab settings are often costly and face various challenges, computational approaches have become a practical complement. In particular, predicting SLs can be formulated as a link prediction task on a graph of interacting genes. Although matrix factorization techniques have been widely adopted in link prediction, they focus on mapping genes to latent representations in isolation, without aggregating information from neighboring genes. Graph convolutional networks (GCN) can capture such neighborhood dependency in a graph. However, it is still challenging to apply GCN for SL prediction as SL interactions are extremely sparse, which is more likely to cause overfitting.

Results
In this article, we propose a novel dual-dropout GCN (DDGCN) for learning more robust gene representations for SL prediction. We employ both coarse-grained node dropout and fine-grained edge dropout to address the issue that standard dropout in vanilla GCN is often inadequate in reducing overfitting on sparse graphs. In particular, coarse-grained node dropout can efficiently and systematically enforce dropout at the node (gene) level, while fine-grained edge dropout can further fine-tune the dropout at the interaction (edge) level. We further present a theoretical framework to justify our model architecture. Finally, we conduct extensive experiments on human SL datasets and the results demonstrate the superior performance of our model in comparison with state-of-the-art methods.

Availability and implementation
DDGCN is implemented in Python 3.7, open-source and freely available at https://github.com/CXX1113/Dual-DropoutGCN.

Supplementary information
Supplementary data are available at Bioinformatics online.
A phylogenetic C interpreter for TNT
Authors: Goloboff Pablo A , Morales Martín E 
Published: March 2020

Abstract

Motivation
TNT (a widely used program for phylogenetic analysis) includes an interpreter for a scripting language, but that implementation is nonstandard and uses several conventions of its own. This article describes the implementation and basic usage of a C interpreter (with all the ISO essentials) now included in TNT. A phylogenetic library includes functions that can be used for manipulating trees and data, as well as other phylogeny-specific tasks. This greatly extends the capabilities of TNT.

Availability and implementation
Versions of TNT including the C interpreter for scripts can be downloaded from http://www.lillo.org.ar/phylogeny/tnt/.
A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models
Authors: Wen Jia , Ford Colby T , Janies Daniel , Shi Xinghua 
Published: March 2020

AbstractMotivationEpistasis reflects the distortion on a particular trait or phenotype resulting from the combinatorial effect of two or more genes or genetic variants. Epistasis is an important genetic foundation underlying quantitative traits in many organisms as well as in complex human diseases. However, there are two major barriers in identifying epistasis using large genomic datasets. One is that epistasis analysis will induce over-fitting of an over-saturated model with the high-dimensionality of a genomic dataset. Therefore, the problem of identifying epistasis demands efficient statistical methods. The second barrier comes from the intensive computing time for epistasis analysis, even when the appropriate model and data are specified.ResultsIn this study, we combine statistical techniques and computational techniques to scale up epistasis analysis using Empirical Bayesian Elastic Net (EBEN) models. Specifically, we first apply a matrix manipulation strategy for pre-computing the correlation matrix and pre-filter to narrow down the search space for epistasis analysis. We then develop a parallelized approach to further accelerate the modeling process. Our experiments on synthetic and empirical genomic data demonstrate that our parallelized methods offer tens of fold speed up in comparison with the classical EBEN method which runs in a sequential manner. We applied our parallelized approach to a yeast dataset, and we were able to identify both main and epistatic effects of genetic variants associated with traits such as fitness.Availability and implementationThe software is available at github.com/shilab/parEBEN.
Plant 3D (P3D): a plant phenotyping toolkit for 3D point clouds
Authors: Ziamtsov Illia , Navlakha Saket 
Published: March 2020

Abstract

Motivation
Developing methods to efficiently analyze 3D point cloud data of plant architectures remain challenging for many phenotyping applications. Here, we describe a tool that tackles four core phenotyping tasks: classification of cloud points into stem and lamina points, graph skeletonization of the stem points, segmentation of individual lamina and whole leaf labeling. These four tasks are critical for numerous downstream phenotyping goals, such as quantifying plant biomass, performing morphological analyses of plant shapes and uncovering genotype to phenotype relationships. The Plant 3D tool provides an intuitive graphical user interface, a fast 3D rendering engine for visualizing plants with millions of cloud points, and several graph-theoretic and machine-learning algorithms for 3D architecture analyses.

Availability and implementation
P3D is open-source and implemented in C++. Source code and Windows installer are freely available at https://github.com/iziamtso/P3D/.

Contact
iziamtso@ucsd.edu or navlakha@cshl.edu

Supplementary information
Supplementary data are available at Bioinformatics online.
Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus
Authors: Liu Sen , Zheng Qiang , Wang Zhiying 
Published: March 2020

AbstractMotivationSince December 2019, the newly identified coronavirus SARS-CoV-2 has caused a massive health crisis worldwide and resulted in over 70 000 COVID-19 infections so far. Clinical drugs targeting SARS-CoV-2 are urgently needed to decrease the high fatality rate of confirmed COVID-19 patients. Traditional de novo drug discovery needs more than 10 years, so drug repurposing seems the best option currently to find potential drugs for treating COVID-19.ResultsCompared with traditional non-covalent drugs, covalent drugs have attracted escalating attention recent years due to their advantages in potential specificity upon careful design, efficiency and patient burden. We recently developed a computational protocol named as SCAR (steric-clashes alleviating receptors) for discovering covalent drugs. In this work, we used the SCAR protocol to identify possible covalent drugs (approved or clinically tested) targeting the main protease (3CLpro) of SARS-CoV-2. We identified 11 potential hits, among which at least six hits were exclusively enriched by the SCAR protocol. Since the preclinical or clinical information of these identified drugs is already available, they might be ready for being clinically tested in the treatment of COVID-19.Contactsenliu.ctgu@gmail.com
A peacock bass (Cichla) functional novelty relaxes a constraint imposed by the classic cichlid pharyngeal jaw innovation
Authors: Burress Edward D , Wainwright Peter C 
Published: March 2020

AbstractInnovations may provide access to new resources but often result in significant trade-offs. Pharyngognathy is a classic pharyngeal jaw innovation in which the left and right lower pharyngeal jaw (LPJ) bones are united into a single structure, producing a strong bite but reduced gape. Throughout cichlids, pharyngeal suturing occurs along the entire medial border between LPJ bones, except in peacock bass (Cichla), where these bones are connected by ligaments only in their anterior region. We show that this limited attachment permits the jaw bones to spread apart and we link this feature to an increase in pharyngeal gape that is comparable to non-pharyngognathous species. The capacity of the LPJ bones to spread apart is strongest in juveniles and is mostly lost during development. Juvenile Cichla exhibit size-specific pharyngeal gape similar to non-pharyngognathous percomorphs; however, adults exhibit pharyngeal gape on par with other predatory cichlids. Relaxation of pharyngeal suturing offsets a major deleterious consequence of pharyngognathy by reducing gape limitation and we propose this may accelerate the ontogenetic transition to piscivory. Partial reversal of the classic cichlid pharyngeal jaw innovation highlights the functional trade-offs that often accompany innovations and may be a major cause of variation in their macroevolutionary consequences.
Posterior shoulder instability: a systematic review
Authors: Longo Umile Giuseppe , Ciuffreda Mauro , Locher Joel , Casciaro Carlo , Mannering Nicholas , Maffulli Nicola , Denaro Vincenzo 
Published: March 2020

Abstract

Introduction
This review aims to provide information on outcomes of surgical procedures for soft tissue or bony glenoid and/or humeral abnormalities in case of posterior shoulder instability.

Source of data
A systematic review of the literature according to the PRISMA guidelines was performed. A comprehensive search of PubMed, Medline, CINAHL, Cochrane, Embase, Ovid and Google Scholar databases using various combinations of the keywords ‘shoulder’, ‘posterior instability’, ‘dislocation’, ‘reversed bony bankart’, ‘reversed Hill Sachs’, and ‘capsulolabral’ was performed.

Areas of agreement
A total of 847 shoulders in 810 patients were included. A redislocation event occurred in 33 (8.7%) of 411 shoulders with soft tissue abnormalities and in 12 (9.1%) of 132 shoulders with bony abnormalities of the glenoid, humeral head or both.

Areas of controversy
The optimal treatment modalities for posterior shoulder dislocation remain to be defined.

Growing points
Operative stabilization for posterior shoulder instability should be lesion-specific and should correct all components of the posterior instability.

Areas timely for developing research
Future prospective studies should aim to establish the optimal treatment modalities for posterior shoulder instability.
MicroRNA-135a-induced formation of CD133+ subpopulation with cancer stem cell properties in cervical cancer
Authors: Leung Carmen O N , Deng Wen , Ye Tian-Min , Ngan Hextan Y S , Tsao Sai Wah , Cheung Annie N Y , Ziru Niu , Yuen Dominic C K , Pang Ronald T K , Yeung William S B 
Published: March 2020

AbstractCancer stem cells (CSCs) play significant roles in tumor initiation. MicroRNA-135a (miR-135a) induced the formation of a CD133+ subpopulation from a human papillomavirus-immortalized cervical epithelial cell line. Compared with the CD133− cells, the CD133+ cells expressed higher levels of miR-135a and OCT4, exhibited significantly higher tumorsphere forming capacity and the time required for tumorsphere formation was shortened in the second generation. Serum induction suppressed the expression of CD133, OCT4 and miR-135a, but increased expression of involucrin in the miR-135a-induced CD133+ cells. The miR-135a-induced CD133+ cells were tumorigenic in a limiting dilution approach in vivo. The cells expressed significantly higher level of active β-catenin and OCT4 than the CD133− counterpart. Wnt3a enhanced the expression of OCT4 and CD133 in cervical cancer cells but failed to enhance CD133 transcription in normal cervical cells. Wnt3a stimulation also increased tumorsphere size and self-renewal of miR-135a-induced CD133+ subpopulation. Wnt/β-catenin inhibition suppressed tumorsphere formation while Wnt3a partially nullified the inhibitory effect. Taken together, miR-135a induced the formation of a subpopulation of cells with CSC properties both in vitro and in vivo and the Wnt/β-catenin signaling pathway is essential to maintain its tumorigenicity.
Calcium and phosphate levels after kidney transplantation and long-term patient and allograft survival
Authors: Chevarria Julio , Sexton Donal J , Murray Susan L , Adeel Chaudhry E , O’Kelly Patrick , Williams Yvonne E , O’Seaghdha Conall M , Little Dilly M , Conlon Peter J 
Published: March 2020

Abstract

Background
Non-traditional cardiovascular risk factors, including calcium and phosphate derangement, may play a role in mortality in renal transplant. The data regarding this effect are conflicting. Our aim was to assess the impact of calcium and phosphate derangements in the first 90 days post-transplant on allograft and recipient outcomes.

Methods
We performed a retrospective cohort review of all-adult, first renal transplants in the Republic of Ireland between 1999 and 2015. We divided patients into tertiles based on serum phosphate and calcium levels post-transplant. We assessed their effect on death-censored graft survival and all-cause mortality. We used Stata for statistical analysis and did survival analysis and spline curves to assess the association.

Results
We included 1525 renal transplant recipients. Of the total, 86.3% had hypophosphataemia and 36.1% hypercalcaemia. Patients in the lowest phosphate tertile were younger, more likely female, had lower weight, more time on dialysis, received a kidney from a younger donor, had less delayed graft function and better transplant function compared with other tertiles. Patients in the highest calcium tertile were younger, more likely male, had higher body mass index, more time on dialysis and better transplant function. Adjusting for differences between groups, we were unable to show any difference in death-censored graft failure [phosphate = 1.14, 95% confidence interval (CI) 0.92–1.41; calcium = 0.98, 95% CI 0.80–1.20] or all-cause mortality (phosphate = 1.10, 95% CI 0.91–1.32; calcium = 0.96, 95% CI 0.81–1.13) based on tertiles of calcium or phosphate in the initial 90 days.

Conclusions
Hypophosphataemia and hypercalcaemia are common occurrences post-kidney transplant. We have identified different risk factors for these metabolic derangements. The calcium and phosphate levels exhibit no independent association with death-censored graft failure and mortality.
Effect of bicuspid aortic valve phenotype on progression of aortic stenosis
Authors: Shen Mylène , Tastet Lionel , Capoulade Romain , Arsenault Marie , Bédard Élisabeth , Clavel Marie-Annick , Pibarot Philippe 
Published: March 2020

Abstract

Aims
To compare the progression of aortic stenosis (AS) in patients with bicuspid aortic valve (BAV) or tricuspid aortic valve (TAV).

Methods and results
One hundred and forty-one patients with mild-to-moderate AS, recruited prospectively in the PROGRESSA study, were included in this sub-analysis. Baseline clinical, Doppler echocardiography and multidetector computed tomography characteristics were compared between BAV (n = 32) and TAV (n = 109) patients. The 2-year haemodynamic [i.e. peak aortic jet velocity (Vpeak) and mean transvalvular gradient (MG)] and anatomic [i.e. aortic valve calcification density (AVCd) and aortic valve calcification density ratio (AVCd ratio)] progression of AS were compared between the two valve phenotypes. The 2-year progression rate of Vpeak was: 16 (−0 to 40) vs. 17 (3–35) cm/s, P = 0.95; of MG was: 1.8 (−0.7 to 5.8) vs. 2.6 (0.4–4.8) mmHg, P = 0.56; of AVCd was 32 (2–109) vs. 52 (25–85) AU/cm2, P = 0.15; and of AVCd ratio was: 0.08 (0.01–0.23) vs. 0.12 (0.06–0.18), P = 0.16 in patients with BAV vs. TAV. In univariable analyses, BAV was not associated with AS progression (all, P ≥ 0.26). However, with further adjustment for age, AS baseline severity, and several risk factors (i.e. sex, history of hypertension, creatinine level, diabetes, metabolic syndrome), BAV was independently associated with faster haemodynamic (Vpeak: β = 0.31, P = 0.02) and anatomic (AVCd: β = 0.26, P = 0.03 and AVCd ratio: β = 0.26, P = 0.03) progression of AS.

Conclusion
In patients with mild-to-moderate AS, patients with BAV have faster haemodynamic and anatomic progression of AS when compared to TAV patients with similar age and risk profile. This study highlights the importance and necessity to closely monitor patients with BAV and to adequately control and treat their risk factors.

Clinical trial registration
https://clinicaltrials.gov Unique identifier: NCT01679431.
Incremental value of diastolic stress test in identifying subclinical heart failure in patients with diabetes mellitus
Authors: Nishi Tomoko , Kobayashi Yukari , Christle Jeffrey W , Cauwenberghs Nicholas , Boralkar Kalyani , Moneghetti Kegan , Amsallem Myriam , Hedman Kristofer , Contrepois Kévin , Myers Jonathan , Mahaffey Kenneth W , Schnittger Ingela , Kuznetsova Tatiana , Palaniappan Latha , Haddad Francois 
Published: March 2020

Abstract

Aims
Resting echocardiography is a valuable method for detecting subclinical heart failure (HF) in patients with diabetes mellitus (DM). However, few studies have assessed the incremental value of diastolic stress for detecting subclinical HF in this population.

Methods and results
Asymptomatic patients with Type 2 DM were prospectively enrolled. Subclinical HF was assessed using systolic dysfunction (left ventricular longitudinal strain &lt;16% at rest and &lt;19% after exercise in absolute value), abnormal cardiac morphology, or diastolic dysfunction (E/e′ &gt; 10). Metabolic equivalents (METs) were calculated using treadmill speed and grade, and functional capacity was assessed by percent-predicted METs (ppMETs). Among 161 patients studied (mean age of 59 ± 11 years and 57% male sex), subclinical HF was observed in 68% at rest and in 79% with exercise. Among characteristics, diastolic stress had the highest yield in improving detection of HF with 57% of abnormal cases after exercise and 45% at rest. Patients with revealed diastolic dysfunction during stress had significantly lower exercise capacity than patients with normal diastolic stress (7.3 ± 2.1 vs. 8.8 ± 2.5, P &lt; 0.001 for peak METs and 91 ± 30% vs. 105 ± 30%, P = 0.04 for ppMETs). On multivariable modelling found that age (beta = −0.33), male sex (beta = 0.21), body mass index (beta = −0.49), and exercise E/e′ &gt;10 (beta = −0.17) were independently associated with peak METs (combined R2 = 0.46). A network correlation map revealed the connectivity of peak METs and diastolic properties as central features in patients with DM.

Conclusion
Diastolic stress test improves the detection of subclinical HF in patients with diabetes mellitus.
Implementation of appropriate use criteria for cardiology tests and procedures: a systematic review and meta-analysis
Authors: Winchester David E , Merritt Justin , Waheed Nida , Norton Hannah , Manja Veena , Shah Nishant R , Helfrich Christian D 
Published: March 2020

Abstract

Aims
The American College of Cardiology appropriate use criteria (AUC) provide clinicians with evidence-informed recommendations for cardiac care. Adopting AUC into clinical workflows may present challenges, and there may be specific implementation strategies that are effective in promoting effective use of AUC. We sought to assess the effect of implementing AUC in clinical practice.

Methods and results
We conducted a meta-analysis of studies found through a systematic search of the MEDLINE, Web of Science, Cochrane, or CINAHL databases. Peer-reviewed manuscripts published after 2005 that reported on the implementation of AUC for a cardiovascular test or procedure were included. The main outcome was to determine if AUC implementation was associated with a reduction in inappropriate/rarely appropriate care. Of the 18 included studies, the majority used pre/post-cohort designs; few (n = 3) were randomized trials. Most studies used multiple strategies (n = 12, 66.7%). Education was the most common individual intervention strategy (n = 13, 72.2%), followed by audit and feedback (n = 8, 44.4%) and computerized physician order entry (n = 6, 33.3%). No studies reported on formal use of stakeholder engagement or ‘nudges’. In meta-analysis, AUC implementation was associated with a reduction in inappropriate/rarely appropriate care (odds ratio 0.62, 95% confidence interval 0.49–0.78). Funnel plot suggests the possibility of publication bias.

Conclusion
We found most published efforts to implement AUC observed reductions in inappropriate/rarely appropriate care. Studies rarely explored how or why the implementation strategy was effective. Because interventions were infrequently tested in isolation, it is difficult to make observations about their effectiveness as stand-alone strategies.

Study registration
PROSPERO 2018 CRD42018091602. Available from https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42018091602.