bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effective responses: Protestants, Catholics and the provision of health care in the post-war Kivus
Authors: Seay Laura 
                      E. 
Published: March 2013

In extremely weak states, why are some civil society organisations better at providing health care than others? The case of health-care provision in the Kivu provinces of the eastern DRC provides a useful context in which to examine this question. Faced with the negative effects of more than 15 years of conflict, civil society organisations are the only institutions capable of providing social services. This article uses a series of case studies of local, faith-based health-care providers to argue that a number of historical, demographic and institutional factors cause some groups to develop stronger social capital networks than others. This in turn affects the degree of effectiveness that an organisation will have in providing social services in the state's absence. In doing so, they effectively substitute for the state in its role as a provider and regulator of public goods.
[Réponses efficaces : les Protestants, les Catholiques et la prévention des soins sanitaires dans le Kivu d'après-guerre]. Dans les états extrêmement faibles, pourquoi certaines organisations de la société civile sont plus efficaces pour fournir les soins sanitaires que d'autres? Le cas de prévention des soins sanitaires dans les provinces du Kivu à l'est de la RDC fournit un contexte pertinent pour examiner cette question. Faisant face aux effets négatifs de plus de 15 ans de conflits, les organisations de la société civile sont les seules institutions capables de fournir des services sociaux. Cet article utilise une série d'études de cas de fournisseurs de soins de santé confessionnels opérant au niveau local, pour soutenir qu'un certain nombre de facteurs historiques, démographiques et institutionnels permettent à certains groupes de développer de plus forts réseaux sociaux que d'autres. Ceci affecte à son tour le degré d'efficacité d'une organisation dans la fourniture de services sociaux en l'absence de l'État. De cette manière, ils se substituent effectivement à l'État dans son rôle de fournisseur et régulateur de biens publics.

Mots-clés : RDC ; soins de santé, religion ; les Protestants, les Catholiques ; Kivu
Ontogenetic Development of the Digestive Tract in Larvae of American Shad
Authors: Hong X Y , Zhu X P , Chen K C , Pan D B , Li K B 
Published: March 2013

Abstract
The American Shad Alosa sapidissima was introduced into China for aquaculture in 2003. The histological characteristics of the digestive tract of American Shad larvae were examined from hatching to 33 d after hatching (DAH) with the aim of cultivating the larvae efficiently. The fertilized American Shad eggs were imported from Oregon and incubated in barrels with spring water maintained at 20.3–21.9°C in Qingyuan, Guangdong Province, China. The larvae were transferred to cement pools (water temperature at 24.0–25.0°C) at 13 DAH. Larvae were fed Artemia nauplii starting at 3 DAH, Artemia nauplii supplemented with gradually increasing proportions of commercial formulated feed after 18 DAH, and then only the formulated feed by 30 DAH. Based on the source of nutrition and structural changes in the digestive tract, larval development was divided into three stages: (1) lecitotrophic (0–2 DAH), (2) lecitoexotrophic (3 DAH), and (3) exotrophic (4–33 DAH). At 0 DAH of the lecitotrophic stage, the digestive system was undifferentiated and contained a large acidophilic yolk sac. By 1 DAH, the mouth and anus opened, the liver appeared, and the buccopharynx and intestine began to differentiate. The lecitoexotrophic stage began at the start of exogenous feeding, which led to the disappearance of the yolk sac. During the exotrophic stage, the esophagus could be differentiated into two different regions by 4 DAH. The intestinal tract developed quickly and differentiated into an obvious foregut and hindgut by 11 DAH. The primary stomach formed by 8 DAH and completely developed by 19 DAH with the presence of a few gastric glands. By 25 DAH, many gastric glands and a number of pyloric ceca were observed. The results of the study show the quick development of the digestive system in American Shad and we suggest initiating the weaning process at 23–25 DAH in the larvae.
EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection
Authors: Chu Hsueh-Ting , Hsiao William W. L. , Chen Jen-Chih , Yeh Tze-Jung , Tsai Mong-Hsun , Lin Han , Liu Yen-Wenn , Lee Sheng-An , Chen Chaur-Chin , Tsao Theresa T. H. , Kao Cheng-Yan 
Published: March 2013

Abstract
Motivation: High-accuracy de novo assembly of the short sequencing reads from RNA-Seq technology is very challenging. We introduce a de novo assembly algorithm, EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo. This algorithm uses an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in RNA-Seq data.
Results: EBARDenovo resolves the complications of RNA-Seq assembly arising from sequencing errors, repetitive sequences and aberrant chimeric amplicons. In a series of assembly experiments, our algorithm is the most accurate among the examined programs, including de Bruijn graph assemblers, Trinity and Oases.
Availability and implementation: EBARDenovo is available at http://ebardenovo.sourceforge.net/. This software package (with patent pending) is free of charge for academic use only.
Contact: cykao@csie.ntu.edu.tw, htchu@asia.edu.tw or postergrey@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package
Authors: Kemena Carsten , Bussotti Giovanni , Capriotti Emidio , Marti-Renom Marc A. , Notredame Cedric 
Published: March 2013

Abstract
Motivation: Aligning RNAs is useful to search for homologous genes, study evolutionary relationships, detect conserved regions and identify any patterns that may be of biological relevance. Poor levels of conservation among homologs, however, make it difficult to compare RNA sequences, even when considering closely evolutionary related sequences.
Results: We describe SARA-Coffee, a tertiary structure-based multiple RNA aligner, which has been validated using BRAliDARTS, a new benchmark framework designed for evaluating tertiary structure–based multiple RNA aligners. We provide two methods to measure the capacity of alignments to match corresponding secondary and tertiary structure features. On this benchmark, SARA-Coffee outperforms both regular aligners and those using secondary structure information. Furthermore, we show that on sequences in which &lt;60% of the nucleotides form base pairs, primary sequence methods usually perform better than secondary-structure aware aligners.
Availability and implementation: The package and the datasets are available from http://www.tcoffee.org/Projects/saracoffee and http://structure.biofold.org/sara/.
Contact: cedric.notredame@crg.es
Supplementary information: Supplementary data are available at Bioinformatics online
SplicingCompass: differential splicing detection using RNA-Seq data
Authors: Aschoff Moritz , Hotz-Wagenblatt Agnes , Glatting Karl-Heinz , Fischer Matthias , Eils Roland , König Rainer 
Published: March 2013

AbstractMotivation: Alternative splicing is central for cellular processes and substantially increases transcriptome and proteome diversity. Aberrant splicing events often have pathological consequences and are associated with various diseases and cancer types. The emergence of next-generation RNA sequencing (RNA-seq) provides an exciting new technology to analyse alternative splicing on a large scale. However, algorithms that enable the analysis of alternative splicing from short-read sequencing are not fully established yet and there are still no standard solutions available for a variety of data analysis tasks.Results: We present a new method and software to predict genes that are differentially spliced between two different conditions using RNA-seq data. Our method uses geometric angles between the high dimensional vectors of exon read counts. With this, differential splicing can be detected even if the splicing events are composed of higher complexity and involve previously unknown splicing patterns. We applied our approach to two case studies including neuroblastoma tumour data with favourable and unfavourable clinical courses. We show the validity of our predictions as well as the applicability of our method in the context of patient clustering. We verified our predictions by several methods including simulated experiments and complementary in silico analyses. We found a significant number of exons with specific regulatory splicing factor motifs for predicted genes and a substantial number of publications linking those genes to alternative splicing. Furthermore, we could successfully exploit splicing information to cluster tissues and patients. Finally, we found additional evidence of splicing diversity for many predicted genes in normalized read coverage plots and in reads that span exon–exon junctions.Availability: SplicingCompass is licensed under the GNU GPL and freely available as a package in the statistical language R at http://www.ichip.de/software/SplicingCompass.htmlContact: m.aschoff@dkfz.de or r.koenig@dkfz.deSupplementary information: Supplementary data are available at Bioinformatics online.
RCPedia: a database of retrocopied genes
Authors: Navarro Fábio C. P. , Galante Pedro A. F. 
Published: March 2013

Abstract
Motivation: Retrocopies are copies of mature RNAs that are usually devoid of regulatory sequences and introns. They have routinely been classified as processed pseudo-genes with little or no biological relevance. However, recent findings have revealed functional roles for retrocopies, as well as their high frequency in some organisms, such as primates. Despite their increasing importance, there is no user-friendly and publicly available resource for the study of retrocopies.
Results: Here, we present RCPedia, an integrative and user-friendly database designed for the study of retrocopied genes. RCPedia contains a complete catalogue of the retrocopies that are known to be present in human and five other primate genomes, their genomic context, inter-species conservation and gene expression data. RCPedia also offers a streamlined data representation and an efficient query system.
Availability and implementation: RCPedia is available at http://www.bioinfo.mochsl.org.br/rcpedia.
Contact: pgalante@mochsl.org.br
Supplementary information: Supplementary data are available at Bioinformatics online.
Direct distance measurements to SN 2009ip
Authors: Potashov M. , Blinnikov S. , Baklanov P. , Dolgov A. 
Published: March 2013

Abstract
We demonstrate the applicability of our new method (the Dense Shell Method or DSM) for the determination of astronomical distances by calculating the distance to SN 2009ip. The distance to this supernova has been accurately determined in the standard approach via the cosmic distance ladder and has been found to be 20.4 Mpc. Our direct method, assuming the most reasonable parameter values, gives a very close result, namely ≈20.1 ± 0.8 (68 per cent CL) Mpc to SN 2009ip.
Effect of Milling Temperature and Postmilling Cooling Procedures on Rice Milling Quality Appraisals
Authors: Pan Zhongli , Khir Ragab , Thompson James F. 
Published: March 2013

ABSTRACTThe objective of this research was to study the effects of different milling conditions and postmilling handling procedures on appraised milling quality of rough rice. Rough rice (M202) with moisture content of 11.5 ± 0.2% was used for this study. The samples were milled with a McGill number 3 mill under four milling conditions, including normal milling, milling at high temperature, milling with cooling using ice water, and room temperature water. The milled rice samples were cooled in closed and open plastic containers and in open pans with three temperatures: 15, 23, and 35°C. The effects of milling and postmilling conditions on milled rice temperature, moisture loss, cooling rate, single and multiple fissuring rates, total rice yield (TRY), head rice yield (HRY), whiteness index (WI), and total lipid content (TLC) were evaluated. Results showed that high single and multiple fissuring rates and low TRY and HRY were inherent in improper milling and postmilling conditions. Single fissuring rates were 15.9 and 17.6% and multiple fissuring rates were 3.5 and 7.2% for rice samples milled under normal and high‐temperature conditions, respectively. Cooling methods that used open containers and pans had more moisture losses and further resulted in lowering appraised milling quality than methods that used closed containers. Low‐temperature milling conditions followed by cooling in closed containers significantly reduced single and multiple fissuring rates and improved TRY and HRY by 0.9 and 1.5 percentage points, respectively. The effects of tested milling and postmilling conditions on WI and TLC were not significant. Obtained results constitute valuable information for developing milling and cooling procedures to achieve consistent, accurate, and reliable milling quality appraisals for rough rice.
Validity of the Lipid Sink as a Mechanism for the Reversal of Local Anesthetic Systemic Toxicity
Authors: Kuo Ilin , Akpa Belinda S. 
Published: March 2013

Abstract

Background:

In vitro observations support the lipid sink theory of therapeutic action by confirming the capacity of lipid emulsions to successfully uptake bupivacaine from aqueous media. However, competing hypotheses and some in/ex vivo small animal studies suggest that a metabolic or positive inotropic effect underlies the dramatic effects of lipid therapy. Controlled clinical tests to establish causality and mechanism of action are an impossibility. In an effort to quantitatively probe the merits of a “sink” mechanism, a physiologically based pharmacokinetic model has been developed that considers the binding action of plasma lipid.

Methods:
The model includes no fitting parameters and accounts for concentration dependence of plasma protein and lipid:anesthetic binding as well as the metabolism of the lipid scavenger. Predicted pharmacokinetics were validated by comparison with data from healthy volunteers administered a nontoxic dose of bupivacaine. The model was augmented to simulate lipid therapy and extended to the case of accidental IV infusion of bupivacaine at levels known to cause systemic toxicity.

Results:
The model yielded quantitative agreement with available pharmacokinetic data. Simulated lipid infusion following an IV overdose was predicted to yield (1) an increase in total plasma concentration, (2) a decrease in unbound concentration, and (3) a decrease in tissue content of bupivacaine.

Conclusions:
Results suggest that the timescale on which tissue content is reduced varies from organ to organ, with the concentration in the heart falling by 11% within 3 min. This initial study suggests that, in isolation, the lipid sink is insufficient to guarantee a reversal of systemic toxicity.
Protein-Coding cis-Natural Antisense Transcripts Have High and Broad Expression in Arabidopsis
Authors: Zhan Shuhua , Lukens Lewis 
Published: March 2013

Abstract
Pairs of genes within eukaryotic genomes are often located on opposite DNA strands such that transcription generates cis-natural sense antisense transcripts (cis-NATs). This orientation of genes has been associated with the biogenesis of splice variants and natural antisense small RNAs. Here, in an analysis of currently available data, we report that within Arabidopsis (Arabidopsis thaliana), protein-coding cis-NATs are also characterized by high abundance, high coexpression, and broad expression. Our results suggest that a permissive chromatin environment may have led to the proximity of these genes. Compared with other genes, cis-NAT-encoding genes have enriched low-nucleosome-density regions, high levels of histone H3 lysine-9 acetylation, and low levels of H3 lysine-27 trimethylation. Promoters associated with broadly expressed genes are preferentially found in the 5′ regulatory sequences of cis-NAT-encoding genes. Our results further suggest that natural antisense small RNA production from cis-NATs is limited. Small RNAs sequenced from natural antisense small RNA biogenesis mutants including dcl1, dcl2, dcl3, and rdr6 map to cis-NATs as frequently as small RNAs sequenced from wild-type plants. Future work will investigate if the positive transcriptional regulation of overlapping protein-coding genes contributes to the prevalence of these genes within other eukaryotic genomes.
The influence of ERP implementation on the division of power at the production‐sales interface
Authors: de Vries Jan , Boonstra Albert 
Published: March 2013

PurposeThe purpose of this paper is to develop and validate a model that demonstrates the influence of enterprise resource planning (ERP) implementation on the power and interests of actors at the production‐sales interface, and vice versa.Design/methodology/approachAn empirical in‐depth longitudinal case study examines how a medium‐sized company in the graphics industry implemented an ERP system and how this has affected the interests and power distribution between the manufacturing and sales departments.FindingsThe case study reveals that the power division among key players at the production‐sales interface has been affected by the ERP implementation. These changes influence their attitudes and behaviours as well as the usage of the ERP system.Research limitations/implicationsLimitations are associated with the inherent weaknesses of any research based on a single‐case study: theoretical, but not statistical, generalisations are possible.Practical implicationsThe findings imply that those implementing ERP systems in production‐sales environments should, from the outset of the project, identify potential changes in the division of power and seek to reconcile stakeholder interests.Originality/valueThis is one of the few studies that has examined in‐depth the potential effects of ERP implementation on power division at the production‐sales interface.
Logistics supplier integration in the automotive industry
Authors: Bennett David , Klug Florian 
Published: March 2013

PurposeIn recent decades the automotive industry has established a variety of new forms of logistics integration between automobile assemblers and their suppliers, in particular those in the first tier. The purpose of this paper is to outline which form of logistics integration original equipment manufacturer (OEM) assembly plants use to link up with proximate suppliers, and to classify and compare different types of logistics supplier integration.Design/methodology/approachThe data and insights for this paper come from a literature review of research and practitioner papers and studies to survey logistics integration models in theory and practice. In addition, data are collected through semi‐structured interviews and site visits.FindingsThe main findings are summarised in five conditions which characterise logistics supplier integration in the automotive industry. These conditions vary significantly between local dedicated supply as discussed in this paper and the traditional supply, which is distant and scattered around suppliers. These main conditions are “geographical proximity”, “delivery contents, volume and sequence”, “shared investment and asset specificity”, “information sharing and information technology system integration” as well as “transport system”. Although all of the five conditions were considered relevant for the description of existing integration forms, only the “geographical proximity” dimension is emerged as most suited for a formal typology. Therefore, a seven‐step integration model was developed which allows for a categorisation and comparison of existing logistics integration forms of proximate supply.Research limitations/implicationsThis research aims to support the academic study of cross‐company and inter‐organisational supplier integration by providing consistent criteria for cross‐site comparisons. A holistic and consistent understanding of different logistics integration types will be necessary, which will help in evaluating the actual integration forms such as supplier parks.Originality/valueThe majority of studies into the supplier integration phenomenon conclude that logistical concerns are the driving factor behind supplier co‐location. Therefore, the focus of this research is on the spectrum of vertical integration in logistics between the vehicle manufacturers and their suppliers.
An evaluation of problem‐based assessment in teaching operations management
Authors: Bamford David , Karjalainen Katri , Jenavs Ernest 
Published: March 2013

PurposeThe aim of this paper is to respond to calls for in‐depth studies of production and operations management (OM) teaching by providing an analysis of the relative effectiveness of a continuous problem‐based assessment and a traditional final exam assessment in OM.Design/methodology/approachAn undergraduate OM module is used to assess how well a problem‐based assessment method performs against a more traditional final exam in terms of impact on student learning, student classification and feasibility. Quantitative data on student performance, feedback and satisfaction are used.FindingsThe analysis shows that the problem‐based assessment provides a better learning experience for the students, but is a worse classificatory of student results than the conventional exam. In terms of feasibility, problem‐based assessment can be a cost‐effective assessment method.Research limitations/implicationsThis study analyses the assessment method used on one module for nine years; to increase the generalizability of the findings further research is needed with different modules and contexts.Practical implicationsThis paper gives guidance to OM educators on how to improve assessment methods to achieve both improved learning effects as well as an accurate classification of student performance.Originality/valueThis study extends the literature on problem‐based learning to assessments and provides an empirical analysis of one such method. This study also provides detailed analysis of different assessment methods in OM based on longitudinal data.
Identifying critical enablers and pathways to high performance supply chain quality management
Authors: Lin Chinho , Kuei Chu‐hua , Chai Kang‐Wei 
Published: March 2013

PurposeThe aim of this paper is threefold: first, to examine the content of supply chain quality management (SCQM); second, to identify the structure of SCQM; and third, to show ways for finding improvement opportunities and organizing individual institution's resources/actions into collective performance outcomes.Design/methodology/approachTo meet the goals of this work, the paper uses abductive reasoning and two qualitative methods: content analysis and formal concept analysis (FCA). Primary data were collected from both original design manufacturers (ODMs) and original equipment manufacturers (OEMs) in Taiwan.FindingsAccording to the qualitative empirical study, modern enterprises need to pay immediate attention to the following two pathways: a compliance approach and a voluntary approach. For the former, three strategic content variables are identified: training programs, ISO, and supplier quality audit programs. As for initiating a voluntary effort, modern lead firms need to instill “motivation” into a supply chain quality system.Practical implicationsThe findings based on the abductive model reveal numerous strategic and tactical enablers, key sequences to move firms from their current situation to their preferred one, and critical opportunities for supply chain‐wide quality system designs.Originality/valueThis study will be of great value to supply chain policy makers, supply chain operators, and decision makers in lead firms in a supply chain setting and their channel partners. The proactive use of the authors' proposed research procedure is indispensable to effective supply chain quality planning.