bluuebunny/crossref_metadata_2025_split huggingface dataset:
Venous leg ulcer in the context of chronic venous disease
Authors: Sánchez F S Lozano , Roura J Marinel Io , Carrasco E Carrasco , González-Porras J R , Rodríguez J R Escudero , Nevarez I Sánchez , Sánchez S Díaz ,   Representing The Sociedades Españolas De Angiología Y Cirugía Vascular (Seacv), Capítulo Español De Flebologia, The Médicos De Atención Primaria (Semergen), And Medicina Familiar Y Comunitaria (Semfyc)
Published: April 2013

Objectives Chronic venous disease (CVD) is a frequent disorder with a high socioeconomic impact. Little is known about the possible differences between healed ulcer (C5 group) and active ulcer (C6 group) in terms of disease severity and quality of life (QoL). Our aim was to determine the possible differences in severity disease and QoL between the C5–C6 and C1 (control) group. Methods Data from a national, multicentre, observational and cross-sectional study ( n = 1598) were used to compare three groups of CVD: C1 ( n = 243), C5 ( n = 136) and C6 ( n = 70). CVD severity was assessed with the Venous Clinical Severity Score (VCSS) and QoL with the Short Form 12 Health Survey (SF-12) and Chronic Lower Limb Venous Insufficiency Questionnaire (CIVIQ-20). Results Patients with active ulcers had a higher mean total VCSS than patients with healed ulcers ( P < 0.05). Both SF-12 and CIVIQ-20 QoL questionnaires indicated a poorer QoL in patients with ulcers than in those with C1 ( P < 0.05). Compared with the C5 group, patients with active ulcers (C6) had lower QoL scores, but the differences were not statistically significant. Conclusions Patients with venous leg ulcers (C5–C6) are associated with high severity and poor QoL. However, the healing of a leg ulcer did not contribute to improvement of QoL.
Non-ST-elevation myocardial infarction following foam ultrasound-guided sclerotherapy
Authors: Stephens R , Dunn S 
Published: April 2013

The objective of the study was to describe a very rare complication of foam ultrasound-guided sclerotherapy (FUGS). An unusual case of persisting chest discomfort following FUGS in a 61-year-old woman led to a diagnosis of non-ST-elevation myocardial infarction. The patient was found to have a patent foramen ovale (PFO). The differential diagnoses of paradoxical embolism, gas embolism or vasospasm are discussed, with reference to relevant literature. A hypothesis of post sclerotherapy release of endothelin-1 (in a patient with a known PFO) leading to sustained coronary artery spasm causing sufficient myocardial damage to be reflected in elevated troponin levels is suggested. Any episode of chest tightness or pain following FUGS should be considered as possibly cardiac in origin. Sustained symptoms warrant admission to hospital for troponin monitoring and ECG assessment.
Implementation of the Liverpool Care Pathway (LCP) for the Dying Patient in the Inpatient Hospice Setting
Authors: Leo Silvia Di , Bono Laura , Romoli Vittoria , West Emily , Ambrosio Raffaella , Gallucci Michele , Pilastri Paola , Ciura Pietro La , Morino Piero , Piazza Massimo , Valenti Danila , Franceschini Catia , Costantini Massimo 
Published: April 2013

Background: The Liverpool Care Pathway (LCP) is extensively used in hospices, but the literature on the process of implementation is scarce. Aim: Developing, piloting, and preliminarily assessing the LCP program within the inpatient hospice setting. Methods: This is a phase 0-1 study, according to the Medical Research Council (MRC) Framework, divided into three phases: literature review on LCP in hospice and development of the Italian version of the LCP program (LCP-I), development of a procedure for assessing the quality of the implementation process and assessing the feasibility of the implementation process, and piloting the procedure in 7 inpatient Italian hospices. Results: The LCP was implemented in all the hospices involved. A high proportion of physicians (50%-100%) and nurses (94%-100%) attended the self-education program. The self-implementation of the LCP-I program was completed in all hospices. The proportion of patients who died on LCP-I ranged between 35.6% and 89.1%. Professionals from 2 hospices reported a positive impact of the LCP-I. Conversely, professionals from 2 hospices did not recognize a positive impact of the program and did not agree to maintain the LCP-I in hospice. Finally, professionals from the other 3 hospices reported intermediate evaluations (1 stopped to use the LCP-I). Some weaknesses emerged from the external audits, related to the self-education and the self-implementation approach. Professionals required an external support from a trained palliative care team with reference to both phases. Conclusions: The LCP-I implementation within hospices is feasible, and the process of implementation is evaluable. Issues that occurred within the implementation process suggest the introduction of an external support from a trained palliative care team in implementing the LCP program.
Evaluating a Police and Journalism Joint Training Initiative
Authors: Davies Kayt 
Published: April 2013

In early 2010, the Edith Cowan University (ECU) journalism programme and the Western Australia Police Academy Detective Training School launched a novel collaboration that involved running joint training days, in which a ‘media pack’ of journalism students interview trainee detectives about mock crimes they have been tasked with investigating. The training improved the trainee journalists’ and detectives’ understanding about the constraints the other parties face. It also made them more confident about their ability to elicit and convey accurate information, and more willing to attempt to do so than before the training.  This article presents a description of the training days and the rationale behind them from detective and journalism educator perspectives, including the minimal costs involved in time and resources. It also presents the results of an evaluation, involving before-and-after questionnaires completed by participants. The article also reviews the scant literature about the dynamics of the relationship between journalists and detectives and suggests that training related to the dynamic is important for journalism students given that police public relations departments and polices are blossoming in Australia and throughout the Asia-Pacific region.
Commentary
Authors: Tere Nidhi Shendurnikar 
Published: April 2013

A university degree was once considered to be the least requisite to become a journalist in India. A sense for news, writing skills and a burning desire for truth were all that mattered. Times changed and so did the face of journalism in India. From a mission during the freedom movement to a commercially laden venture; journalists transformed from crusaders to those enslaved by advertising and revenue concerns. A subtle but decisive development that took place alongside was the formalization of journalism education in the country (1940–50).1 The need to educate and train media professionals was recognized and infrastructure and institutes laid down for the same. This was only the beginning of the popularity and spread of journalism education in India. Today the presence of audio-visual media, new media and other interactive media has provided a boost to journalismem education, in technical as well as academic terms. It is now not restricted to the traditional domain but includes many inter-disciplinary aspects. We have witnessed the blossoming of many institutes2 having their stake in media education apart from government universities and courses offered by media house.3 The article examines issues of quality in media education even as the number of institutions offering journalism programmes proliferate. As a nation, do we want to invest only in growing number of educational institutes or in quality education? Small town India is emerging fast on the media education map. How will it compete with media education in urban metros? Addressing these and other critical issues calls for an innovative role on part of media educators and improved training techniques in media education.
International Pediatric Multiple Sclerosis Study Group criteria for pediatric multiple sclerosis and immune-mediated central nervous system demyelinating disorders: revisions to the 2007 definitions
Authors: Krupp Lauren B , Tardieu Marc , Amato Maria Pia , Banwell Brenda , Chitnis Tanuja , Dale Russell C , Ghezzi Angelo , Hintzen Rogier , Kornberg Andrew , Pohl Daniela , Rostasy Kevin , Tenembaum Silvia , Wassmer Evangeline ,   for the International Pediatric Multiple Sclerosis Study Group
Published: April 2013

Background: There has been tremendous growth in research in pediatric multiple sclerosis (MS) and immune mediated central nervous system demyelinating disorders since operational definitions for these conditions were first proposed in 2007. Further, the International Pediatric Multiple Sclerosis Study Group (IPMSSG), which proposed the criteria, has expanded substantially in membership and in its international scope. Objective: The purpose of this review is to revise the 2007 definitions in order to incorporate advances in delineating the clinical and neuroradiologic features of these disorders. Methods: Through a consensus process, in which input was sought from the 150 members of the Study Group, criteria were drafted, revised and finalized. Final approval was sought through a web survey. Results: Revised criteria are proposed for pediatric acute disseminated encephalomyelitis, pediatric clinically isolated syndrome, pediatric neuromyelitis optica and pediatric MS. These criteria were approved by 93% or more of the 56 Study Group members who responded to the final survey. Conclusions: These definitions are proposed for clinical and research purposes. Their utility will depend on the outcomes of their application in prospective research.
Wallerian and trans-synaptic degeneration contribute to optic radiation damage in multiple sclerosis: a diffusion tensor MRI study
Authors: Rocca Maria A , Mesaros Sarlota , Preziosa Paolo , Pagani Elisabetta , Stosic-Opincal Tatjana , Dujmovic-Basuroski Irena , Drulovic Jelena , Filippi Massimo 
Published: April 2013

Background: Optic radiation (OR) damage occurs in multiple sclerosis (MS). Objectives: The purpose of this study was to explore the contribution of local and distant mechanisms associated with OR damage in MS. Methods: Diffusion tensor (DT) magnetic resonance imaging (MRI) tractography probability maps of the ORs were derived from 102 MS patients and 11 controls. Between-group differences of OR normal-appearing white matter (NAWM) damage and topographical distribution of OR damage were assessed using quantitative and voxel-wise analyses, considering the influence of previous optic neuritis (ON+) and T2 OR lesions (T2 OR+). Results: OR NAWM diffusivity abnormalities were more severe in ON+ patients vs patients without previous optic neuritis (ON–) and T2 OR+ vs T2 OR– patients. Damage to the anterior portions of the ORs was more severe in ON+ vs ON– patients. Compared to controls and T2 OR– patients, T2 OR+ patients experienced a more distributed pattern of DT MRI abnormalities along the ORs, with an increased axial diffusivity limited to the anterior portions of the ORs. In T2 OR+ group, ON+ vs ON– patients showed DT MRI abnormalities in the middle portion of the ORs, in correspondence with focal lesions. OR damage correlated with OR T2 lesion volume, visual dysfunction and optic nerve atrophy. Conclusions: Both trans-synaptic degeneration secondary to optic nerve damage and Wallerian degeneration due to local T2 lesions contribute to OR damage in MS.
Serum dehydroepiandrosterone sulfate concentration is lower in women with primary aldosteronism
Authors: Chen Ai-Hua , Li Hung-Yuan , Wu Vin-cent , Lin Yen-Hung , Huang Tien-Shang ,   (and the Taiwan Primary Aldosteronism Investigation (TAIPAI) Study Group)
Published: April 2013

Objective: The objective of this article is to measure serum dehydroepiandrosterone sulfate (DHEA-S) concentration in both genders with primary aldosteronism (PA). Materials and methods: The study enrolled 78 subjects with normal controls, 46 subjects with essential hypertension and 85 subjects with PA from October 2007 to June 2011. Subjects with PA were divided into three subtype groups: aldosterone-producing adenoma (APA), bilateral idiopathic hyperplasia (IHA) and PA with negative imaging findings. Results: Women with PA ( n = 49) had lower serum DHEA-S levels compared with normal controls and subjects with essential hypertension ( p < 0.01). In subtype analysis, only female APAs had lower serum DHEA-S levels ( p < 0.01 compared with normal controls, p < 0.01 compared with subjects with essential hypertension). In APA, a significant correlation between tumor size and serum DHEA-S was found in women ( p < 0.01). Conclusion: Our data suggested that serum DHEA-S levels are lower in women with PA. In subtype groups, only women with APA had lower serum DHEA-S. There was no significant difference between subjects with bilateral essential hyperplasia, PA with negative imaging findings, normal controls and subjects with essential hypertension in both genders. The serum DHEA-S level is negatively correlated with the size of APA.
Discovering motifs that induce sequencing errors
Authors: Allhoff Manuel , Schönhuth Alexander , Martin Marcel , Costa Ivan G , Rahmann Sven , Marschall Tobias 
Published: April 2013

AbstractBackgroundElevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS). Beyond routinely handled generic sources of errors, certain base calling errors relate to specific sequence patterns. Statistically principled ways to associate sequence patterns with base calling errors have not been previously described. Extant approaches either incur decisive losses in power, due to relating errors with individual genomic positions rather than motifs, or do not properly distinguish between motif-induced and sequence-unspecific sources of errors.ResultsHere, for the first time, we describe a statistically rigorous framework for the discovery of motifs that induce sequencing errors. We apply our method to several datasets from Illumina GA IIx, HiSeq 2000, and MiSeq sequencers. We confirm previously known error-causing sequence contexts and report new more specific ones.ConclusionsChecking for error-inducing motifs should be included into SNP calling pipelines to avoid false positives. To facilitate filtering of sets of putative SNPs, we provide tracks of error-prone genomic positions (in BED format).Availabilityhttp://discovering-cse.googlecode.com
An optimized algorithm for detecting and annotating regional differential methylation
Authors: Li Sheng , Garrett-Bakelman Francine E , Akalin Altuna , Zumbo Paul , Levine Ross , To Bik L , Lewis Ian D , Brown Anna L , D'Andrea Richard J , Melnick Ari , Mason Christopher E 
Published: April 2013

Abstract

Background
DNA methylation profiling reveals important differentially methylated regions (DMRs) of the genome that are altered during development or that are perturbed by disease. To date, few programs exist for regional analysis of enriched or whole-genome bisulfate conversion sequencing data, even though such data are increasingly common. Here, we describe an open-source, optimized method for determining empirically based DMRs (eDMR) from high-throughput sequence data that is applicable to enriched whole-genome methylation profiling datasets, as well as other globally enriched epigenetic modification data.

Results
Here we show that our bimodal distribution model and weighted cost function for optimized regional methylation analysis provides accurate boundaries of regions harboring significant epigenetic modifications. Our algorithm takes the spatial distribution of CpGs into account for the enrichment assay, allowing for optimization of the definition of empirical regions for differential methylation. Combined with the dependent adjustment for regional p-value combination and DMR annotation, we provide a method that may be applied to a variety of datasets for rapid DMR analysis. Our method classifies both the directionality of DMRs and their genome-wide distribution, and we have observed that shows clinical relevance through correct stratification of two Acute Myeloid Leukemia (AML) tumor sub-types.

Conclusions
Our weighted optimization algorithm eDMR for calling DMRs extends an established DMR R pipeline (methylKit) and provides a needed resource in epigenomics. Our method enables an accurate and scalable way of finding DMRs in high-throughput methylation sequencing experiments. eDMR is available for download at http://code.google.com/p/edmr/.
Joint genotype inference with germline and somatic mutations
Authors: Bareke Eric , Saillour Virginie , Spinella Jean-François , Vidal Ramon , Healy Jasmine , Sinnett Daniel , Csűrös Miklós 
Published: April 2013

AbstractThe joint sequencing of related genomes has become an important means to discover rare variants. Normal-tumor genome pairs are routinely sequenced together to find somatic mutations and their associations with different cancers. Parental and sibling genomes revealde novogermline mutations and inheritance patterns related to Mendelian diseases.Acute lymphoblastic leukemia (ALL) is the most common paediatric cancer and the leading cause of cancer-related death among children. With the aim of uncovering the full spectrum of germline and somatic genetic alterations in childhood ALL genomes, we conducted whole-exome re-sequencing on a unique cohort of over 120 exomes of childhood ALL quartets, each comprising a patient's tumor and matched-normal material, and DNA from both parents. We developed a general probabilistic model for such quartet sequencing reads mapped to the reference human genome. The model is used to infer joint genotypes at homologous loci across a normal-tumor genome pair and two parental genomes.We describe the algorithms and data structures for genotype inference, model parameter training. We implemented the methods in an open-source software package (QUADGT) that uses the standard file formats of the 1000 Genomes Project. Our method's utility is illustrated on quartets from the ALL cohort.
Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing
Authors: Ueno Saneyoshi , Klopp Christophe , Leplé Jean Charles , Derory Jérémy , Noirot Céline , Léger Valérie , Prince Elodie , Kremer Antoine , Plomion Christophe , Le Provost Grégoire 
Published: April 2013

AbstractBackgroundIn temperate regions, the time lag between vegetative bud burst and bud set determines the duration of the growing season of trees (i.e. the duration of wood biomass production). Dormancy, the period during which the plant is not growing, allows trees to avoid cold injury resulting from exposure to low temperatures. An understanding of the molecular machinery controlling the shift between these two phenological states is of key importance in the context of climatic change. The objective of this study was to identify genes upregulated during endo- and ecodormancy, the two main stages of bud dormancy. Sessile oak is a widely distributed European white oak species. A forcing test on young trees was first carried out to identify the period most likely to correspond to these two stages. Total RNA was then extracted from apical buds displaying endo- and ecodormancy. This RNA was used for the generation of cDNA libraries, and in-depth transcriptome characterization was performed with 454 FLX pyrosequencing technology.ResultsPyrosequencing produced a total of 495,915 reads. The data were cleaned, duplicated reads removed, and sequences were mapped onto the oak UniGene data. Digital gene expression analysis was performed, with bothRstatistics and the R-Bioconductor packages (edgeR and DESeq), on 6,471 contigs with read numbers ≥ 5 within any contigs. The number of sequences displaying significant differences in expression level (read abundance) between endo- and ecodormancy conditions ranged from 75 to 161, depending on the algorithm used. 13 genes displaying significant differences between conditions were selected for further analysis, and 11 of these genes, including those for glutathione-S-transferase (GST) and dehydrin xero2 (XERO2) were validated by quantitative PCR.ConclusionsThe identification and functional annotation of differentially expressed genes involved in the “response to abscisic acid”, “response to cold stress” and “response to oxidative stress” categories constitutes a major step towards characterization of the molecular network underlying vegetative bud dormancy, an important life history trait of long-lived organisms.
High throughput transcriptome analysis of lipid metabolism in Syrian hamster liver in absence of an annotated genome
Authors: Schmucki Roland , Berrera Marco , Küng Erich , Lee Serene , Thasler Wolfgang E , Grüner Sabine , Ebeling Martin , Certa Ulrich 
Published: April 2013

AbstractBackgroundWhole transcriptome analyses are an essential tool for understanding disease mechanisms. Approaches based on next-generation sequencing provide fast and affordable data but rely on the availability of annotated genomes. However, there are many areas in biomedical research that require non-standard animal models for which genome information is not available. This includes the Syrian hamsterMesocricetus auratusas an important model for dyslipidaemia because it mirrors many aspects of human disease and pharmacological responses. We show that complementary use of two independent next generation sequencing technologies combined with mapping to multiple genome databases allows unambiguous transcript annotation and quantitative transcript imaging. We refer to this approach as “triple match sequencing” (TMS).ResultsContigs assembled from a normalized Roche 454 hamster liver library comprising 1.2 million long reads were used to identify 10’800 unique transcripts based on homology to RefSeq database entries from human, mouse, and rat. For mRNA quantification we mapped 82 million SAGE tags (SOLiD) from the same RNA source to the annotated hamster liver transcriptome contigs. We compared the liver transcriptome of hamster with equivalent data from human, rat, minipig, and cynomolgus monkeys to highlight differential gene expression with focus on lipid metabolism. We identify a cluster of five genes functionally related to HDL metabolism that is expressed in human, cynomolgus, minipig, and hamster but lacking in rat as a non-responder species for lipid lowering drugs.ConclusionsThe TMS approach is suited for fast and inexpensive transcript profiling in cells or tissues of species where a fully annotated genome is not available. The continuously growing number of well annotated reference genomes will further empower reliable transcript identification and thereby raise the utility of the method for any species of interest.