bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timing of ECMO Initiation Impacts Survival in Influenza-Associated ARDS
Authors: Steimer Desiree , Hernandez Omar , Mason David , Schwartz Gary 
Published: May 2018

AbstractIn the past decade, extracorporeal membrane oxygenation (ECMO) has emerged as an innovative therapy for influenza-associated acute respiratory distress syndrome (ARDS). Despite its promising results, the ideal timing of ECMO initiation for these patients remains unclear. Retrospective analysis of a single institution experience with venovenous ECMO for influenza-induced ARDS was performed. Twenty-one patients were identified and categorized into early (0–2 days), standard (3–6 days), or late (more than 7 days) cannulation cohorts. Patients cannulated within 48 hours of admission had 80% survival rate at 90 days. Comparatively, the standard and late cannulation cohorts had an observed 90-day survival rate of 60 and 16.7%, respectively.
Benefits and Risks of Prophylactic Cerebrospinal Fluid Catheter and Evoked Potential Monitoring in Symptomatic Spinal Cord Ischemia Low-Risk Thoracic Endovascular Aortic Repair
Authors: Maier Sven , Shcherbakova Maria , Beyersdorf Friedhelm , Benk Christoph , Kari Fabian Alexander , Siepe Matthias , Czerny Martin , Rylski Bartosz 
Published: May 2018

Background To assess risks and benefits of a standardized strategy to prevent symptomatic spinal cord ischemia (SSCI) after thoracic endovascular repair (TEVAR) using routine cerebrospinal fluid (CSF) catheter placement and evoked potential (EP) monitoring.
Methods One hundred and ninety-five patients underwent 223 SSCI low-risk TEVAR procedures between 1998 and 2014. CSF catheter was used to measure CSF pressure and drain CSF if necessary throughout the procedure and up to 24 hours thereafter. EPs were used to monitor spinal cord integrity throughout the procedure.
Results Underlying pathologies included descending thoracic aortic aneurysm in 115 (52%), type B aortic dissection in 85 (38%), traumatic aortic rupture in 16 (7%), and others in 7 (3%) patients. CSF catheter was inserted before TEVAR in 116 procedures (52%). Active CSF draining was required in 29 patients (25%). The CSF catheter caused no major and 11 (10%) minor complications. EP were monitored during 88 (40%) procedures. We observed a reduction in the amplitude, prolonged latencies, or complete signal loss in nine procedures. There were no EP monitoring-related complications. SSCI incidence was higher in patients without CSF drainage (0.8% vs 4.7%, p = 0.031).
Conclusion Use of CSF drainage is associated with a significant lower incidence of SSCI after SSCI low-risk TEVAR than nonuse, whereas the complication rate associated with CSF drainage insertion or removal is very low. Routine EP monitoring is a useful tool to detect immediate arterial inflow obstruction to the spinal cord. The combination of these two methods serves as a safe and reliable standardized strategy in reducing the incidence of SSCI to a minimum.
The Feasibility of Thoracoscopic Left Pneumonectomy
Authors: Xu Hao , Zhang Linyou 
Published: May 2018

Objective In this study, we describe our experience with video-assisted thoracoscopic surgery (VATS) left pneumonectomy as a treatment for advanced malignant and benign diseases.Methods Patients who underwent VATS left pneumonectomy in our clinic between October 2013 and August 2017 were retrospectively evaluated. VATS pneumonectomy was successfully completed in 46 patients. We reviewed and analyzed the characteristics of the patients in addition to intraoperative parameters, chest tube duration, length of hospital stay, morbidity, and mortality.
Results A total of 46 patients underwent VATS left pneumonectomy. Of these, 43 patients had malignant tumors and 3 patients had destroyed lung. The histologic types were squamous cell carcinoma in 24 patients, adenocarcinoma in 11, large cell carcinoma in 2, sarcomatoid carcinoma in 1, follicular dendritic cell sarcoma in 1, and small cell carcinoma in 4. Primary lung cancers were classified as stage IA1 in 2 patients, IA2 in 2, IA3 in 1, IB in 3, IIA in 3, IIB in 11, IIIA in 18, and IIIB in 3. The mean operation time was 160.54 ± 43.44 minutes, and the mean blood loss was 401.09 ± 284.32 mL. There was no perioperative mortality and no secretion retention and bronchopleural fistula. Arrhythmia was found in three patients. Pneumonia was found in four patients. The median follow-up time in this cohort was 25 months. A total of 15 patients (34.8%) developed recurrent diseases, 12 developed distant or multiple metastasis, and 3 developed locoregional recurrence.
Conclusion VATS pneumonectomy is a safe, feasible treatment for complicated diseases that induces acceptable damage and has lower morbidity.
Lung Ultrasound Findings in Congenital Pulmonary Airway Malformation
Authors: Mokhtari Mostafa , Durand Philippe , Raimondi Francesco , Migliaro Fiorella , Letourneau Alexandra , Tissières Pierre , De Luca Daniele , Yousef Nadya 
Published: May 2018

Background and Objective Congenital pulmonary airway malformation (CPAM) is a group of rare congenital malformations of the lung and airways. Lung ultrasound (LU) is increasingly used to diagnose neonatal respiratory diseases since it is quick, easy to learn, and radiation-free, but no formal data exist for congenital lung malformations. We aimed to describe LU findings in CPAM neonates needing neonatal intensive care unit (NICU) admission and to compare them with a control population.
Methods A retrospective review of CPAM cases from three tertiary academic NICUs over 3 years (2014–2016) identified five patients with CPAM who had undergone LU examination. LU was compared with chest radiograms and computed tomography (CT) scans that were used as references.
Results CPAM lesions were easily identified and corresponded well with CT scans; they varied from a single large cystic lesion, multiple hypoechoic lesions, and/or consolidation. The first two LU findings have not been described in other respiratory conditions and were not found in controls.
Conclusion We provide the first description of LU findings in neonates with CPAM. LU may be used to confirm antenatally diagnosed CPAM and to suspect CPAM in infants with respiratory distress if cystic lung lesions are revealed. Further studies are necessary to define the place of LU in the management of CPAM.
Protein threading using residue co-variation and deep learning
Authors: Zhu Jianwei , Wang Sheng , Bu Dongbo , Xu Jinbo 
Published: May 2018

Abstract

Motivation
Template-based modeling, including homology modeling and protein threading, is a popular method for protein 3D structure prediction. However, alignment generation and template selection for protein sequences without close templates remain very challenging.

Results
We present a new method called DeepThreader to improve protein threading, including both alignment generation and template selection, by making use of deep learning (DL) and residue co-variation information. Our method first employs DL to predict inter-residue distance distribution from residue co-variation and sequential information (e.g. sequence profile and predicted secondary structure), and then builds sequence-template alignment by integrating predicted distance information and sequential features through an ADMM algorithm. Experimental results suggest that predicted inter-residue distance is helpful to both protein alignment and template selection especially for protein sequences without very close templates, and that our method outperforms currently popular homology modeling method HHpred and threading method CNFpred by a large margin and greatly outperforms the latest contact-assisted protein threading method EigenTHREADER.

Availability and implementation
http://raptorx.uchicago.edu/

Supplementary information
Supplementary data are available at Bioinformatics online.
Modeling one thousand intron length distributions with fitild
Authors: Gotoh Osamu 
Published: May 2018

Abstract

Motivation
Intron length distribution (ILD) is a specific feature of a genome that exhibits extensive species-specific variation. Whereas ILD contributes to up to 30% of the total information content for intron recognition in some species, rendering it an important component of computational gene prediction, very few studies have been conducted to quantitatively characterize ILDs of various species.

Results
We developed a set of computer programs (fitild, compild, etc.) to build statistical models of ILDs and compare them with one another. Each ILD of more than 1000 genomes was fitted with fitild to a statistical model consisting of one, two, or three components of Frechet distributions. Several measures of distances between ILDs were calculated by compild. A theoretical model was presented to better understand the origin of the observed shape of an ILD.

Availability and implementation
The C++ source codes are available at https://github.com/ogotoh/fitild.git/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks
Authors: Pan Xiaoyong , Shen Hong-Bin 
Published: May 2018

Abstract

Motivation
RNA-binding proteins (RBPs) take over 5–10% of the eukaryotic proteome and play key roles in many biological processes, e.g. gene regulation. Experimental detection of RBP binding sites is still time-intensive and high-costly. Instead, computational prediction of the RBP binding sites using patterns learned from existing annotation knowledge is a fast approach. From the biological point of view, the local structure context derived from local sequences will be recognized by specific RBPs. However, in computational modeling using deep learning, to our best knowledge, only global representations of entire RNA sequences are employed. So far, the local sequence information is ignored in the deep model construction process.

Results
In this study, we present a computational method iDeepE to predict RNA–protein binding sites from RNA sequences by combining global and local convolutional neural networks (CNNs). For the global CNN, we pad the RNA sequences into the same length. For the local CNN, we split a RNA sequence into multiple overlapping fixed-length subsequences, where each subsequence is a signal channel of the whole sequence. Next, we train deep CNNs for multiple subsequences and the padded sequences to learn high-level features, respectively. Finally, the outputs from local and global CNNs are combined to improve the prediction. iDeepE demonstrates a better performance over state-of-the-art methods on two large-scale datasets derived from CLIP-seq. We also find that the local CNN runs 1.8 times faster than the global CNN with comparable performance when using GPUs. Our results show that iDeepE has captured experimentally verified binding motifs.

Availability and implementation
https://github.com/xypan1232/iDeepE

Supplementary information
Supplementary data are available at Bioinformatics online.
Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids
Authors: Dorier Julien , Goundaroulis Dimos , Benedetti Fabrizio , Stasiak Andrzej 
Published: May 2018

Abstract

Summary
The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the curve into a loop, which alters the geometry of curve. Knoto-ID allows evaluating the entanglement of open curves without the need to close them, using the recent concept of knotoids which is a generalization of the classical knot theory to open curves. Knoto-ID can analyse the global topology of the full chain as well as the local topology by exhaustively studying all subchains or only determining the knotted core. Knoto-ID permits to localize topologically non-trivial protein folds that are not detected by informatics tools detecting knotted protein folds.

Availability and implementation
Knoto-ID is written in C++ and includes R (www.R-project.org) scripts to generate plots of projections maps, fingerprint matrices and disk matrices. Knoto-ID is distributed under the GNU General Public License (GPL), version 2 or any later version and is available at https://github.com/sib-swiss/Knoto-ID. A binary distribution for Mac OS X, Linux and Windows with detailed user guide and examples can be obtained from https://www.vital-it.ch/software/Knoto-ID.
Improved enzyme annotation with EC-specific cutoffs using DETECT v2
Authors: Nursimulu Nirvana , Xu Leon L , Wasmuth James D , Krukov Ivan , Parkinson John 
Published: May 2018

Abstract

Summary
We present DETECT v2—an enzyme annotation tool which considers the effect of sequence diversity when assigning enzymatic function [as an Enzyme Commission (EC) number] to a protein sequence. In addition to capturing more enzyme classes than the previous version, we now provide EC-specific cutoffs that greatly increase precision and recall of assignments and show its performance in the context of pathways.

Availability and implementation
https://github.com/ParkinsonLab/DETECT-v2

Supplementary information
Supplementary data are available at Bioinformatics online.
polymapR—linkage analysis and genetic map construction from F1 populations of outcrossing polyploids
Authors: Bourke Peter M , van Geest Geert , Voorrips Roeland E , Jansen Johannes , Kranenburg Twan , Shahin Arwa , Visser Richard G F , Arens Paul , Smulders Marinus J M , Maliepaard Chris 
Published: May 2018

Abstract

Motivation
Polyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.

Results
polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.

Availability and implementation
polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR.

Supplementary information
Supplementary data are available at Bioinformatics online.
AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs
Authors: Gorjanc Gregor , Hickey John M 
Published: May 2018

Abstract

Summary
AlphaMate is a flexible program that optimizes selection, maintenance of genetic diversity and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimization of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic. The optimization can maximize genetic gain, minimize group coancestry, minimize inbreeding of individual matings, or maximize genetic gain for a given increase in group coancestry or inbreeding. Users provide a list of candidate individuals with associated gender and selection criteria information (if applicable) and coancestry matrix. Selection criteria and coancestry matrix can be based on pedigree or genome-wide markers. Additional individual or mating specific information can be included to enrich optimization objectives. An example of rapid recurrent genomic selection in wheat demonstrates how AlphaMate can double the efficiency of converting genetic diversity into genetic gain compared to truncation selection. Another example demonstrates the use of genome editing to expand the gain-diversity frontier.

Availability and implementation
Executable versions of AlphaMate for Windows, Mac and Linux platforms are available at http://www.AlphaGenes.roslin.ed.ac.uk/AlphaMate.
Health in All Policies (HiAP) governance: lessons from network governance
Authors: Khayatzadeh-Mahani Akram , Ruckert Arne , Labonté Ronald , Kenis Patrick , Akbari-Javar Mohammad Reza 
Published: May 2018

AbstractThe Health in All Policies (HiAP) approach requires formal and sustained governance structures and mechanisms to ensure that the policies of various non-health sectors maximize positive and minimize negative impacts on population health. In this paper, we demonstrate the usefulness of a network perspective in understanding and contributing to the effectiveness of HiAP. We undertook an exploratory, qualitative case study of a HiAP structure in Iran, the Kerman province Council of Health and Food Security (CHFS) with diverse members from health and non-health sectors. We analyzed relevant policy texts and interviewed 32 policy actors involved in the CHFS. Data were analyzed using within-case analysis and constant comparative methodology. Our findings suggest that CHFS governance from a network perspective drew in practice on elements of two competing network governance modes: the network administrative organization (NAO) and the lead organization mode. Our results also show that a shift from a hierarchical and market-based mode of interaction to a network logic within CHFS has not yet taken place. In addition, CHFS suffers from large membership and an inability to address complex ‘wicked problems’, as well as low trust, legitimacy and goal consensus among its members. Drawing on other HiAP studies and commentaries, insights from organization network theory, and in-depth findings from our case study, we conclude that a NAO may be the most effective mode of governance for tackling complex social problems in HiAP structures. Since similar studies are limited, and our single case study may not be transferable across all contexts, we suggest that further research be undertaken to explore HiAP structures from a network perspective in different institutional and cultural settings. With increasing emphasis given to HiAP approaches in national and international health policy discourse, it is important that comparative knowledge about the effectiveness of HiAP governance arrangements be developed.
Mitochondrial DNA Is a Pro-Inflammatory Damage-Associated Molecular Pattern Released During Active IBD
Authors: Boyapati Ray K , Dorward David A , Tamborska Arina , Kalla Rahul , Ventham Nicholas T , Doherty Mary K , Whitfield Philip D , Gray Mohini , Loane Joseph , Rossi Adriano G , Satsangi Jack , Ho Gwo-tzer 
Published: May 2018

Abstract

Background
Due to common evolutionary origins, mitochondrial DNA (mtDNA) shares many similarities with immunogenic bacterial DNA. MtDNA is recognized as a pro-inflammatory damage-associated molecular pattern (DAMP) with a pathogenic role in several inflammatory diseases. We hypothesised that mtDNA is released during active disease, serving as a key pro-inflammatory factor in inflammatory bowel disease (IBD).

Methods
Between 2014 and 2015, we collected plasma separated within 2 hours of sampling from 97 prospectively recruited IBD patients (67 ulcerative colitis [UC] and 30 Crohn’s disease [CD]) and 40 non-IBD controls. We measured circulating mtDNA using quantitative polymerase chain reaction (amplifying mitochondria COXIII/ND2 genes) and also in mouse colitis induced by dextran sulfate-sodium (DSS). We used a mass spectometry approach to detect free plasma mitochondrial formylated peptides. Furthermore, we examined for mitochondrial damage using electron microscopy (EM) and TLR9 expression, the target for mtDNA, in human intestinal IBD mucosa.

Results
Plasma mtDNA levels were increased in UC and CD (both P &lt; 0.0001) compared with non-IBD controls. These levels were significantly correlated to blood (C-reactive protein, albumin, white cell count), clinical and endoscopic markers of severity, and disease activity. In active UC, we identified 5 mitochondrial formylated peptides (the most abundant being fMMYALF with known chemoattractant function) in plasma. We observed mitochondrial damage in inflamed UC mucosa and significantly higher fecal MtDNA levels (vs non-IBD controls [P &lt; 0.0001]), which supports gut mucosal mitochondrial DAMP release as the primary source. In parallel, plasma mtDNA levels increased during induction of acute DSS colitis and were associated with more severe colitis (P &lt; 0.05). In active IBD, TLR9+ lamina propria inflammatory cells were significantly higher in UC and CD compared with controls (P &lt; 0.05).

Conclusions
We present the first evidence to show that mtDNA is released during active IBD. MtDNA is a potential mechanistic biomarker, and our data point to mtDNA-TLR9 as a therapeutic target in IBD.
On Weyl’s Embedding Problem in Riemannian Manifolds
Authors: Lu Siyuan 
Published: May 2018

Abstract
We consider a priori estimates of Weyl’s embedding problem of $(\mathbb{S}^2, g)$ in general three-dimensional Riemannian manifold $(N^3, \bar g)$. We establish interior $C^2$ estimate under natural geometric assumption. Together with a recent work by Li and Wang [18], we obtain an isometric embedding of $(\mathbb{S}^2,g)$ in Riemannian manifold. In addition, we reprove Weyl’s embedding theorem in space form under the condition that $g\in C^2$ with $D^2g$ Dini continuous.
Why is interstellar object 1I/2017 U1 (‘Oumuamua) rocky, tumbling and possibly very prolate?
Authors: Katz J I 
Published: May 2018

Abstract
The recently discovered first interstellar object 1I/2017 U1 (‘Oumuamua) has brightness that varies by a factor of 10, a range greater than that of any Solar system asteroid, a spectrum characteristic of type D asteroids, and no evidence of evaporating volatiles, contrary to expectation for exo-Oort clouds. ‘Oumuamua is possibly the first example of the proposed ‘Jurads’, objects depleted in volatiles and ejected from planetary systems during the post-main sequence evolution of their parent stars. I suggest that heating by the star’s giant stage fluidized a precursor object as well as driving off any volatiles, causing it to assume the Jacobi ellipsoidal shape of a self-gravitating incompressible liquid. The collision that produced the inferred tumbling motion may have occurred thousands of years after the formation of 1I/2017 U1 ‘Oumuamua. Jacobi ellipsoids have a unique relation among rotation rate, density and axial ratio. The inferred axial ratio ⪆5 suggests a lower bound on the density of 1.6 g cm−3, apparently excluding an icy interior unless it is almost entirely frozen CO2. ‘Oumuamua may be related to accreting objects that pollute white dwarf atmospheres and that may make Soft Gamma Repeaters.