bluuebunny/crossref_metadata_2025_split huggingface dataset:
The EDIBLES survey
Authors: Bacalla Xavier L. , Linnartz Harold , Cox Nick L. J. , Cami Jan , Roueff Evelyne , Smoker Jonathan V. , Farhang Amin , Bouwman Jordy , Zhao Dongfeng 
Published: November 2018

We report cosmic ray ionization rates toward ten reddened stars studied within the framework of the EDIBLES (ESO Diffuse Interstellar Bands Large Exploration Survey) program, using the VLT-UVES. For each sightline, between two and ten individual rotational lines of OH+ have been detected in its (0,0) and (1,0) A3Π − X3Σ− electronic band system. This allows constraining of OH+ column densities toward different objects. Results are also presented for 28 additional sightlines for which only one or rather weak signals are found. An analysis of these data makes it possible to derive the primary cosmic ray ionization rate ζp in the targeted diffuse interstellar clouds. For the ten selected targets, we obtain a range of values for ζp equal to (3.9–16.4) × 10−16 s−1. These values are higher than the numbers derived in previous detections of interstellar OH+ in the far-infrared/submillimeter-wave regions and in other near-ultraviolet studies. This difference is a result of using new OH+ oscillator strength values and a more complete picture of all relevant OH+ formation and destruction routes (including the effect of proton recombinations on PAHs), and the relatively high N(OH+) seen toward those ten targets.
GUV-AP: multifunctional FIJI-based tool for quantitative image analysis of Giant Unilamellar Vesicles
Authors: Sych Taras , Schubert Thomas , Vauchelles Romain , Madl Josef , Omidvar Ramin , Thuenauer Roland , Richert Ludovic , Mély Yves , Römer Winfried 
Published: November 2018

Abstract

Motivation
Giant Unilamellar Vesicles (GUVs) are widely used synthetic membrane systems that mimic native membranes and cellular processes. Various fluorescence imaging techniques can be employed for their characterization. In order to guarantee a fast and unbiased analysis of imaging data, the development of automated recognition and processing steps is required.

Results
We developed a fast and versatile Fiji-based macro for the analysis of digital microscopy images of GUVs. This macro was designed to investigate membrane dye incorporation and protein binding to membranes. Moreover, we propose a fluorescence intensity-based method to quantitatively assess protein binding.

Availability and implementation
The ImageJ distribution package FIJI is freely available online: https://imagej.net/Fiji. The macro file GUV-AP.ijm is available at https://github.com/AG-Roemer/GUV-AP.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Effect of Onset Age of Visual Deprivation on Visual Cortex Surface Area Across-Species
Authors: Andelin Adrian K , Olavarria Jaime F , Fine Ione , Taber Erin N , Schwartz Daniel , Kroenke Christopher D , Stevens Alexander A 
Published: November 2018

Abstract
Blindness early in life induces permanent alterations in brain anatomy, including reduced surface area of primary visual cortex (V1). Bilateral enucleation early in development causes greater reductions in primary visual cortex surface area than at later times. However, the time at which cortical surface area expansion is no longer sensitive to enucleation is not clearly established, despite being an important milestone for cortical development. Using histological and MRI techniques, we investigated how reductions in the surface area of V1 depends on the timing of blindness onset in rats, ferrets and humans. To compare data across species, we translated ages of all species to a common neuro-developmental event-time (ET) scale. Consistently, blindness during early cortical expansion induced large (~40%) reductions in V1 surface area, in rats and ferrets, while blindness occurring later had diminishing effects. Longitudinal measurements on ferrets confirmed that early enucleation disrupted cortical expansion, rather than inducing enhanced pruning. We modeled the ET associated with the conclusion of the effect of blindness on surface area at maturity (ETc), relative to the normal conclusion of visual cortex surface area expansion, (ETdev). A final analysis combining our data with extant published data confirmed that ETc occurred well before ETdev.
Multi-hop assortativities for network classification
Authors: Gutiérrez-Gómez Leonardo , Delvenne Jean-Charles 
Published: November 2018

Abstract
Several social, medical, engineering and biological challenges rely on discovering the functionality of networks from their structure and node metadata, when it is available. For example, in chemoinformatics one might want to detect whether a molecule is toxic based on structure and atomic types, or discover the research field of a scientific collaboration network. Existing techniques rely on counting or measuring structural patterns that are known to show large variations from network to network, such as the number of triangles, or the assortativity of node metadata. We introduce the concept of multi-hop assortativity, that captures the similarity of the nodes situated at the extremities of a randomly selected path of a given length. We show that multi-hop assortativity unifies various existing concepts and offers a versatile family of ‘fingerprints’ to characterize networks. These fingerprints allow in turn to recover the functionalities of a network, with the help of the machine learning toolbox. Our method is evaluated empirically on established social and chemoinformatic network benchmarks. Results reveal that our assortativity based features are competitive providing highly accurate results often outperforming state of the art methods for the network classification task.
NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform
Authors: Calus Szymon T , Ijaz Umer Z , Pinto Ameet J 
Published: November 2018

Abstract

Background
Amplicon sequencing on Illumina sequencing platforms leverages their deep sequencing and multiplexing capacity but is limited in genetic resolution due to short read lengths. While Oxford Nanopore or Pacific Biosciences sequencing platforms overcome this limitation, their application has been limited due to higher error rates or lower data output.

Results
In this study, we introduce an amplicon sequencing workflow, i.e., NanoAmpli-Seq, that builds on the intramolecular-ligated nanopore consensus sequencing (INC-Seq) approach and demonstrate its application for full-length 16S rRNA gene sequencing. NanoAmpli-Seq includes vital improvements to the INC-Seq protocol that reduces sample processing time while significantly improving sequence accuracy. The developed protocol includes chopSeq software for fragmentation and read orientation correction of INC-Seq consensus reads while nanoClust algorithm was designed for read partitioning-based de novo clustering and within cluster consensus calling to obtain accurate full-length 16S rRNA gene sequences.

Conclusions
NanoAmpli-Seq accurately estimates the diversity of tested mock communities with average consensus sequence accuracy of 99.5% for 2D and 1D2 sequencing on the nanopore sequencing platform. Nearly all residual errors in NanoAmpli-Seq sequences originate from deletions in homopolymer regions, indicating that homopolymer aware base calling or error correction may allow for sequencing accuracy comparable to short-read sequencing platforms.
Sodium bicarbonate catheter lock solution reduces hemodialysis catheter loss due to catheter-related thrombosis and blood stream infection: an open-label clinical trial
Authors: El-Hennawy Adel S , Frolova Elena , Romney Wesley A 
Published: November 2018

AbstractBackgroundThere is no ideal lock solution that prevents hemodialysis (HD) catheter loss due to catheter-related thrombosis (CRT) and catheter-related bloodstream infection (CRBSI). Catheter loss is associated with increased hospitalization and high inpatient costs. Sodium bicarbonate (NaHCO3) demonstrates anti-infective and anticoagulation properties with a good safety profile, making it an ideal lock solution development target.The objective of this study was to determine the safety and efficacy of using sodium bicarbonate catheter lock solution (SBCLS) as a means of preventing HD catheter loss due to CRT and CRBSI.MethodsThe study took place in a community hospital in Brooklyn, NY, USA. All admitted patients ≥18 years of age who needed HD treatment through CVC were included in the study. 451 patients included in the study were provided SBCLS or NSCLS post-dialysis. Catheter loss due to CRT or CRBSI was evaluated over a period of 546 days.ResultsA total of 452 patients met the criteria; 1 outlier was excluded, 226 were in the NSCLS group and 225 were in the SBCLS group. There were no significant differences between groups in comorbidities at the outset. The NSCLS group had CRT and CRBSI rates of 4.1 and 2.6/1000 catheter days (CD), respectively, compared with 0.17/1000 CD for both outcomes in the SBCLS group. SBCLS patients had a significantly reduced catheter loss rate due to CRT (P < 0.0001) and CRBSI (P = 0.0004). NSCLS patients had higher odds of losing their catheter due to CRT {odds ratio [OR] 26.6 [95% confidence interval (CI) 3.57–198.52]} and CRBSI [OR 15.9 (95% CI 2.09–121.61)] during the study period.ConclusionThe novel approach of using SBCLS was found to be safe and was statistically superior to normal saline in preventing HD catheter loss due to CRT and CRBSI. NaHCO3 solution is inexpensive, readily available in various settings and holds the potential to decrease hospitalization, length of stay and dialysis-related costs.Trial registrationMaimonides Medical Center Investigational Review Board, Study IRB 2015-06-25-CIH. ClinicalTrials.gov identifier: NCT03627884.
TFound: A Software to Map Cis-Regulatory Elements in Yeast
Authors: Gomes-Silva Adriano , Silva-Rocha Rafael 
Published: November 2018

AbstractTranscription factors (TFs) are responsible for regulating the rate of transcription of genes in all organisms. These factors can be represented computationally by position weight matrices (PWM). TFound was developed to allow the detailed visualization of predicted binding sites of transcription factors in multiple sequences based on the PWMs, by using the graphic user interface (GUI). The tool was loaded with the genome of Saccharomyces cerevisiae and PWMs from the YeTFaSCo database (http://yetfasco.ccbr.utoronto.ca/), also allowing the insertion of new sequences and PWMs. Thus, the user is allowed to load custom PWMs and genomes to perform easily mining and visualization of binding site motifs of cis-regulatory elements of interest, permitting an efficient way to inspect DNA assembly projects for complex synthetic circuits. This work describes the functionality of the current version of the tool, which is coded in Python and is freely available at the repository https://github.com/adri4nogomes/TFound.
Incremental BLAST: incremental addition of new sequence databases through e-value correction
Authors: Dash Sajal , Rahman Sarthok , Hines Heather M. , Feng Wu-chun 
Published: November 2018

AbstractMotivationSearch results from local alignment search tools use statistical parameters sensitive to the size of the database. NCBI BLAST, for example, reports important matches using similarity scores and expect or e-values calculated against database size. Over the course of an investigation, the database grows and the best matches may change. To update the results of a sequence similarity search to find the most optimal hits, bioinformaticians must rerun the BLAST search against the entire database; this translates into irredeemable spent time, money, and computational resources.ResultsWe develop an efficient way to redeem spent BLAST search effort by introducing the Incremental BLAST. This tool makes use of the previous BLAST search results as it conducts new searches on only the incremental part of the database, recomputes statistical metrics such as e-values and combines these two sets of results to produce updated results. We develop statistics for correcting e-values of any BLAST result against any arbitrary sequence database. The experimental results and accuracy analysis demonstrate that Incremental BLAST can provide search results identical to NCBI BLAST at a significantly reduced computational cost. We apply three case studies to showcase different use cases where Incremental BLAST can make biological discovery more efficiently at a reduced cost. This tool can be used to update sequence blasts during the course of genomic and transcriptomic projects, such as in re-annotation projects, and to conduct incremental addition of taxon-specific sequences to a BLAST database. Incremental BLAST performs (1 + δ)/δ times faster than NCBI BLAST for δ fraction of database growth.AvailabilityIncremental BLAST is available at https://bitbucket.org/sajal000/incremental-blast.Contactsajal@vt.eduSupplementary informationSupplementary data are available at https://bitbucket.org/sajal000/incremental-blast
Malaria-induced remodelling of the bone marrow microenvironment mediates loss of haematopoietic stem cell function
Authors: Haltalli Myriam L.R. , Watcham Samuel , Wilson Nicola K. , Eilers Kira , Lipien Alexander , Vainieri Maria L. , Ruivo Nicola , Ang Heather , Sinden Robert E. , Duffy Ken R. , Göttgens Berthold , Blagborough Andrew M. , Celso Cristina Lo 
Published: November 2018

ABSTRACTSevere infections are a major source of stress on haematopoiesis, where consequences for haematopoietic stem cells (HSCs) have only recently started to emerge. HSC function critically depends on the integrity of complex bone marrow niches, which have been shown to be altered during ageing and haematopoietic malignancies. Whether the bone marrow (BM) microenvironment plays a role in mediating the effects of infection on HSCs remains an open question. Here we used an murine model of malaria coupled with intravital microscopy, single cell RNA-Seq, mathematical modelling and transplantation assays to obtain a quantitative understanding of the proliferation dynamics of haematopoietic stem and progenitor cells (HSPCs) duringPlasmodiuminfection. We uncovered that duringPlasmodiuminfection the HSC compartment turns over significantly faster than in steady state, and that a global interferon response and loss of functional HSCs are linked to alterations in BM endothelium function and osteoblasts number. Interventions that targeted osteoblasts uncoupled HSC proliferation and function, thus opening up new avenues for therapeutic interventions that may improve the health of survivors of severe infections.
DeepCapTail: A Deep Learning Framework to Predict Capsid and Tail Proteins of Phage Genomes
Authors: Abid Dhoha , Zhang Liqing 
Published: November 2018

AbstractThe capsid and tail proteins are considered the main structural proteins for phages and also their footprint since they exist only in phage genomes. These proteins are known to lack sequence conservation, making them extremely diverse and thus posing a major challenge to identify and annotate them in genomic sequences. In this study, we aim to overcome this challenge and predict these proteins by using deep neural networks with composition-based features. We develop two models trained with k-mer features to predict capsid and tail proteins respectively. Evaluating the models on two different testing sets shows that they outperform state-of-the-art methods with improved F-1 scores.
High-order finite volume approximation for population density model based on quadratic integrate-and-fire neuron
Authors: Singh Paramjeet , Kumar Santosh , Koksal Mehmet Emir 
Published: November 2018

PurposeThe purpose of this paper is to develop and apply a high-order numerical method based on finite volume approximation for quadratic integrate-and-fire (QIF) neuron model with the help of population density approach.Design/methodology/approachThe authors apply the population density approach for the QIF neuron model to derive the governing equation. The resulting mathematical model cannot be solved with existing analytical or numerical techniques owing to the presence of delay and advance. The numerical scheme is based along the lines of approximation: spatial discretization is performed by weighted essentially non-oscillatory (WENO) finite volume approximation (FVM) and temporal discretization are performed by strong stability-preserving explicit Runge–Kutta (SSPERK) method. Compared with existing schemes of orders 2 and 3 from the literature, the proposed scheme is found to be more efficient and it produces accurate solutions with few grid cells. In addition to this, discontinuity is added in the application of the model equation to illustrate the high performance of the proposed scheme.FindingsThe developed scheme works nicely for the simulation of the resulting model equation. The authors discussed the role of inhibitory and excitatory parts in variation of neuronal firing. The validation of the designed scheme is measured by its comparison with existing schemes in the literature. The efficiency of the designed scheme is demonstrated via numerical simulations.Practical implicationsIt is expected that the present study will be a useful tool to tackle the complex neuron model and related studies.Originality/valueThe novel aspect of this paper is the application of the numerical methods to study the modified version of leaky integrate-and-fire neuron based on a QIF neuron. The model of the current study is inspired from the base model given in Stein (1965) and modified version in Kadalbajoo and Sharma (2005) and Wang and Zhang (2014). The applicability was confirmed by taking some numerical examples.
Role of internal service quality in enhancing patient centricity and internal customer satisfaction
Authors: Prakash Gyan , Srivastava Shefali 
Published: November 2018

Purpose
The purpose of this paper is to identify the antecedents and outcomes of internal service quality (ISQ) in a health-care environment. The relationships among the heterogeneous health-care environment, coordinated care, perceived organisational support (POS), ISQ, internal customer satisfaction and patient-centred care were explored.

Design/methodology/approach
Based on a review of the literature, a structural model was developed. A 37-item questionnaire was circulated among service providers in the health-care system, including doctors, nurses and system staff, all over India. The random sampling method was adopted to collect data. A total of 238 valid responses were received. The data were analysed using structural equation modelling.

Findings
The results show that the heterogeneous environment, coordinated care and POS act as antecedents of ISQ, which drives internal customer satisfaction and patient centricity in health care.

Research limitations/implications
The paper contributes to the health-care literature by identifying the antecedents and consequences of ISQ and developing a structural relationship among ISQ, the heterogeneous health-care environment, coordinated care, POS, internal customer satisfaction and patient-centred care.

Practical implications
Hospital administrators may use various constructs of POS, ISQ and coordinated care to measure process and employee performance, which may aid the design of appropriate processes and improve employee selection. The constructs of patient centricity and internal customer satisfaction may be used as benchmarking tools to facilitate the formulation of immediate corrective actions and policies for future courses of action.

Social implications
This paper highlights how patient centricity may be achieved by focussing on ISQ, coordinated care processes and a facilitative internal environment. This understanding may aid the design of processes that in turn deliver health as a social good in an effective manner.

Originality/value
This paper extends past research on ISQ by showing that ISQ affects internal customer satisfaction and, in turn, the quality of service delivery in the system. In the health-care context, heterogeneity in patient needs, coordinated care and organisational support play crucial roles in determining ISQ, which in turn influences the level of patient-centred care.
Effect of thermal radiation on engine oil nanofluid flow over a permeable wedge under convective heating
Authors: Kotha Gangadhar , Kukkamalla Keziya , Ibrahim S.M. 
Published: November 2018

Purpose
The purpose of this paper is to examine the magneto hydrodynamic flow and heat transfer of nanofluids over a permeable wedge based on engine oil which is under the effects of thermal radiation and convective heating.

Design/methodology/approach
The equations governing the flow are transformed into differential equations by applying similarity transformations. Keller box method is used to bring out the numerical solution.

Findings
The discovery interprets that temperature as well as the velocity of Ag-engine oil nanofluids are more noticeable than Cu-engine oil nanofluids. Thermal boundary layer increases for radiation parameter as well as Biot number. Fluctuations of co-efficient of drag skin friction as well heat transfer rate at the wall are also tested.

Originality/value
Till now, no numerical studies are reported on the heat transfer enhancement of the permeable wedge under thermal radiation on engine oil nanofluid flow by considering convective heating.
Differential clustering of fecal and mucosa‐associated microbiota in ‘healthy’ individuals
Authors: Carstens Adam , Roos Annika , Andreasson Anna , Magnuson Anders , Agréus Lars , Halfvarson Jonas , Engstrand Lars 
Published: November 2018

ObjectiveFecal samples are often used to characterize gut microbiota. However, whether or not fecal microbiota differs from mucosa‐associated microbiota remains largely unknown. This may be specifically relevant in conditions that are characterized by complex mucosal microbe–host interactions, such as Crohn’s disease. We aimed to determine the degree of agreement between fecal and mucosal microbiota profiles in ‘healthy’ individuals, using two commonly used collection procedures.MethodsThe gut microbiota composition of fecal samples (sent at ambient temperature before storage at −70°C) and of colonic biopsies (obtained at endoscopy and immediately stored at −70°C) was determined by sequencing the 16S rRNA gene. Altogether 31 randomly selected ‘healthy’ individuals from the population‐based colonoscopy (Popcol) study were included.ResultsThe fecal samples were characterized by a reduced degree of richness (P < 0.0001) and diversity (P = 0.016), and also differences in several phyla, including a lower relative abundance of Proteobacteria (P < 0.0001) and Verrucomicrobia (P = 0.008) than in biopsies. Only three of 30 individuals had a similar fecal and mucosal microbiota profile, based on weighted UniFrac analysis. A difference in Crohn’s disease dysbiosis‐associated bacteria was observed, including a lower relative abundance of Faecalibacterium (P = 0.004) and a higher relative abundance of Ruminococcus (P = 0.001) in feces than in biopsies.ConclusionsThe observed differences between fecal samples, transported at ambient temperature, and the colonic mucosa‐associated microbiota have implications for the interpretation of the previous literature, and may be specifically relevant to studies on Crohn’s disease.