bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graphite fabric reinforced PAEK composites by novel impregnation-co-film technique
Authors: Marathe Umesh , Padhan Meghashree , Bijwe Jayashree 
Published: June 2020

Abstract
High performance polymers such as Poly(ether ether ketone) (PEEK), Poly(aryl ether ketone) (PAEK), Poly(ether ketone ketone) (PEKK), etc exhibit high melting points, 343 °C, 373 °C and 338 °C respectively and very high melt viscosity. They do not have appropriate solvents, which could open the ways to process their fabric reinforced composites; by impregnation technique followed by compression molding. Film stacking and powder sprinkling are the only possible techniques, which lead to weak crossover points due to non-wetting by the resin and finally resulting in inferior mechanical and interfacial properties and high amount of voids. In order to solve these problems, a novel technique called impregnation-co-film (ICF) is explored in this work. Polyetherimide (PEI) (10 wt% in dichloromethane solution) pre-impregnated graphite fabric prepregs were used before applying film technique followed by compression molding. The study compares properties such as density, void content, flexural strength, impact strength, Interlaminar shear strength (ILSS), thermal stability (in air) and interface by field emission scanning electron microscopy for the composite prepared with film stacking technique and that by impregnation-co-film stacking technique. It was confirmed that the new ICF technique proved to be significantly promising than the older technique almost in all aspects with 120% improvement in ILSS, 127% in flexural strength and 200% decrease in void content.
Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data
Authors: Sarkar Hirak , Srivastava Avi , Bravo Héctor Corrada , Love Michael I , Patro Rob 
Published: June 2020

Abstract

Motivation
Advances in sequencing technology, inference algorithms and differential testing methodology have enabled transcript-level analysis of RNA-seq data. Yet, the inherent inferential uncertainty in transcript-level abundance estimation, even among the most accurate approaches, means that robust transcript-level analysis often remains a challenge. Conversely, gene-level analysis remains a common and robust approach for understanding RNA-seq data, but it coarsens the resulting analysis to the level of genes, even if the data strongly support specific transcript-level effects.

Results
We introduce a new data-driven approach for grouping together transcripts in an experiment based on their inferential uncertainty. Transcripts that share large numbers of ambiguously-mapping fragments with other transcripts, in complex patterns, often cannot have their abundances confidently estimated. Yet, the total transcriptional output of that group of transcripts will have greatly reduced inferential uncertainty, thus allowing more robust and confident downstream analysis. Our approach, implemented in the tool terminus, groups together transcripts in a data-driven manner allowing transcript-level analysis where it can be confidently supported, and deriving transcriptional groups where the inferential uncertainty is too high to support a transcript-level result.

Availability and implementation
Terminus is implemented in Rust, and is freely available and open source. It can be obtained from https://github.com/COMBINE-lab/Terminus.

Supplementary information
Supplementary data are available at Bioinformatics online.
The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction
Authors: Stamboulian Moses , Guerrero Rafael F , Hahn Matthew W , Radivojac Predrag 
Published: June 2020

Abstract

Motivation
The computational prediction of gene function is a key step in making full use of newly sequenced genomes. Function is generally predicted by transferring annotations from homologous genes or proteins for which experimental evidence exists. The ‘ortholog conjecture’ proposes that orthologous genes should be preferred when making such predictions, as they evolve functions more slowly than paralogous genes. Previous research has provided little support for the ortholog conjecture, though the incomplete nature of the data cast doubt on the conclusions.

Results
We use experimental annotations from over 40 000 proteins, drawn from over 80 000 publications, to revisit the ortholog conjecture in two pairs of species: (i) Homo sapiens and Mus musculus and (ii) Saccharomyces cerevisiae and Schizosaccharomyces pombe. By making a distinction between questions about the evolution of function versus questions about the prediction of function, we find strong evidence against the ortholog conjecture in the context of function prediction, though questions about the evolution of function remain difficult to address. In both pairs of species, we quantify the amount of information that would be ignored if paralogs are discarded, as well as the resulting loss in prediction accuracy. Taken as a whole, our results support the view that the types of homologs used for function transfer are largely irrelevant to the task of function prediction. Maximizing the amount of data used for this task, regardless of whether it comes from orthologs or paralogs, is most likely to lead to higher prediction accuracy.

Availability and implementation
https://github.com/predragradivojac/oc.

Supplementary information
Supplementary data are available at Bioinformatics online.
Joint modeling and multiple comparisons with the best of data from a SMART with survival outcomes
Authors: Chao Yan-Cheng , Tran Qui , Tsodikov Alex , Kidwell Kelley M 
Published: June 2020

Summary
A dynamic treatment regimen (DTR) is a sequence of decision rules that can alter treatments or doses based on outcomes from prior treatment. In the case of two lines of treatment, a DTR specifies first-line treatment, and second-line treatment for responders and treatment for non-responders to the first-line treatment. A sequential, multiple assignment, randomized trial (SMART) is one such type of trial that has been designed to assess DTRs. The primary goal of our project is to identify the treatments, covariates, and their interactions result in the best overall survival rate. Many previously proposed methods to analyze data with survival outcomes from a SMART use inverse probability weighting and provide non-parametric estimation of survival rates, but no other information. Other methods have been proposed to identify and estimate the optimal DTR, but inference issues were seldom addressed. We apply a joint modeling approach to provide unbiased survival estimates as a mechanism to quantify baseline and time-varying covariate effects, treatment effects, and their interactions within regimens. The issue of multiple comparisons at specific time points is addressed using multiple comparisons with the best method.
Appropriateness of Antibiotic Prescribing for Acute Sinusitis in Primary Care: A Cross-sectional Study
Authors: Truitt Katie N , Brown Tiffany , Lee Ji Young , Linder Jeffrey A 
Published: June 2020

Abstract
The proportion of sinusitis visits that meet antibiotic prescribing criteria is unknown. Of 425 randomly selected sinusitis visits, 50% (214) met antibiotic prescribing criteria. There was no significant difference in antibiotic prescribing at visits that did (205/214 [96%]) and did not (193/211 [92%]; P = .07) meet antibiotic prescribing criteria.
Oral Capsulized Fecal Microbiota Transplantation for Eradication of Carbapenemase-producing Enterobacteriaceae Colonization With a Metagenomic Perspective
Authors: Bar-Yoseph Haggai , Carasso Shaqed , Shklar Shlomit , Korytny Alexander , Even Dar Razi , Daoud Haneen , Nassar Roni , Maharshak Nitsan , Hussein Khetam , Geffen Yuval , Chowers Yehuda , Geva-Zatorsky Naama , Paul Mical 
Published: June 2020

Abstract

Background
Carbapenemase-producing Enterobacteriaceae (CPE) infections lead to considerable morbidity and mortality. We assessed the potential of fecal microbiota transplantation (FMT) to eradicate CPE carriage and aimed to explain failure or success through microbiome analyses.

Methods
In this prospective cohort study, all consenting eligible CPE carriers received oral capsulized FMT for 2 days. Primary outcome was CPE eradication at 1 month, defined by 3 consecutive negative rectal swabs, the last also negative for carbapenemase gene by polymerase chain reaction. Comprehensive metagenomics analysis of the intestinal microbiome of donors and recipients before and after FMT was performed.

Results
Fifteen CPE carriers received FMT, 13 of whom completed 2 days of treatment. CPE eradication at 1 month was successful in 9/15 and 9/13, respectively. Bacterial communities showed significant changes in both beta and alpha diversity metrics among participants who achieved CPE eradication that were not observed among failures. Post-FMT samples’ beta-diversity clustered according to the treatment outcome, both in taxonomy and in function. We observed a significant decrease in beta diversity in participants who received post-FMT antibiotics. Enterobacteriaceae abundance decreased in post-FMT samples of the responders but increased among failures. Functionally, a clear demarcation between responders (who were similar to the donors) and failures was shown, driven by antimicrobial resistance genes.

Conclusions
Our study provides the biological explanation for the effect of FMT against CPE carriage. Decolonization of CPE by FMT is likely mediated by compositional and functional shifts in the microbiome. Thus, FMT might be an efficient strategy for sustained CPE eradication.

Clinical Trials Registration
NCT03167398.
mAML: an automated machine learning pipeline with a microbiome repository for human disease classification
Authors: Yang Fenglong , Zou Quan 
Published: June 2020

Abstract
Due to the concerted efforts to utilize the microbial features to improve disease prediction capabilities, automated machine learning (AutoML) systems aiming to get rid of the tediousness in manually performing ML tasks are in great demand. Here we developed mAML, an ML model-building pipeline, which can automatically and rapidly generate optimized and interpretable models for personalized microbiome-based classification tasks in a reproducible way. The pipeline is deployed on a web-based platform, while the server is user-friendly and flexible and has been designed to be scalable according to the specific requirements. This pipeline exhibits high performance for 13 benchmark datasets including both binary and multi-class classification tasks. In addition, to facilitate the application of mAML and expand the human disease-related microbiome learning repository, we developed GMrepo ML repository (GMrepo Microbiome Learning repository) from the GMrepo database. The repository involves 120 microbiome-based classification tasks for 85 human-disease phenotypes referring to 12 429 metagenomic samples and 38 643 amplicon samples. The mAML pipeline and the GMrepo ML repository are expected to be important resources for researches in microbiology and algorithm developments.
Database URL: http://lab.malab.cn/soft/mAML
Three-dimensional right ventricular shape and strain in congenital heart disease patients with right ventricular chronic volume loading
Authors: Moceri Pamela , Duchateau Nicolas , Gillon Stéphane , Jaunay Lolita , Baudouy Delphine , Squara Fabien , Ferrari Emile , Sermesant Maxime 
Published: June 2020

Abstract

Aims
Right ventricular (RV) function assessment is crucial in congenital heart disease patients, especially in atrial septal defect (ASD) and repaired Tetralogy of Fallot (TOF) patients with pulmonary regurgitation (PR). In this study, we aimed to analyse both 3D RV shape and deformation to better characterize RV function in ASD and TOF-PR.

Methods and results
We prospectively included 110 patients (≥16 years old) into this case–control study: 27 ASD patients, 28 with TOF, and 55 sex- and age-matched healthy controls. Endocardial tracking was performed on 3D transthoracic RV echocardiographic sequences and output RV meshes were post-processed to extract local curvature and deformation. Differences in shape and deformation patterns between subgroups were quantified both globally and locally. Curvature highlights differences in RV shape between controls and patients while ASD and TOF-PR patients are similar. Conversely, strain highlights differences between controls and TOF-PR patients while ASD and controls are similar [global area strain: −31.5 ± 5.8% (controls), −34.1 ± 7.9% (ASD), −24.8 ± 5.7% (TOF-PR), P &lt; 0.001, similar significance for longitudinal and circumferential strains]. The regional and local analysis highlighted differences in particular in the RV free wall and the apical septum.

Conclusion
Chronic RV volume loading results in similar RV shape remodelling in both ASD and TOF patients while strain analysis demonstrated that RV strain is only reduced in the TOF group. This suggests a fundamentally different RV remodelling process between both conditions.
Comparing traditional aortic valve surgery and transapical approach to transcatheter aortic valve implant
Authors: Buzzatti Nicola , Sala Alessandra , Alfieri Ottavio 
Published: June 2020

Abstract
During the last 15 years, transcatheter aortic valve implant (TAVI) has become a valid alternative to surgical aortic valve replacement in symptomatic patients with severe aortic stenosis, and high or intermediate operative risk. Transcatheter aortic valve implant could be approached through various access sites, among which the transapical has long been one of the most popular. Through the years, this procedure has shown results similar to the standard surgical approach, but not as good as the same procedure via the transfemoral approach. For this reason, along with continuous technological advances, the transfemoral approach is used, presently, in 90% of the patient, while the transapical route has been limited, progressively, to a minority of patients. Currently the Heart Team should decide, in every single patient, between conventional surgery and TAVI. In clinical practice, TAVI is favoured in high-risk patients, and in the elderly at intermediate surgical risk with favourable anatomical features. In patients in whom TAVI is preferable to surgery, but have ‘non-usable’ femoral approach, alternative routes, such as transaxillary or transapical, could be considered.
Atrial fibrillation ablation in heart failure
Authors: Balla Cristina , Cappato Riccardo 
Published: June 2020

Abstract
Atrial fibrillation (AF) and heart failure (HF) commonly coexist in the same patient and either condition predisposes to the other. Several mechanisms promote the pathophysiological relationship between AF and HF, reducing quality of life, increasing the risk of stroke, and worsening HF progression. Although restoration and maintenance of sinus rhythm would be ideal for those patients, several trials comparing rhythm and rate control failed to show a benefit of rhythm control strategy, achieved with pharmacological therapy, in terms of hospitalization for HF or death. Catheter ablation is a well-established option for symptomatic AF patients, resistant to drug therapy, with normal cardiac function. Several recent studies have shown an improvement in clinical outcomes after AF ablation in HF patients highlighting the emerging role of the invasive approach in this subset of patients. However, several concerns regarding patients’ selection and standardization of the procedure still remain to be addressed.
How important is blood pressure variability?
Authors: Rosei Enrico Agabiti , Chiarini Giulia , Rizzoni Damiano 
Published: June 2020

Abstract
Arterial blood pressure (BP) is a continuous variable, with a physiology characterized by significant variability stemming from the complex interaction among haemodynamic factors, neuronal reflexes, as well as hormonal, behavioural, and environmental stimuli. The homoeostatic response accounts for the physiologic variability in BP in normotensive individuals, which is more evident in hypertensive patients. Blood pressure variability is a complex phenomenon, which could be classified in various types: very short term (beat to beat), short term (during 24 h), mid-term (day by day), long term (&lt;5 years), and very long term (&gt;5 years). Accurate measurement of BP variability represents a complex and often controversial endeavour, despite several methodological approaches are available. Albeit a prognostic significance has been demonstrated for some indicators of BP variability, the clinical significance of this measurement is still uncertain. In fact, none of the indicators presently available for BP variability, including early morning BP rise, substantially affects, and redefines, the cardiovascular risk of the hypertensive patient, over and beyond the mere BP values. Accordingly, in defining the cardiovascular risk, the focus should be on the absolute BP values, which remain the most relevant risk factor, and the one more susceptible to modification with both non-pharmacologic and pharmacologic treatment.
Right ventricular electromechanical abnormalities in Brugada syndrome: is this a cardiomyopathy?
Authors: Pappone Carlo , Monasky Michelle M , Micaglio Emanuele , Ciconte Giuseppe 
Published: June 2020

Abstract
Brugada syndrome (BrS) has been often described as a purely electrical disease. However, current dogma surrounding this concept has shifted to accept that BrS is associated with structural abnormalities. Brugada syndrome is now associated with epicardial surface and interstitial fibrosis, reduced gap junction expression, increased collagen, and reduced contractility. The ventricular arrhythmias observed in BrS have been linked to an arrhythmogenic substrate (AS) located rather consistently in the right ventricular outflow tract, sparking much debate as to the significance of this anatomical position. The size of the AS is dynamic and can be altered due to a number of factors. A larger AS is associated with reduced contractility, and this impaired mechanical function may be responsible for syncopal episodes in BrS patients in the absence of arrhythmic events. While BrS is generally regarded as a channelopathy, recent studies have now identified also mutations in genes encoding for sarcomeric proteins to be associated with BrS. Future studies should evaluate electromechanical coupling in BrS, including calcium handling and sarcomeric alterations, and evaluate whether BrS should be classified as a cardiomyopathy.
The revolution of the anti-diabetic drugs in cardiology
Authors: Verdecchia Paolo , Angeli Fabio , Cavallini Claudio , Aita Adolfo , Turturiello Dario , Reboldi Gianpaolo 
Published: June 2020

Abstract
Beginning in December 2008, under the auspices of Food and Drug Administration, numerous controlled clinical trial were planned, and in part completed, concerning the cardiovascular (CV) effects of hypoglycaemic drug in patients with Type 2 diabetes mellitus. At least 9 studies have been concluded, 13 are still open, and 4 have been initiated and closed ahead of time. Of the nine completed studies, three concerned inhibitor of the dipeptidyl peptidase 4 (inhibitors of DPP-4), four the glucagon-like peptide 1 agonist (GLP-1 agonist), and two the inhibitor of sodium-glucose co-transporter-2 (inhibitors of SGLT-2). Only four studies demonstrated the superiority, and not the mere ‘non-inferiority’, of the anti-diabetic drugs compared to placebo, in addition to standard treatment, in terms of reduction of the primary endpoint (CV death, non-fatal myocardial infarction, and non-fatal stroke). Two of the four studies regarded GLP-1 analogues (liraglutide and semaglutide), and two inhibitors of SGLT-2 (empaglifozin and canaglifozin). As a whole, these studies provided solid data supporting major beneficial CV effects of anti-diabetic drugs. During the next 3–4 years, an equal number of studies will be completed and published, so we will soon have the ‘final word’ on this issue. In the meantime, the clinical cardiologist should become familiar with these drugs, selecting the patients able to gain the best clinical advantage from this treatment, also by establishing a close relationship with the diabetologist.
To whom recommend intensive treatment for hypertension?
Authors: Volpe Massimo , Gallo Giovanna 
Published: June 2020

Abstract
Arterial hypertension is the main identifiable cardiovascular risk factor, and although the benefit of blood pressure reduction is universally acknowledged, the scientific community has long been divided over the therapeutic blood pressure targets to be reached, also considering the estimated overall cardiovascular risk and the presence of individual risk factors and associated comorbidities. During the last few years, numerous clinical studies and meta-analyses, in particular, the SPRINT study, have been published, demonstrating the advantages of an intensive antihypertensive treatment, over a target blood pressure value (&lt;140/90 mmHg), in the reduction of major cardiovascular events, myocardial infarction, stroke, heart failure, and all-causes cardiovascular mortality. Stemming from these results the major International Guidelines revisited the therapeutic objectives, recommending blood pressure value &lt;130/80 mmHg for the vast majority of hypertensive patients until the age of 65 and suggesting a reduction of the target also in the elderly. Numerous studies and meta-analyses demonstrated that the reduction of the risk of coronary or cerebral events, and of all-causes cardiovascular mortality, is independent from the baseline value of blood pressure and the individual estimated risk. It has been also demonstrated that an early institution of antihypertensive treatment is associated with a faster realization of the recommended targets, and consequent significant benefits in terms of reduction of the incidence of myocardial infarction, heart failure, and major cardiovascular events, particularly when blood pressure control is achieved during the first 6 months of treatment, and even better during first 3 months. Other studies outlined that combination therapy with two or more drugs, mainly in a single pill configuration, are superior in reaching the recommended therapeutic targets. This is the reason why this strategy is strongly supported by the European Society of Cardiology/European Society of Hypertension (ESC/ESH) 2018 Guidelines, specifically the use of renin–angiotensin–aldosterone system inhibitors [angiotensin-converting enzyme (ACE) inhibitors and Sartans], in combination with calcium antagonist and/or thiazide diuretics, with the option to add antagonist of mineralcorticoid receptors, when an adequate blood pressure control has not been reached, or other classes of drugs, such as beta-blockers, when specific clinical indications are present, first and foremost ischaemic cardiomyopathy or heart failure. The newly proposed therapeutic goals are particularly important in high-risk patients, such as patients with previous cardiovascular events, diabetes mellitus, renal insufficiency, and patients older than 65 years of age.
Patenting a living microbial cell: 40th anniversary of US Supreme Court decision Diamond versus Chakrabarty
Authors: Silver Simon 
Published: June 2020

ABSTRACT
Patents for microbiology and biotechnology are generally for a process (for example DNA cloning; and polymerase chain reaction, PCR) and not for the microbe itself. The patent for oil degrading bacteria was different in that it covered the modified microbial cell itself, a Pseudomonas strain with laboratory-assembled plasmids that encoded the bacterial degradation of multiple components of crude oil. It was first applied for in 1972, initially refused by the patent office on the basis that it was a living organism, and then eight years later in June 1980 allowed by the US Supreme Court ruling that this did not matter and the only issue was whether it was a novel manufactured product.