bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hazard Mitigation of Unstable Volcanic Edifices
Authors: Acocella Valerio , Puglisi Giuseppe 
Published: October 2010

Because of their continuous and relatively rapid growth, volcanoes are inherently unstable, with instabilities ranging from slow volcano spreading to sudden flank collapse. Instability may induce magma ascent and eruption, mainly through dikes, to such an extent that it may significantly control the evolution of volcanic edifices and their associated hazards. Understanding what controls the development of the instability of a volcanic edifice is therefore crucial for hazard assessment and mitigation.For example, what are the hazards associated with volcanic flank instability, and under what conditions do these hazards occur? What can we learn about flank motion by studying an unstable volcano? Addressing these questions is the goal of the Etna Flank project, which, after 2 years, has provided constraints on the characteristics and hazards of volcano instability at Italy's Mount Etna.
ChEBI, an Open-access Chemistry Resource for the Life Sciences: Facilities for On-line Submission and Curation
Authors: Ennis Marcus 
Published: October 2010

AbstractChEBI (Chemical Entities of Biological Interest) is a database of ‘small’ molecular entities structured around a chemical ontology. It contains almost 600,000 entries, of which approximately 20,000 have been manually curated, as well as entries for groups (parts of molecular entities) and classes of entities. It provides a wide range of information such as chemical nomenclature, structures and related chemical values, and establishes interrelationships between entities in the ontology, in terms of both structure and role. ChEBI places a strong focus on quality, with exceptional efforts being applied to upholding IUPAC nomenclature recommendations and best IUPAC practices when drawing chemical structures.To invite the community to participate more directly in the future growth and development of ChEBI, we have developed a web-based software utility to enable direct user submissions. Users are encouraged to carry out as much of their own manual curation as possible, e.g. by adding multiple synonyms and database cross-references, and by creating multiple relationships within the ontology. The submissions are automatically validated for uniqueness (both of name and chemical structure) and correctness (such as checking that no non-allowed cycles have inadvertently been created in the ontology graph structure, and that the ontology relationships which have been specified are allowed between entities of the relevant types). Once a submission has passed the required validations, it is submitted to the ChEBI database, at which time it receives its unique ChEBI identifier. It will then become visible to the public (as a preliminary entry) as part of the monthly ChEBI release. To date, ChEBI has received over 750 such external submissions.
UniProt Knowledgebase: a hub of integrated data
Authors: Magrane Michele , Consortium UniProt 
Published: October 2010

AbstractData integration plays an increasingly important role in bringing together the large amounts of diverse information spread across disparate resources and presenting a comprehensive overview of these data to the scientific community. The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialised data collections. UniProtKB also integrates data such as protein sequences, protein-protein interactions, Gene Ontology terms and official gene nomenclature from a range of resources. All information in UniProtKB is attributed to its original source, allowing users to trace the provenance of all data. In addition, UniProtKB data is made freely available in a range of formats to facilitate integration with other databases and the UniProt Consortium is committed to using and promoting common data exchange formats and technologies. This approach ensures that information is captured in the most appropriate resource for subsequent integration with other databases and also ensures maximum curation efficiency by preventing duplication of efforts across multiple resources. How UniProt achieves this data capture and integration will be presented. The UniProt resource is available at "www.uniprot.org":http://www.uniprot.org.
Prevalence and Phenotype of Childhood Apraxia of Speech in Youth With Galactosemia
Authors: Shriberg Lawrence D. , Potter Nancy L. , Strand Edythe A. 
Published: October 2010

PurposeIn this article, the authors address the hypothesis that the severe and persistent speech disorder reported in persons with galactosemia meets contemporary diagnostic criteria for Childhood Apraxia of Speech (CAS). A positive finding for CAS in this rare metabolic disorder has the potential to impact treatment of persons with galactosemia and inform explanatory perspectives on CAS in neurological, neurodevelopmental, and idiopathic contexts.MethodThirty-three youth with galactosemia and significant prior or persistent speech sound disorder were assessed in their homes in 17 states. Participants completed a protocol yielding information on their cognitive, structural, sensorimotor, language, speech, prosody, and voice status and function.ResultsEight of the 33 participants (24%) met contemporary diagnostic criteria for CAS. Two participants, 1 of whom was among the 8 with CAS, met criteria for ataxic or hyperkinetic dysarthria. Groupwise findings for the remaining 24 participants are consistent with a classification category termedMotor Speech Disorder–Not Otherwise Specified(Shriberg, Fourakis et al., 2010a).ConclusionThe authors estimate the prevalence of CAS in galactosemia at 18 per hundred—180 times the estimated risk for idiopathic CAS. Findings support the need to study risk factors for the high occurrence of motor speech disorders in galactosemia despite early compliant dietary management.
Graphene and its one-dimensional patterns: from basic properties towards applications
Authors: Do Van Nam , Pham Thanh Huy 
Published: October 2010

Abstract
Graphene, a carbon material discovered in 2004 by a group of scientists at the University of Manchester, UK, has been attracting significant attention in both fundamental and applied studies. Due to the rapid increase in the number of articles on this material since its discovery, a range of readers, particularly those just beginning to learn about this material, are turning to various different sources. The purpose of this article is to create a bridge between the key aspects of this material in experimental and theoretical investigations, as well as in fundamental and applied studies, aiming to provide a basic understanding of this material for those who are new to it. The presentation in this article is thus not particularly academic. The content focuses on four themes, including fabrication methods, basic properties, potential for application and some typical research directions for this magic carbon material.
SmashCell: a software framework for the analysis of single-cell amplified genome sequences
Authors: Harrington Eoghan D. , Arumugam Manimozhiyan , Raes Jeroen , Bork Peer , Relman David A. 
Published: October 2010

Abstract
Summary: Recent advances in single-cell manipulation technology, whole genome amplification and high-throughput sequencing have now made it possible to sequence the genome of an individual cell. The bioinformatic analysis of these genomes, however, is far more complicated than the analysis of those generated using traditional, culture-based methods. In order to simplify this analysis, we have developed SmashCell (Simple Metagenomics Analysis SHell-for sequences from single Cells). It is designed to automate the main steps in microbial genome analysis—assembly, gene prediction, functional annotation—in a way that allows parameter and algorithm exploration at each step in the process. It also manages the data created by these analyses and provides visualization methods for rapid analysis of the results.
Availability: The SmashCell source code and a comprehensive manual are available at http://asiago.stanford.edu/SmashCell
Contact: eoghanh@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data
Authors: Ivakhno Sergii , Royce Tom , Cox Anthony J. , Evers Dirk J. , Cheetham R. Keira , Tavaré Simon 
Published: October 2010

Abstract
Motivation: Copy number abnormalities (CNAs) represent an important type of genetic mutation that can lead to abnormal cell growth and proliferation. New high-throughput sequencing technologies promise comprehensive characterization of CNAs. In contrast to microarrays, where probe design follows a carefully developed protocol, reads represent a random sample from a library and may be prone to representation biases due to GC content and other factors. The discrimination between true and false positive CNAs becomes an important issue.
Results: We present a novel approach, called CNAseg, to identify CNAs from second-generation sequencing data. It uses depth of coverage to estimate copy number states and flowcell-to-flowcell variability in cancer and normal samples to control the false positive rate. We tested the method using the COLO-829 melanoma cell line sequenced to 40-fold coverage. An extensive simulation scheme was developed to recreate different scenarios of copy number changes and depth of coverage by altering a real dataset with spiked-in CNAs. Comparison to alternative approaches using both real and simulated datasets showed that CNAseg achieves superior precision and improved sensitivity estimates.
Availability: The CNAseg package and test data are available at http://www.compbio.group.cam.ac.uk/software.html.
Contact: Sergii.Ivakhno@cancer.org.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Etiology of Esophageal Food Impactions in Children
Authors: Hurtado Christine Waasdorp , Furuta Glenn T , Kramer Robert E 
Published: October 2010

ABSTRACTObjective:The aim of the study was to measure clinicopathological features of children presenting to a tertiary care emergency department with esophageal food impaction.Materials and Methods:A retrospective chart review of children with esophageal food impaction seen between January 1, 2005 and June 30, 2009, including all patients from age 1 month to 18 years with esophageal food impaction at a pediatric emergency department, was performed.Results:Initial screening ofInternational Classification of Disease, 9th Revision, discharge diagnosis identified 698 children with an esophageal foreign body. Of this group, 72 esophageal food impaction events were identified in 65 children (69% boys), 49 of whom required endoscopic intervention. Endoscopic appearances of the esophageal mucosa were abnormal in 40 (82%), revealing evidence of esophagitis (55%) or stricture (27%). Twenty‐four of the subjects had biopsies taken at the time of endoscopy. Inflammation, described as increased eosinophils, basilar hyperplasia, rete peg elongation, and/or microabscess, was present in 76% of mucosal samples. Follow‐up endoscopy in 12 children identified an etiology in 9, five of whom were found to have eosinophilic esophagitis.Conclusions:The majority of children with esophageal food impaction who underwent endoscopic evaluation and biopsy have an underlying potentially treatable cause. We therefore recommend that all of the children with esophageal food impaction have mucosal biopsies at the time of endoscopic disimpaction with appropriate follow‐up to allow for diagnosis and management of the underlying etiology.
Surgery in Children With Crohn Disease Refractory to Medical Therapy
Authors: Pacilli Maurizio , Eaton Simon , Fell John M , Rawat David , Clarke Simon , Haddad Munther J 
Published: October 2010

ABSTRACTObjective:The aim of this study was to evaluate the results of surgery in children with Crohn disease (CD) not responding to medical therapy and establish whether surgery improves growth and nutrition.Patients and Methods:Children with CD diagnosed between 1998 and 2008 were reviewed. Relapse was defined by Harvey‐Bradshaw index >5. Data, reported as median (range), were compared by Fisher exact test and repeated‐measures ANOVA.Results:One hundred forty‐one children, ages 12.7 years (3.5–16.8), were identified; 27 (19%) required surgery 14.5 months (1.1–61.8) after diagnosis. Twenty‐one had elective surgery (19 isolated ileocaecal disease and stricture, 2 diffuse disease of ileum); 6 had emergency surgery (3 peritonitis, 2 haemorrhage, 1 perforation). Surgery included 18 ileocaecal resection and end‐to‐end anastomosis, 5 stoma formation, 2 left hemicolectomy and end‐to‐end anastomosis, and 2 stricturoplasty. Follow‐up was 2.5 years (1–9.4). Growth and nutrition improved by 6 and 12 months after surgery, with a significant increase in weight z score (P < 0.0001), height z score (P < 0.0001), albumin (30 [13–36] vs 39 [30–46] vs 40 [33–45], P < 0.0001), and haemoglobin [10 (6.8–13.2) vs 11.7 (8.2–13.7) vs 12.0 (9.3–14.7), P < 0.0001]. All patients of the received azathioprine (2–2.5 mg · kg−1 · day−1) after surgery. Fifteen patients (55%) relapsed with a modified Harvey‐Bradshaw index of 8 (6–11) within 11.5 months (4.2–33.4). Of these, 5 patients (18%) relapsed within 1 year. Five patients (18%) had further surgery (2 anastomotic strictures, 2 diseased stoma, and 1 enterocutaneous fistula).Conclusions:Growth and nutrition following surgery for CD improve, but there is a high relapse rate. Despite this, the improved growth and nutrition before relapse may be beneficial during puberty and justify surgery in children not responding to medications.
Gluten‐free Sourdough Wheat Baked Goods Appear Safe for Young Celiac Patients: A Pilot Study
Authors: Di Cagno Raffaella , Barbato Maria , Di Camillo Chiara , Rizzello Carlo Giuseppe , De Angelis Maria , Giuliani Giammaria , De Vincenzi Massimo , Gobbetti Marco , Cucchiara Salvatore 
Published: October 2010

ABSTRACTObjectives:This study was aimed at showing the safety, for young patients with celiac disease (CD), of sweet baked goods made of wheat flour, which was rendered gluten‐free during sourdough fermentation.Methods and Results:As shown by R5 antibody‐based sandwich and competitive enzyme‐linked immunosorbent assay (ELISA), selected lactobacilli and fungal proteases, routinely used in bakeries, degraded gluten to <10 ppm during sourdough fermentation. The resulting flour was mainly a mixture of water‐/salt‐soluble low‐size peptides and free amino acids. Gliadin and glutenin fractions extracted from the pepsin‐trypsin (PT) digest of the fermented wheat flour induced the expression of interferon (IFN)‐γ at the level comparable with the negative control. After fermentation, the wheat flour was spray dried and used for making sweet baked goods. Eight patients with CD in remission were enrolled for the clinical challenge, and they daily consumed 200 g of sweet baked goods equivalent to 10 g of native gluten. Hematology, serology (total serum IgA, IgG and IgA antigluten, endomysial and tissue transglutaminase IgA antibodies), and intestinal permeability analyses were carried out over time. One patient interrupted the trial after 15 days and another after 30 days only due to difficulties in the compliance of the daily consumption. All of the other patients showed normal values of hematology, serology, and intestinal permeability during 60 days of challenge.Conclusions:This study showed that a wheat flour–fermented product, having gluten completely degraded, is not toxic for patients with CD. Nevertheless, these foods should not be recommended for patients with celiac disease until a formal trial has been done.
Neonatal immune function and inflammatory illnesses in later life: lessons to be learnt from the developing world?
Authors: Lisciandro J. G. , Van Den Biggelaar A. H. J. 
Published: October 2010

SummaryWith the emergence of allergic and autoimmune diseases in populations that have started to transit to a western lifestyle, there has been an increasing interest in the role of environmental factors modulating early immune function. Yet, most of the information concerning neonatal immune function has been derived from studies in westernized countries. We postulate that comparative studies of early immune development in children born under conditions that are typical for a westernized vs. that of a still more traditional setting will provide a crucial insight into the environmental‐driven immunological mechanisms that are responsible for the world‐wide rise in inflammatory disorders. In this review, we summarize the current understanding of early‐life immune function in humans in general and the literature on some major lifestyle factors that may influence neonatal immune function and potentially the risk for disease in later life. An understanding of the mechanisms of ‘prenatal/early‐life programming’ in populations living in traditional compared with modern societies is crucial to develop strategies to prevent a further rise in ‘western diseases’ such as allergic disorders. Indications exist that prenatal conditioning of the innate immune system by low‐grade inflammatory responses is key to inducing more tightly regulated postnatal adaptive immune responses. Cite this as: J. G. Lisciandro and A. H. J. van den Biggelaar, Clinical & Experimental Allergy, 2010 (40) 1719–1731.
STUDIES ON THE DECOMPOSITION OF PLANT MATERIAL IN SOIL. IV. THE EFFECT OF RATE OF ADDITION
Authors: JENKINSON D. S. 
Published: October 2010

SummaryDifferent amounts of ryegrass roots and tops, both uniformly labelled with 1
4 C, were mixed with soil and allowed to decompose for 155 days under controlled conditions in the laboratory at 25°C. Initially the roots decomposed more slowly than the tops but by 155 days this difference had disappeared. About a third of the added plant C remained in the soil at the end of 155 days, about as much as when the same plant materials were incubated in the same soils for 6 months in the field.To a first approximation, the amount of labelled CO2–C evolved was directly proportional to the amount of labelled plant C added. This held throughout the incubations. However, a slightly smaller percentage of the added plant C was evolved with small additions than with large, although this effect was on the limits of detection. Slightly more labelled plant C was retained in a soil rich in organic matter (2.43% C) than in an otherwise similar soil with less organic matter (0.97% C).
Continuing connections: the experiences of retired and senior working nurse mentors
Authors: McDonald Glenda , Mohan Shantala , Jackson Debra , Vickers Margaret H , Wilkes Lesley 
Published: October 2010

Aims and objectives.  This paper reports the benefits and challenges of a mentoring programme through which retired and senior nurses continued to support and nurture nurses and midwives currently working in the health system.Background.  Nursing has an ageing workforce and faces significant loss of expertise because of retirements. Previously, mentoring programmes have been instituted in a range of nursing contexts and they have been a retention strategy for older nurses and midwives.Design.  Mentors and their mentees worked together towards mutually agreed on professional and personal goals. They were asked to meet or speak together a minimum of twice per month for at least six months.Method.  As part of a collective case study, 15 mentoring dyads were established. Participants and mentors took part in qualitative, semi‐structured interviews about their perceptions and experiences of the mentoring programme. Interviews were audio‐taped, transcribed and analysed thematically.Results.  Mentors reported the mentoring experience to be rewarding experience that enabled them to re‐connect with nursing‐related activities and brought new challenges in retirement. They perceived the mentees were visibly helped by their support and influence.Conclusions.  The mentors studied reinforced a positive self‐concept as nurses and midwives in their mentees and assisted their development. Retired nurses and midwives in particular may have several characteristics that make them effective mentors.Relevance to clinical practice.  Potential benefits are demonstrated for nurses and midwives vulnerable to workplace adversity, especially those new to Australia who may have limited professional and social networks. For health organisations, mentoring programmes may be an innovative method of retention that engages both mid‐career nurses and midwives and those recently retired.
The relationships between organisational citizenship behaviour, job satisfaction and turnover intention
Authors: Tsai Yafang , Wu Shih‐Wang 
Published: October 2010

Aim. This study aims to explore the relationships between organisational citizenship behaviour, job satisfaction and turnover intention.Background. Because of the changing health policies landscape, Taiwan’s hospital administrators are facing major cost reduction challenges. Specifically, the high turnover rate of nurses represents a hindrance and a human resource cost. This study focuses on ways of reducing the employee turnover rate through enhanced organisational citizenship behaviour and job satisfaction.Design. A cross‐sectional study.Methods. This study focuses on hospital nurses in Taiwan. Our research samples were obtained from one medical centre, three regional hospitals and seven district hospitals. Out of 300 questionnaires distributed among samples, 237 were completed and returned. Pearson’s correlation was used to test for relationships among the main variables. One‐way analysis of variance and Scheffé’spost hocanalysis were employed to test the influence of demographic data on the main variables.Results. The results reveal that the nurses’ job satisfaction has a significantly positive correlation with organisational citizenship behaviour and a negative correlation with turnover intention.Conclusions. This study has proven that the turnover intention of clinical nurses is related to their organisational citizenship behaviour and job satisfaction. Hospital administrators can reduce the turnover intention by meeting nurses’ needs and by promoting their organisational citizenship behaviour.Relevance to clinical practice. Organisational citizenship behaviour involves behaviour that encourages staff to endeavour to voluntarily improve organisational performance without lobbying for compensation. Employees’ job satisfaction includes satisfaction with the working environment or welfare programme in the context of human resource initiatives. Similarly, human resource protocols may serve as the starting point for promoting staff organisational citizenship behaviour. Administrators in clinical healthcare are encouraged to meet their employees’ working needs through human resource practices.