bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis
Authors: Johnson Benjamin K. , Scholz Matthew B. , Teal Tracy K. , Abramovitch Robert B. 
Published: July 2015

ABSTRACTSummarySPARTA is a reference-based bacterial RNA-seq analysis workflow application for single-end Illumina reads. SPARTA is turnkey software that simplifies the process of analyzing RNA-seq data sets, making bacterial RNA-seq analysis a routine process that can be undertaken on a personal computer or in the classroom. The easy-to-install, complete workflow processes whole transcriptome shotgun sequencing data files by trimming reads and removing adapters, mapping reads to a reference, counting gene features, calculating differential gene expression, and, importantly, checking for potential batch effects within the data set. SPARTA outputs quality analysis reports, gene feature counts and differential gene expression tables and scatterplots. The workflow is implemented in Python for file management and sequential execution of each analysis step and is available for Mac OS X, Microsoft Windows, and Linux. To promote the use of SPARTA as a teaching platform, a web-based tutorial is available explaining how RNA-seq data are processed and analyzed by the software.Availability and ImplementationTutorial and workflow can be found at sparta.readthedocs.org. Teaching materials are located atsparta-teaching.readthedocs.org. Source code can be downloaded atwww.github.com/abramovitchMSU/, implemented in Python and supported on Mac OS X, Linux, and MS Windows.ContactRobert B. Abramovitch (abramov5@msu.edu)Supplemental InformationSupplementary data are available atBioinformaticsonline.
Livestock market data for modeling disease spread among US cattle
Authors: Carroll Ian T. , Bansal Shweta 
Published: July 2015

AbstractTransportation of livestock carries the risk of spreading foreign animal diseases, leading to costly public and private sector expenditures on disease containment and eradication. Livestock movement tracing systems in Europe, Australia and Japan have allowed epidemiologists to model the risks engendered by transportation of live animals and prepare responses designed to protect the livestock industry. Within the US, data on livestock movement is not sufficient for direct parameterization of models for disease spread, but network models that assimilate limited data provide a path forward in model development to inform preparedness for disease outbreaks in the US. Here, we develop a novel data stream, the information publicly reported by US livestock markets on the origin of cattle consigned at live auctions, and demonstrate the potential for estimating a national-scale network model of cattle movement. By aggregating auction reports generated weekly at markets in several states, including some archived reports spanning several years, we obtain a market-oriented sample of edges from the dynamic cattle transportation network in the US. We first propose a sampling framework that allows inference about shipments originating from operations not explicitly sampled and consigned at non-reporting livestock markets in the US, and we report key predictors that are influential in extrapolating beyond our opportunistic sample. As a demonstration of the utility gained from the data and fitted parameters, we model the critical role of market biosecurity procedures in the context of a spatially homogeneous but temporally dynamic representation of cattle movements following an introduction of a foreign animal disease. We conclude that auction market data fills critical gaps in our ability to model intrastate cattle movement for infectious disease dynamics, particularly with an ability to addresses the capacity of markets to amplify or control a livestock disease outbreak.Author SummaryWe have automated the collection of previously unavailable cattle movement data, allowing us to aggregate details on the origins of cattle sold at live-auction markets in the US. Using our novel dataset, we demonstrate potential to infer a complete dynamic transportation network that would drive disease transmission in models of potential US livestock epidemics.
Capacity gaps in post disaster construction
&
demolition waste management
Authors: Karunasena Gayani , Amaratunga Dilanthi 
Published: July 2015

Purpose
– The purpose of this paper is to focus on the identification of the existing capacities of post disaster C
&
D waste management in developing countries, with a special emphasis on Sri Lanka to determine the capacity gaps and related influencing factors.

Design/methodology/approach
– Multiple case studies and expert interviews were conducted to gather primary information on the existing capacities of disaster C
&
D waste management. Three case studies, including 15 individuals and six experts representing government, non-government institutions and others, were selected.

Findings
– The results revealed the existing capacities, capacity gaps and influencing factors for post disaster C
&
D waste management in the areas of skills and confidence building, links and collaborations, continuity and sustainability, research and development, communication and coordination, organisational implementation and investment in infrastructure.

Research limitations/implications
– This study limited disaster C
&
D waste to debris generated from totally or partially damaged buildings and infrastructure as a direct impact of natural disasters or from demolished buildings and infrastructure at rehabilitation or at early recovery stages.

Originality/value
– The research enabled an analysis of existing capacities and identified capacity gaps in post disaster C
&
D waste management with influencing factors developing countries.
The impact of mobile phone penetration on African inequality
Authors: Asongu Simplice 
Published: July 2015

Purpose
– The purpose of this paper is to complement theoretical and qualitative literature with empirical evidence on the income-redistributive effect of mobile phone penetration in 52 African countries.

Design/methodology/approach
– Robust ordinary least squares and two stage least squares empirical strategies are employed.

Findings
– The findings suggest that mobile penetration is pro-poor, as it has a positive income equality effect.

Social implications
– “Mobile phone”-oriented poverty reduction channels are discussed.

Originality/value
– It deviates from mainstream country-specific and microeconomic survey-based approaches in the literature and provides the first macroeconomic assessment of the “mobile phone”-inequality nexus.
The potential of community entrepreneurship for neighbourhood revitalization in the United Kingdom and the United States
Authors: Varady David , Kleinhans Reinout , van Ham Maarten 
Published: July 2015

Purpose– The aim of this paper is to assess the current potential of community entrepreneurship in neighbourhood revitalisation in the US and the UK. The global economic crisis has had a major impact on government spending for urban regeneration. In the context of these austerity regimes, in many European countries, community entrepreneurship and active citizenship are increasingly considered as a means to continue small-scale urban revitalisation. This paper investigates recent literature on both British community enterprises (CEs) and American community development corporations (CDCs).Design/methodology/approach– Starting from a seminal article, this paper reviews literature focusing on the role of CEs and CDCs in neighbourhood revitalisation. Differences and similarities are analysed, taking into account national context differences.Findings– While CDCs have a relatively successful record in affordable housing production in distressed areas, CDCs are fundamentally limited in terms of reversing processes of community decline. CEs in the UK have focused on non-housing issues.Research limitations/implications– This paper asks the question what CEs can learn from CDCs in terms of scope, aims, strategies, accountability, assets and partnerships with public and private actors. However, a systematic literature review has not been conducted.Originality/value– This comparison reveals not only similarities but also differences with regard to aims, organisational characteristics, cooperation on multiple scales and community participation. Apart from lessons that can be learned, this paper provides recommendations for further research that should cover the lack of empirical evidence in this field.
Comparing entrepreneurial communities
Authors: Paul Justin , Shrivastava Archana 
Published: July 2015

Purpose– The purpose of this paper is to compare entrepreneurial attributes of MBA students, the next generation business people, from two important Asian countries, India from South Asia and Japan from East Asia (India, being an emerging country and Japan, a developed country).Design/methodology/approach– Survey responses from MBA students in India and Japan were measured on an entrepreneurial personality index. Bateman and Crant’s scale consisting of 17 traits is used to identify if entrepreneurial traits are a learned cultural behaviour or intrinsic personality factors.Findings– Although the findings indicate that India has benefitted from entrepreneurship in the information technology and information technology-enabled service ventures during the past two decades, the country still has a long way to go when compared to developed countries like Japan, where entrepreneurship is widespread.Research limitations/implications– The results are based on a single survey, using cross-sectional data.Originality/value– The level of entrepreneurship differs considerably across countries and periods. The authors put forward a theoretical framework to denote the linkage between entrepreneurial attitude, pro-active personality and culture, besides highlighting the three pillars of entrepreneurship.
Continental‐scale variation in seaweed host‐associated bacterial communities is a function of host condition, not geography
Authors: Marzinelli Ezequiel M. , Campbell Alexandra H. , Zozaya Valdes Enrique , Vergés Adriana , Nielsen Shaun , Wernberg Thomas , de Bettignies Thibaut , Bennett Scott , Caporaso J. Gregory , Thomas Torsten , Steinberg Peter D. 
Published: July 2015

SummaryInteractions between hosts and associated microbial communities can fundamentally shape the development and ecology of ‘holobionts’, from humans to marine habitat‐forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large‐scale drivers of host‐associated microbial communities are largely unknown. Using 16S‐rRNA gene sequencing, we characterized 260 seaweed‐associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a ‘core’ microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale.
Long‐term neurodevelopmental outcome after selective feticide in monochorionic pregnancies
Authors: van Klink JMM , Koopman HM , Middeldorp JM , Klumper FJ , Rijken M , Oepkes D , Lopriore E 
Published: July 2015

ObjectiveTo assess the incidence of and risk factors for adverse long‐term neurodevelopmental outcome in complicated monochorionic pregnancies treated with selective feticide at our centre between 2000 and 2011.DesignObservational cohort study.SettingNational referral centre for fetal therapy (Leiden University Medical Centre, the Netherlands).PopulationNeurodevelopmental outcome was assessed in 74 long‐term survivors.MethodsChildren, at least 2 years of age, underwent an assessment of neurologic, motor and cognitive development using standardised psychometric tests and the parents completed a behavioural questionnaire.Main outcome measuresA composite outcome termed neurodevelopmental impairment including cerebral palsy (GMFCS II‐V), cognitive and/or motor test score of <70, bilateral blindness or bilateral deafness requiring amplification.ResultsA total of 131 monochorionic pregnancies were treated with selective feticide at the Leiden University Medical Centre. Overall survival rate was 88/131 (67%). Long‐term outcome was assessed in 74/88 (84%). Neurodevelopmental impairment was detected in 5/74 [6.8%, 95% confidence interval (CI), 1.1–12.5] of survivors. Overall adverse outcome, including perinatal mortality or neurodevelopmental impairment was 48/131 (36.6%). In multivariate analysis, parental educational level was associated with cognitive test scores (regression coefficient B 3.9, 95% CI 1.8–6.0). Behavioural problems were reported in 10/69 (14.5%).ConclusionsAdverse long‐term outcome in survivor twins of complicated monochorionic pregnancies treated with selective feticide appears to be more prevalent than in the general population. Cognitive test scores were associated with parental educational level.Tweetable abstractNeurodevelopmental impairment after selective feticide was detected in 5/74 (6.8%, 95% CI 1.1–12.5) of survivors.
Model to predict inpatient mortality from information gathered at presentation to an emergency department: The Triage Information Mortality Model (TIMM)
Authors: Teubner David JO , Considine Julie , Hakendorf Paul , Kim Susan , Bersten Andrew D 
Published: July 2015

AbstractObjectivesTo derive and validate a mortality prediction model from information available at ED triage.MethodsMultivariable logistic regression of variables from administrative datasets to predict inpatient mortality of patients admitted through an ED. Accuracy of the model was assessed using the receiver operating characteristic area under the curve (ROC‐AUC) and calibration using the Hosmer–Lemeshow goodness of fit test. The model was derived, internally validated and externally validated. Derivation and internal validation were in a tertiary referral hospital and external validation was in an urban community hospital.ResultsThe ROC‐AUC for the derivation set was 0.859 (95% CI 0.856–0.865), for the internal validation set was 0.848 (95% CI 0.840–0.856) and for the external validation set was 0.837 (95% CI 0.823–0.851). Calibration assessed by the Hosmer–Lemeshow goodness of fit test was good.ConclusionsThe model successfully predicts inpatient mortality from information available at the point of triage in the ED.
High‐throughput monitoring of wild bee diversity and abundance via mitogenomics
Authors: Tang Min , Hardman Chloe J. , Ji Yinqiu , Meng Guanliang , Liu Shanlin , Tan Meihua , Yang Shenzhou , Moss Ellen D. , Wang Jiaxin , Yang Chenxue , Bruce Catharine , Nevard Tim , Potts Simon G. , Zhou Xin , Yu Douglas W. 
Published: July 2015

Summary

Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high‐throughput identification pipeline.

We show that the metagenomic mining and resequencing of mitochondrial genomes (mitogenomics) can be applied successfully to bulk samples of wild bees. We assembled the mitogenomes of 48 UK bee species and then shotgun‐sequenced total DNA extracted from 204 whole bees that had been collected in 10 pan‐trap samples from farms in England and been identified morphologically to 33 species. Each sample data set was mapped against the 48 reference mitogenomes.

The morphological and mitogenomic data sets were highly congruent. Out of 63 total species detections in the morphological data set, the mitogenomic data set made 59 correct detections (93·7% detection rate) and detected six more species (putative false positives). Direct inspection and an analysis with species‐specific primers suggested that these putative false positives were most likely due to incorrect morphological IDs. Read frequency significantly predicted species biomass frequency (R2 = 24·9%). Species lists, biomass frequencies, extrapolated species richness and community structure were recovered with less error than in a metabarcoding pipeline.

Mitogenomics automates the onerous task of taxonomic identification, even for cryptic species, allowing the tracking of changes in species richness and distributions. A mitogenomic pipeline should thus be able to contain costs, maintain consistently high‐quality data over long time series, incorporate retrospective taxonomic revisions and provide an auditable evidence trail. Mitogenomic data sets also provide estimates of species counts within samples and thus have potential for tracking population trajectories.
Corporate fraud culture: Re‐examining the corporate governance and performance relation
Authors: Tan David T. , Chapple Larelle , Walsh Kathleen D. 
Published: July 2015

AbstractWe analyse the corporate governance and performance relation, when conditioning on corporate fraud, for fraud firms during 2000 – 2007. Fraud firms are identified as either self‐ reported fraud events, or subject to regulatory investigation. We use the inverse Mills ratio procedure to account for firms' (unobservable) fraud culture in the dynamic system GMM model of the performance‐ governance relation. We find that corporate governance is an endogenously determined characteristic that has no causal impact on firm performance when conditioning on fraud. Fraud is a significant regulatory event but its overall economic impact at the firm level is highly variable.
Development and Characterization of the Arterial Windkessel and Its Role During Left Ventricular Assist Device Assistance
Authors: Capoccia Massimo 
Published: July 2015

AbstractModeling of the cardiovascular system is challenging, but it has the potential to further advance our understanding of normal and pathological conditions. Morphology and function are closely related. The arterial system provides steady blood flow to each organ and damps out wave fluctuations as a consequence of intermittent ventricular ejection. These actions can be approached separately in terms of mathematical relationships between pressure and flow. Lumped parameter models are helpful for the study of the interactions between the heart and the arterial system. The arterial windkessel model still plays a significant role despite its limitations. This review aims to discuss the model and its modifications and derive the fundamental equations by applying electric circuits theory. In addition, its role during left ventricular assist device assistance is explored and discussed in relation to rotary blood pumps.
Acute Myocardial Infarction Complicated by Cardiogenic Shock: An Algorithm‐Based Extracorporeal Membrane Oxygenation Program Can Improve Clinical Outcomes
Authors: Unai Shinya , Tanaka Daizo , Ruggiero Nicholas , Hirose Hitoshi , Cavarocchi Nicholas C. 
Published: July 2015

AbstractExtracorporeal membrane oxygenation (ECMO) in our institution resulted in near total mortality prior to the establishment of an algorithm‐based program in July 2010. We hypothesized that an algorithm‐based ECMO program improves the outcome of patients with acute myocardial infarction complicated with cardiogenic shock. Between March 2003 and July 2013, 29 patients underwent emergent catheterization for acute myocardial infarction due to left main or proximal left anterior descending artery occlusion complicated with cardiogenic shock (defined as systolic blood pressure <90 mm Hg despite multiple inotropes, with or without intra‐aortic balloon pump, lactic acidosis). Of 29 patients, 15 patients were treated before July 2010 (Group 1, old program), and 14 patients were treated after July 2010 (Group 2, new program). There were no significant differences in the baseline characteristics, including age, sex, coronary risk factors, and left ventricular ejection fraction between the two groups. Cardiopulmonary resuscitation prior to ECMO was performed in two cases (13%) in Group 1 and four cases (29%) in Group 2. ECMO support was performed in one case (6.7%) in Group 1 and six cases (43%) in Group 2. The 30‐day survival of Group 1 versus Group 2 was 40 versus 79% (P = 0.03), and 1‐year survival rate was 20 versus 56% (P = 0.01). The survival rate for patients who underwent ECMO was 0% in Group 1 versus 83% in Group 2 (P = 0.09). In Group 2, the mean duration on ECMO was 9.8 ± 5.9 days. Of the six patients who required ECMO in Group 2, 100% were successfully weaned off ECMO or were bridged to ventricular assist device implantation. Initiation of an algorithm‐based ECMO program improved the outcomes in patients with acute myocardial infarction complicated by cardiogenic shock.
Evaluation of a Spiral Groove Geometry for Improvement of Hemolysis Level in a Hydrodynamically Levitated Centrifugal Blood Pump
Authors: Murashige Tomotaka , Kosaka Ryo , Sakota Daisuke , Nishida Masahiro , Kawaguchi Yasuo , Yamane Takashi , Maruyama Osamu 
Published: July 2015

AbstractThe purpose of this study is to evaluate a spiral groove geometry for a thrust bearing to improve the hemolysis level in a hydrodynamically levitated centrifugal blood pump. We compared three geometric models: (i) the groove width is the same as the ridge width at any given polar coordinate (conventional model); (ii) the groove width contracts inward from 9.7 to 0.5 mm (contraction model); and (iii) the groove width expands inward from 0.5 to 4.2 mm (expansion model). To evaluate the hemolysis level, an impeller levitation performance test and in vitro hemolysis test were conducted using a mock circulation loop. In these tests, the driving conditions were set at a pressure head of 200 mm Hg and a flow rate of 4.0 L/min. As a result of the impeller levitation performance test, the bottom bearing gaps of the contraction and conventional models were 88 and 25 μm, respectively. The impeller of the expansion model touched the bottom housing. In the hemolysis test, the relative normalized index of hemolysis (NIH) ratios of the contraction model in comparison with BPX‐80 and HPM‐15 were 0.6 and 0.9, respectively. In contrast, the relative NIH ratios of the conventional model in comparison with BPX‐80 and HPM‐15 were 9.6 and 13.7, respectively. We confirmed that the contraction model achieved a large bearing gap and improved the hemolysis level in a hydrodynamically levitated centrifugal blood pump.