bluuebunny/crossref_metadata_2025_split huggingface dataset:
LncRNAnet: long non-coding RNA identification using deep learning
Authors: Baek Junghwan , Lee Byunghan , Kwon Sunyoung , Yoon Sungroh 
Published: May 2018

AbstractMotivationLong non-coding RNAs (lncRNAs) are important regulatory elements in biological processes. LncRNAs share similar sequence characteristics with messenger RNAs, but they play completely different roles, thus providing novel insights for biological studies. The development of next-generation sequencing has helped in the discovery of lncRNA transcripts. However, the experimental verification of numerous transcriptomes is time consuming and costly. To alleviate these issues, a computational approach is needed to distinguish lncRNAs from the transcriptomes.ResultsWe present a deep learning-based approach, lncRNAnet, to identify lncRNAs that incorporates recurrent neural networks for RNA sequence modeling and convolutional neural networks for detecting stop codons to obtain an open reading frame indicator. lncRNAnet performed clearly better than the other tools for sequences of short lengths, on which most lncRNAs are distributed. In addition, lncRNAnet successfully learned features and showed 7.83%, 5.76%, 5.30% and 3.78% improvements over the alternatives on a human test set in terms of specificity, accuracy, F1-score and area under the curve, respectively.Availability and implementationData and codes are available in http://data.snu.ac.kr/pub/lncRNAnet.
NGL viewer: web-based molecular graphics for large complexes
Authors: Rose Alexander S , Bradley Anthony R , Valasatava Yana , Duarte Jose M , Prlić Andreas , Rose Peter W 
Published: May 2018

Abstract

Motivation
The interactive visualization of very large macromolecular complexes on the web is becoming a challenging problem as experimental techniques advance at an unprecedented rate and deliver structures of increasing size.

Results
We have tackled this problem by developing highly memory-efficient and scalable extensions for the NGL WebGL-based molecular viewer and by using Macromolecular Transmission Format (MMTF), a binary and compressed MMTF. These enable NGL to download and render molecular complexes with millions of atoms interactively on desktop computers and smartphones alike, making it a tool of choice for web-based molecular visualization in research and education.

Availability and implementation
The source code is freely available under the MIT license at github.com/arose/ngl and distributed on NPM (npmjs.com/package/ngl). MMTF-JavaScript encoders and decoders are available at github.com/rcsb/mmtf-javascript.
A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data
Authors: Kong Yunchuan , Yu Tianwei 
Published: May 2018

Abstract

Motivation
Gene expression data represents a unique challenge in predictive model building, because of the small number of samples (n) compared with the huge amount of features (p). This ‘n≪p’ property has hampered application of deep learning techniques for disease outcome classification. Sparse learning by incorporating external gene network information could be a potential solution to this issue. Still, the problem is very challenging because (i) there are tens of thousands of features and only hundreds of training samples, (ii) the scale-free structure of the gene network is unfriendly to the setup of convolutional neural networks.

Results
To address these issues and build a robust classification model, we propose the Graph-Embedded Deep Feedforward Networks (GEDFN), to integrate external relational information of features into the deep neural network architecture. The method is able to achieve sparse connection between network layers to prevent overfitting. To validate the method’s capability, we conducted both simulation experiments and real data analysis using a breast invasive carcinoma RNA-seq dataset and a kidney renal clear cell carcinoma RNA-seq dataset from The Cancer Genome Atlas. The resulting high classification accuracy and easily interpretable feature selection results suggest the method is a useful addition to the current graph-guided classification models and feature selection procedures.

Availability and implementation
The method is available at https://github.com/yunchuankong/GEDFN.

Supplementary information
Supplementary data are available at Bioinformatics online.
TomoEED: fast edge-enhancing denoising of tomographic volumes
Authors: Moreno J J , Martínez-Sánchez A , Martínez J A , Garzón E M , Fernández J J 
Published: May 2018

Abstract

Summary
TomoEED is an optimized software tool for fast feature-preserving noise filtering of large 3D tomographic volumes on CPUs and GPUs. The tool is based on the anisotropic nonlinear diffusion method. It has been developed with special emphasis in the reduction of the computational demands by using different strategies, from the algorithmic to the high performance computing perspectives. TomoEED manages to filter large volumes in a matter of minutes in standard computers.

Availability and implementation
TomoEED has been developed in C. It is available for Linux platforms at http://www.cnb.csic.es/%7ejjfernandez/tomoeed.

Supplementary information
Supplementary data are available at Bioinformatics online.
Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files
Authors: Roberson Elisha D O 
Published: May 2018

Abstract

Summary
Many genomic features are defined not by exact sequence matches, but by degenerate nucleotide motifs that represent multiple compatible matches. While there are databases cataloging genomic features, such as the location of transcription factor motifs, for commonly used model species, identifying the locations of novel motifs, known motifs in non-model genomes, or known motifs in personal whole-genomes is difficult. I designed motif scraper to overcome this limitation, allowing for efficient, multiprocessor motif searches in any FASTA file.

Availability and implementation
The motif scraper package (MIT license) is available via PyPI, and the Python source is available on GitHub at https://github.com/RobersonLab/motif_scraper.
Zero-inflated generalized Dirichlet multinomial regression model for microbiome compositional data analysis
Authors: Tang Zheng-Zheng , Chen Guanhua 
Published: May 2018

SummaryThere is heightened interest in using high-throughput sequencing technologies to quantify abundances of microbial taxa and linking the abundance to human diseases and traits. Proper modeling of multivariate taxon counts is essential to the power of detecting this association. Existing models are limited in handling excessive zero observations in taxon counts and in flexibly accommodating complex correlation structures and dispersion patterns among taxa. In this article, we develop a new probability distribution, zero-inflated generalized Dirichlet multinomial (ZIGDM), that overcomes these limitations in modeling multivariate taxon counts. Based on this distribution, we propose a ZIGDM regression model to link microbial abundances to covariates (e.g. disease status) and develop a fast expectation–maximization algorithm to efficiently estimate parameters in the model. The derived tests enable us to reveal rich patterns of variation in microbial compositions including differential mean and dispersion. The advantages of the proposed methods are demonstrated through simulation studies and an analysis of a gut microbiome dataset.
Strange Duality on Rational Surfaces II: Higher-Rank Cases
Authors: Yuan Yao 
Published: May 2018

Abstract
We study Le Potier’s strange duality conjecture on a rational surface. We focus on the strange duality map $SD_{c_n^r,L}$ that involves the moduli space of rank $r$ sheaves with trivial 1st Chern class and 2nd Chern class $n$, and the moduli space of one-dimensional sheaves with determinant $L$ and Euler characteristic 0. We show there is an exact sequence relating the map $SD_{c_r^r,L}$ to $SD_{c^{r-1}_{r},L}$ and $SD_{c_r^r,L\otimes K_X}$ for all $r\geq 1$ under some conditions on $X$ and $L$ that applies to a large number of cases on $\mathbb{P}^2$ or Hirzebruch surfaces. Also on $\mathbb{P}^2$ we show that for any $r&gt;0$, $SD_{c^r_r,dH}$ is an isomorphism for $d=1,2$, injective for $d=3,$ and moreover $SD_{c_3^3,rH}$ and $SD_{c_3^2,rH}$ are injective. At the end we prove that the map $SD_{c_n^2,L}$ ($n\geq 2$) is an isomorphism for $X=\mathbb{P}^2$ or Fano rational-ruled surfaces and $g_L=3$, and hence so is $SD_{c_3^3,L}$ as a corollary of our main result.
tableone: An open source Python package for producing summary statistics for research papers
Authors: Pollard Tom J , Johnson Alistair E W , Raffa Jesse D , Mark Roger G 
Published: May 2018

AbstractObjectivesIn quantitative research, understanding basic parameters of the study population is key for interpretation of the results. As a result, it is typical for the first table (“Table 1”) of a research paper to include summary statistics for the study data. Our objectives are 2-fold. First, we seek to provide a simple, reproducible method for providing summary statistics for research papers in the Python programming language. Second, we seek to use the package to improve the quality of summary statistics reported in research papers.Materials and MethodsThe tableone package is developed following good practice guidelines for scientific computing and all code is made available under a permissive MIT License. A testing framework runs on a continuous integration server, helping to maintain code stability. Issues are tracked openly and public contributions are encouraged.ResultsThe tableone software package automatically compiles summary statistics into publishable formats such as CSV, HTML, and LaTeX. An executable Jupyter Notebook demonstrates application of the package to a subset of data from the MIMIC-III database. Tests such as Tukey’s rule for outlier detection and Hartigan’s Dip Test for modality are computed to highlight potential issues in summarizing the data.Discussion and ConclusionWe present open source software for researchers to facilitate carrying out reproducible studies in Python, an increasingly popular language in scientific research. The toolkit is intended to mature over time with community feedback and input. Development of a common tool for summarizing data may help to promote good practice when used as a supplement to existing guidelines and recommendations. We encourage use of tableone alongside other methods of descriptive statistics and, in particular, visualization to ensure appropriate data handling. We also suggest seeking guidance from a statistician when using tableone for a research study, especially prior to submitting the study for publication.
On the existence of a luminosity threshold of GRB jets in massive stars
Authors: Aloy M A , Cuesta-Martínez C , Obergaulinger M 
Published: May 2018

ABSTRACT
Motivated by the many associations of gamma-ray bursts (GRBs) with energetic supernova (SN) explosions, we study the propagation of relativistic jets within the progenitor star in which an SN shock wave may be launched briefly before the jets start to propagate. Based on analytic considerations and verified with an extensive set of 2D axisymmetric relativistic hydrodynamic simulations, we have estimated a threshold intrinsic jet luminosity, $L_{\rm j}^{\rm thr}$, for successfully launching a jet. This threshold depends on the structure of the progenitor and, thus, it is sensitive to its mass and to its metallicity. For a prototype host of cosmological long GRBs, a low-metallicity star of 35 M⊙, it is $L_{\rm j}^{\rm thr}\simeq 1.35\times 10^{49}$ erg s−1. The observed equivalent isotropic gamma-ray luminosity, $L_{\rm \gamma ,iso,BO} \simeq 4 \epsilon _\gamma L_{\rm j} \theta _{\rm BO}^{-2}$, crucially depends on the jet opening angle after breakout, θBO, and on the efficiency for converting the intrinsic jet luminosity into γ-radiation, εγ. Highly energetic jets can produce low-luminosity events if either their opening angle after the breakout is large, which is found in our models, or if the conversion efficiency of kinetic and internal energy into radiation is low enough. Beyond this theoretical analysis, we show how the presence of an SN shock wave may reduce this luminosity threshold by means of numerical simulations. We foresee that the high-energy transients released by jets produced near the luminosity threshold will be more similar to llGRBs or X-ray flashes than to GRBs.
The Cumulative Impact of Harm Reduction on the Swiss HIV Epidemic: Cohort Study, Mathematical Model, and Phylogenetic Analysis
Authors: Marzel Alex , Kusejko Katharina , Weber Rainer , Bruggmann Philip , Rauch Andri , Roth Jan A , Bernasconi Enos , Calmy Alexandra , Cavassini Matthias , Hoffmann Matthias , Böni Jürg , Yerly Sabine , Klimkait Thomas , Perreau Matthieu , Günthard Huldrych F , Kouyos Roger D ,   Swiss HIV Cohort Study, Anagnostopoulos A , Battegay M , Bernasconi E , Böni J , Braun D L , Bucher H C , Calmy A , Cavassini M , Ciuffi A , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux C A , Günthard H F , Haerry D , Hasse B , Hirsch H H , Hoffmann M , Hösli I , Huber M , Kahlert C , Kaiser L , Keiser O , Klimkait T , Kouyos R D , Kovari H , Ledergerber B , Martinetti G , Martinez de Tejada B , Marzolini C , Metzner K J , Müller N , Nicca D , Paioni P , Pantaleo G , Perreau M , Rauch A , Rudin C , Scherrer A U , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Vernazza P , Wandeler G , Weber R , Yerly S 
Published: May 2018

AbstractBackgroundHuman immunodeficiency virus (HIV) transmission among injecting drug users (IDUs) is increasing in the United States due to the recent opioid epidemic and is the leading mode of transmission in Eastern Europe.MethodsTo evaluate the overall impact of HIV harm reduction, we combined (1) data from the Swiss HIV Cohort Study and public sources with (2) a mathematical model expressed as a system of ordinary differential equations. The model reconstructs the national epidemic from the first case in 1980 until 2015. Phylogenetic cluster analysis of HIV-1 pol sequences was used to quantify the epidemic spillover from IDUs to the general population.ResultsOverall, harm reduction prevented 15903 (range, 15359–16448) HIV infections among IDUs until the end of 2015, 5446 acquired immune deficiency syndrome (AIDS) deaths (range, 5142–5752), and a peak HIV prevalence of 50.7%. Introduction of harm reduction 2 years earlier could have halved the epidemic, preventing 3161 (range, 822–5499) HIV infections and 1468 (range, 609–2326) AIDS deaths. Suddenly discontinuing all harm reduction in 2005 would have resulted in outbreak re-emergence with 1351 (range, 779–1925) additional HIV cases. Without harm reduction, the estimated additional number of heterosexuals infected by HIV-positive IDUs is estimated to have been 2540 (range, 2453–2627), which is equivalent to the total national reported incidence among heterosexuals in the period of 2007 to 2015.ConclusionsOur results suggest that a paramount, population-level impact occurred because of the harm reduction package, beyond factors that can be explained by a reduction in risk behavior and a decrease in the number of drug users over time.
Towards a Definition for Health Care–Associated Infection
Authors: Friedman N Deborah , Levit Dana , Taleb Eyal , Marcus Gil , Michaeli Leah , Broide Mor , Mengesha Bethlehem , Zaidenstein Ronit , Lazarovitch Tsilia , Dadon Mor , Kaye Keith S , Marchaim Dror 
Published: May 2018

Abstract

Background
Health care–associated infection (HcAI) is a term frequently used to describe community-onset infections likely to be caused by multidrug-resistant organisms (MDROs). The most frequently used definition was developed at Duke University Medical Center in 2002 (Duke-2002). Although some professional societies have based management recommendations on Duke-2002 (or modifications thereof), neither Duke-2002 nor other variations have had their performance measured.

Methods
A case–control study was conducted at Assaf Harofeh Medical Center (AHMC) of consecutive adult bloodstream infections (BSIs). A multivariable model was used to develop a prediction score for HcAI, measured by the presence of MDRO infection on admission. The performances of this new score and previously developed definitions at predicting MDRO infection on admission were measured.

Results
Of the 504 BSI patients enrolled, 315 had a BSI on admission and 189 had a nosocomial BSI. Patients with MDRO-BSI on admission (n = 100) resembled patients with nosocomial infections (n = 189) in terms of epidemiological characteristics, illness acuity, and outcomes more than patients with non-MDRO-BSI on admission (n = 215). The performances of both the newly developed score and the Duke-2002 definition to predict MDRO infection on admission were suboptimal (area under the receiver operating characteric curve, 0.76 and 0.68, respectively).

Conclusions
Although the term HcAI is frequently used, its definition does not perform well at predicting MDRO infection present on admission to the hospital. A validated score that calculates the risk of MDRO infection on admission is still needed to guide daily practice and improve patient outcomes.
Robot-Assisted Responsive Neurostimulator System Placement in Medically Intractable Epilepsy: Instrumentation and Technique
Authors: McGovern Robert A , Alomar Soha , Bingaman William E , Gonzalez-Martinez Jorge 
Published: May 2018

Abstract

BACKGROUND
The management of medically refractory epilepsy patients who are not surgical candidates has remained challenging. Closed loop—or responsive—neurostimulation (RNS) is now an established therapy for the treatment of epilepsy with specific indications. The RNS® system (NeuroPace Inc, Mountainview, California) has recently been shown to be effective in reducing the seizure frequency of partial onset seizures. The electrode design consists of either intracerebral depth electrodes or subdural strip electrodes, and stereotaxis is typically used to guide placement into the EZ. Details on the operative techniques used to place these electrodes have been lacking.

OBJECTIVE
To address the advantage of using a robotic-assisted technique to place depth electrodes for RNS® system placement compared to the typical frame-based or frameless stereotactic systems.

METHODS
We retrospectively reviewed our single center, technical operative experience with RNS® system placement using robotic assistance from 2014 to 2016 via chart review.

RESULTS
Twelve patients underwent RNS® system placement using robotic assistance. Mean operative time was 121 min for a median of 2 depth electrodes with mean deviation from intended target of ∼3 mm in x, y, and z planes. Two patients developed wound infections, 1 of whom was reimplanted. Seizures were reduced by ∼40% at 2 yr, similar to the results seen in the open label portion of the pivotal RNS trial.

CONCLUSION
Robotic-assisted stereotaxis can be used to provide a stable and accurate stereotactic platform for insertion of intracerebral RNS electrodes, representing a safe, efficient and accurate procedure.
Spatially resolved spectroscopy of non-thermal X-rays in RX J1713.7−3946 with Chandra
Authors: Okuno Tomoyuki , Tanaka Takaaki , Uchida Hiroyuki , Matsumura Hideaki , Tsuru Takeshi Go 
Published: May 2018

Abstract
The young shell-type supernova remnant (SNR) RX J1713.7−3946 has been studied as a suitable target to test the SNR paradigm for the origin of Galactic cosmic rays. We present a spatially resolved spectroscopy of the non-thermal X-ray emission in RX J1713.7−3946 with Chandra. In order to obtain X-ray properties of the filamentary structures and their surrounding regions, we divide the southeastern (SE), southwestern (SW), and northwestern (NW) parts of the SNR into subregions on the typical order of several 10" and extract spectra from each subregion. Their photon indices are significantly different among the subregions, with a range of 1.8 &lt; Γ &lt; 3. In the SE part, the clear filaments are harder (Γ ∼ 2.0) than the surrounding regions. This is a common feature often observed in young SNRs and naturally interpreted as a consequence of synchrotron cooling. On the other hand, the bright filamentary regions do not necessarily coincide with the hardest regions in the SW and NW parts. We also find the SW filamentary region is relatively rather soft (Γ ∼ 2.7). In addition, we find that hard regions with photon indices of 2.0–2.2 exist around the bright emission although the hard regions lie in the downstream region and the bright emission does not appear to be the blast wave shock front. Both the aforementioned characteristic regions in SW are located close to peaks of the interstellar gas. We discuss possible origins of the spatial variation of the photon indices, paying particular attention to the shock–cloud interactions.
Changes in Teaching Hospitals’ Community Benefit Spending After Implementation of the Affordable Care Act
Authors: Alberti Philip M. , Sutton Karey M. , Baker Matthew 
Published: May 2018

Purpose
U.S. teaching hospitals that qualify as 501(c)(3) organizations (a not-for-profit designation) are required to demonstrate community benefit annually. Increases in health insurance access driven by Affordable Care Act (ACA) implementation, along with new regulations, research opportunities, and educational expectations, may be changing hospitals’ allocations of community benefit dollars. This study aimed to describe changes in teaching hospitals’ community benefit spending between 2012 (pre-ACA implementation) and 2015 (post-ACA implementation), and to explore differences in spending changes between hospitals in Medicaid expansion and nonexpansion states.

Method
In 2017, for each teaching hospital member of the Association of American Medical Colleges’ (AAMC’s) Council of Teaching Hospitals and Health Systems required to submit Form 990s to the Internal Revenue Service, the authors sought community benefit spending data for 2012 and 2015 as reported on Schedule H.

Results
The analysis included 169 pairs of Form 990s representing 184 AAMC member teaching hospitals (93% of 198 eligible hospitals). Compared with 2012, hospitals in 2015 spent $3.1 billion (20.14%) more on community benefit despite spending $804 million (16.17%) less on charity care. Hospitals in Medicaid expansion states increased spending on subsidized health services and Medicaid shortfalls at rates higher than hospitals in nonexpansion states. The latter increased spending at higher rates on community health improvement and cash/in-kind contributions.

Conclusions
After ACA implementation, teaching hospitals increased their overall community benefit spending while their charity care spending declined. Changes in community benefit spending differed according to states’ Medicaid expansion status, demonstrating hospitals’ responsiveness to state and local realities.
Neuromodulation in Pediatrics
Authors: Kim Eugene , Gamble Sean , Schwartz Adina , Cucchiaro Giovanni 
Published: May 2018

Objectives:
Neuromodulation, particularly intrathecal drug delivery systems and spinal cord stimulators (SCSs), can be a valuable tool when treating chronic pain in adults. However, there is a paucity of literature with regard to its use in pediatrics.

Materials and Methods:
We present a series of 14 children and adolescents with intractable pain who received a SCS or a pump for the intrathecal delivery of medications between 2010 and 2016 at our institution.

Results:
During the study period, we placed 10 intrathecal pumps and 4 SCSs with an average age of 17 years old. Pain scores significantly improved after the implant (P<0.007) and function improved in 79% of patients. Opioid use was also significantly reduced. Three patients eventually had their device removed due to psychiatric comorbidities. Four patients had complications that were treated without further sequelae.

Conclusions:
Neuromodulation can offer important options in treating some pediatric chronic pain patients. In-depth knowledge of primary disease and strict patient selection in the context of the patient’s social situation is vital to successful treatment.