bluuebunny/crossref_metadata_2025_split huggingface dataset:
High prevalence of metabolic syndrome in an elderly Croatian population – a multicentre study
Authors: Pašalić Daria , Dodig Slavica , Čorović Naima , Pizent Alica , Jurasović Jasna , Pavlović Mladen 
Published: December 2010

AbstractObjectiveTo investigate the prevalence and characteristics of metabolic syndrome (MetS) in a healthy elderly Croatian population.DesignCross-sectional study consisting of a health check including anthropometric measures and food questionnaires as well as analysis of biochemical parameters related to MetS. The diagnostic criteria of the International Diabetes Federation (IDF) were used for diagnosis of MetS.SettingFour centres in continental (Virovitica and Zagreb) and Adriatic coast (Split and Omiš) regions of Croatia.SubjectsFree-living elderly persons aged 70–90 years (n320).ResultsSignificantly lower MetS prevalence was found among participants from small urban centres compared with those from large urban centres (59·1 %v. 69·6 %;P= 0·051). Participants without MetS consumed wine more frequently (P= 0·05) than those with MetS. Compared with their peers with HDL cholesterol (HDL-C) <1·03 mmol/l, more male participants with HDL-C ≥1·03 mmol/l consumed wine (P= 0·04) or pelagic fish (P= 0·03). The prevalence of participants with TAG ≥1·7 mmol/l was higher in wine non-consumers (P= 0·05) than in wine consumers. Multivariate analysis with age and gender as covariates showed a significant inverse association of wine consumption with total cholesterol (P< 0·001), a positive association with HDL-C (P< 0·001) and a marginally inverse association with TAG (P= 0·06). In the male population, alkaline phosphatase and γ-glutamyl transferase activities were higher in participants with MetS (P< 0·05).ConclusionsHigh MetS prevalence was observed in an elderly Croatian population. Data showed that moderate consumption of wine and/or pelagic fish has a protective role against MetS in the population studied.
Electronic Resource Management Systems: Manage Online Library Spend and Increase the Value of the Library
Authors: Kingan Rory 
Published: December 2010

AbstractThis paper, originally presented at the BIALL Conference in June 2010 by Rory Kingan, introduces the concept of Electronic Resource Management systems and how they can help law libraries deliver better value from online services. The goals and functions of these systems are presented, benefits that firms are achieving with them are described and several advanced uses are discussed.
Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature
Authors: Doughty Emily , Kertesz-Farkas Attila , Bodenreider Olivier , Thompson Gary , Adadey Asa , Peterson Thomas , Kann Maricel G. 
Published: December 2010

Abstract
Motivation: A major goal of biomedical research in personalized medicine is to find relationships between mutations and their corresponding disease phenotypes. However, most of the disease-related mutational data are currently buried in the biomedical literature in textual form and lack the necessary structure to allow easy retrieval and visualization. We introduce a high-throughput computational method for the identification of relevant disease mutations in PubMed abstracts applied to prostate (PCa) and breast cancer (BCa) mutations.
Results: We developed the extractor of mutations (EMU) tool to identify mutations and their associated genes. We benchmarked EMU against MutationFinder—a tool to extract point mutations from text. Our results show that both methods achieve comparable performance on two manually curated datasets. We also benchmarked EMU's performance for extracting the complete mutational information and phenotype. Remarkably, we show that one of the steps in our approach, a filter based on sequence analysis, increases the precision for that task from 0.34 to 0.59 (PCa) and from 0.39 to 0.61 (BCa). We also show that this high-throughput approach can be extended to other diseases.
Discussion: Our method improves the current status of disease-mutation databases by significantly increasing the number of annotated mutations. We found 51 and 128 mutations manually verified to be related to PCa and Bca, respectively, that are not currently annotated for these cancer types in the OMIM or Swiss-Prot databases. EMU's retrieval performance represents a 2-fold improvement in the number of annotated mutations for PCa and BCa. We further show that our method can benefit from full-text analysis once there is an increase in Open Access availability of full-text articles.
Availability: Freely available at: http://bioinf.umbc.edu/EMU/ftp.
Contact: mkann@umbc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data
Authors: Lan Xun , Bonneville Russell , Apostolos Jeff , Wu Wangcheng , Jin Victor X 
Published: December 2010

Abstract
Summary: ChIP-based technology is becoming the leading technology to globally profile thousands of transcription factors and elucidate the transcriptional regulation mechanisms in living cells. It has evolved rapidly in recent years, from hybridization with spotted or tiling microarray (ChIP-chip), to pair-end tag sequencing (ChIP-PET), to current massively parallel sequencing (ChIP-seq). Although there are many tools available for identifying binding sites (peaks) for ChIP-chip and ChIP-seq, few of them are available as easy-accessible online web tools for processing both ChIP-chip and ChIP-seq data for the ChIP-based user community. As such, we have developed a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Our web tool W-ChIPeaks employed a probe-based (or bin-based) enrichment threshold to define peaks and applied statistical methods to control false discovery rate for identified peaks. The web tool includes two different web interfaces: PELT for ChIP-chip, BELT for ChIP-seq, where both were tested on previously published experimental data. The novel features of our tool include a comprehensive output for identified peaks with GFF, BED, bedGraph and .wig formats, annotated genes to which these peaks are related, a graphical interpretation and visualization of the results via a user-friendly web interface.
Availability: http://motif.bmi.ohio-state.edu/W-ChIPeaks/.
Contact: victor.jin@osumc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Both Plant and Bacterial Nitrate Reductases Contribute to Nitric Oxide Production in Medicago truncatula Nitrogen-Fixing Nodules
Authors: Horchani Faouzi , Prévot Marianne , Boscari Alexandre , Evangelisti Edouard , Meilhoc Eliane , Bruand Claude , Raymond Philippe , Boncompagni Eric , Aschi-Smiti Samira , Puppo Alain , Brouquisse Renaud 
Published: December 2010

Abstract
Nitric oxide (NO) is a signaling and defense molecule of major importance in living organisms. In the model legume Medicago truncatula, NO production has been detected in the nitrogen fixation zone of the nodule, but the systems responsible for its synthesis are yet unknown and its role in symbiosis is far from being elucidated. In this work, using pharmacological and genetic approaches, we explored the enzymatic source of NO production in M. truncatula-Sinorhizobium meliloti nodules under normoxic and hypoxic conditions. When transferred from normoxia to hypoxia, nodule NO production was rapidly increased, indicating that NO production capacity is present in functioning nodules and may be promptly up-regulated in response to decreased oxygen availability. Contrary to roots and leaves, nodule NO production was stimulated by nitrate and nitrite and inhibited by tungstate, a nitrate reductase inhibitor. Nodules obtained with either plant nitrate reductase RNA interference double knockdown (MtNR1/2) or bacterial nitrate reductase-deficient (napA) and nitrite reductase-deficient (nirK) mutants, or both, exhibited reduced nitrate or nitrite reductase activities and NO production levels. Moreover, NO production in nodules was found to be inhibited by electron transfer chain inhibitors, and nodule energy state (ATP-ADP ratio) was significantly reduced when nodules were incubated in the presence of tungstate. Our data indicate that both plant and bacterial nitrate reductase and electron transfer chains are involved in NO synthesis. We propose the existence of a nitrate-NO respiration process in nodules that could play a role in the maintenance of the energy status required for nitrogen fixation under oxygen-limiting conditions.
Tracking Changes of Lymphocyte Subsets and Pre‐inflammatory Mediators in Full‐term Neonates with Suspected or Documented Infection
Authors: Hotoura E. , Giapros V. , Kostoula A. , Spirou P. , Andronikou S. 
Published: December 2010

AbstractInvestigation was made of changes in immune system parameters during the course of neonatal infection. The study population consisted of 95 full‐term neonates matched for chronological age and sex, divided into three groups: suspected infection (n = 20), sepsis (n = 25), infection‐free control subjects (n = 50). Serial measurements were made of the cytokines interleukin‐6 (IL‐6), interleukin‐1b (IL‐1b) and tumour necrosis factor‐α (TNF‐α), lymphocyte subsets [CD3+, CD4+, CD8+, natural killer (NK) cells and B cells], the immunoglobulins (Ig) (IgG, IgM and IgA), C‐reactive protein (CRP), and the total blood count, before, 2 days after initiation of treatment and after stopping treatment (time periods first, second and third, respectively). IL6, TNF‐α, IL1‐b and CRP were higher at the first time period in the sepsis group, and IL6 and TNF‐α continued to be higher in this group at the second period. IL‐6 and TNF‐α were precise sepsis predictors with sensitivity and specificity of 0.92, 0.98 and 0.91, 0.92, respectively. NK cells, B cells, CD3+, CD4+, CD8+ were higher in the sepsis and suspected infection groups, but the ratios CD3+/CD4+, CD3+/CD8+, CD4+/CD8+ showed no difference from the controls. IgG was lower and IgM higher in the sepsis group. In the control subjects CD3+, CD4+, CD8+ lymphocytes increased with increasing age. It is concluded that IL‐6 and TNF are good diagnostic markers of sepsis in full‐term neonates. Lymphocyte subsets were affected by both the clinical condition and the chronological age. NK and B cells may be elevated in suspected and documented sepsis, and further studies are needed to determine their clinical significance.
The Human NADPH Oxidase: Primary and Secondary Defects Impairing the Respiratory Burst Function and the Microbicidal Ability of Phagocytes
Authors: de Oliveira‐Junior E. B. , Bustamante J. , Newburger P. E. , Condino‐Neto A. 
Published: December 2010

AbstractPhagocytes, such as granulocytes and monocytes/macrophages, contain a membrane‐associated NADPH oxidase that produces superoxide leading to other reactive oxygen species with microbicidal, tumoricidal and inflammatory activities. Primary defects in oxidase activity in chronic granulomatous disease (CGD) lead to severe, life‐threatening infections that demonstrate the importance of the oxygen‐dependent microbicidal system in host defence. Other immunological disturbances may secondarily affect the NADPH oxidase system, impair the microbicidal activity of phagocytes and predispose the host to recurrent infections. This article reviews the primary defects of the human NADPH oxidase leading to classical CGD, and more recently discovered immunological defects secondarily affecting phagocyte respiratory burst function and resulting in primary immunodeficiencies with varied phenotypes, including susceptibilities to pyogenic or mycobacterial infections.
Antiretroviral Therapy‐Induced Dominant Interleukin‐2 HIV‐1 Gag CD4+ T Cell Response: Evidence of Functional Recovery of HIV‐1‐Specific CD4+ T Cells
Authors: Tsalimalma K. , Kordossis T. , Choremi‐Papadopoulou E. 
Published: December 2010

AbstractProlonged antiretroviral treatment (ART) significantly changes the cytokine secretion capacities of HIV‐1‐specific T cells. However, it is unclear whether these changes result from decreased viremia or they correspond to true functional recovery of viral‐specific immune response. To study this issue, we analysed the quantitative and qualitative differences of HIV‐1‐specific and polyclonal CD4+ and CD8+ T cells between 26 naive and 52 treated individuals. HIV‐1 Gag and staphylococcal enterotoxin B (SEB)‐reactive T cells were determined by flowcytometric intracellular secretion of IFN‐γ or/and ΙL‐2. ART resulted in increase of single IL‐2 and decrease of single IFN‐γ‐secreting HIV‐1 CD4+ T cells, while both cytokines secreting HIV‐1 CD4+ T cells were presented in comparable frequencies in both groups. Viral loads correlated negatively with single IL‐2 and positively with single IFN‐γ‐secreting HIV‐1 CD4+ cells. Single IL‐2 HIV‐1 CD4+ T cells correlated positively with both cytokines secreting polyclonal CD8+ T cells. By qualitative analysis, a dominant IL‐2 HIV‐1 CD4+ T cell response (>70% single IL‐2) was identified only in ART suppressed patients, who also generated increased dual specific polyclonal CD8+ T cells. Polyfunctional HIV‐1 CD4+ T cell responses were detected even in naive individuals with high viremia. In conclusion, the presence of dominant IL‐2 HIV‐1 CD4+ T cell response, associated with increased CD8+ T cells capable to produce IL‐2, indicates that the recovery of HIV‐1‐specific CD4+ T cell functionality under ART is a feasible goal. Furthermore, polyfunctional HIV‐1 CD4+ T cell responses seem not to be directly involved in viral replication control.
Surveillance of community antimicrobial use in resource‐constrained settings – experience from five pilot projects
Authors: Holloway Kathleen , Mathai Elisabeth , Gray Andy ,   on behalf of the Community‐Based Surveillance of Antimicrobial Use and Resistance in Resource‐Constrained Settings Project Group
Published: December 2010

SummaryObjective  To investigate the feasibility of surveillance of antimicrobial use in the community in resource‐constrained settings. Overuse and misuse of antimicrobial medicines is contributing to the development of resistance. The WHO Global Strategy for Containment of Antimicrobial Resistance recommends surveillance of use at all levels of the health sector but this is not done in most low and middle income countries.Methods  Pilot projects were established in three sites in India (Delhi, Mumbai and Vellore) and 2 in South Africa (Brits and Durban). Antimicrobial use data were collected monthly from both public and private facilities. Each pilot site sought to document 30 patient encounters where antimicrobials were provided from 7 to 30 facilities per month. Antimicrobial use was expressed as the percentage of patients receiving a specific antimicrobial and as the number of defined daily doses of each specific antibiotic per 100 patients attending the facility per month.Results  In all sites, there was extensive use of antimicrobials, with older agents being used more in the public sector and newer agents in the private sector. Although methodological differences limit the comparability of data, use appeared to be higher in India than in South Africa. Expressing antimicrobial use as the percentage of patients receiving a specific antimicrobial was more easily computed. Defined daily dose measure was useful in demonstrating differences in dosing and duration.Conclusion  All pilot sites provided data on antimicrobial use but also raised several issues related to methodology and logistics of long‐term surveillance in community settings under resource constraints. Use measured as percentage of prescriptions is easier and more reliable in these settings.
Fine‐tuned coupling between human parahippocampal ripples and sleep spindles
Authors: Clemens Zsófia , Mölle Matthias , Erőss Loránd , Jakus Rita , Rásonyi György , Halász Péter , Born Jan 
Published: December 2010

AbstractSleep‐associated memory consolidation is thought to rely on coordinated information transfer between the hippocampus and neocortex brought about during slow wave sleep (SWS) by distinct local field potential oscillations. Specifically, findings in animals have led to the concept that ripples originating from hippocampus combine with spindles to provide a fine‐tuned temporal frame for a persistent transfer of memory‐related information to the neocortex. The present study focused on characterizing the temporal relationship between parahippocampal ripple activity (80–140 Hz) and spindles recorded from frontal, parietal and parahippocampal cortices in 12 epilepsy patients implanted with parahippocampal foramen ovale electrodes. Overall, parietal and parahippocampal spindles showed closer relationships to parahippocampal ripple activity than frontal spindles, with the latter following parietal and parahippocampal spindles at a variable delay of up to 0.5 s. On a timescale of seconds, ripple activity showed a continuous increase before the peak of parietal and parahippocampal spindles, and decreased thereafter. At a fine timescale of milliseconds, parahippocampal ripple activity was tightly phase‐locked to the troughs of these spindles. The demonstration of spindle phase‐locked ripple activity in humans is consistent with the idea of a temporally fine‐tuned hippocampus‐to‐neocortex transfer of information taking place during SWS.
SMALL‐AREA ESTIMATION OF POVERTY: THE AID INDUSTRY STANDARD AND ITS ALTERNATIVES
Authors: Haslett S. J. , Jones G. 
Published: December 2010

SummarySmall‐area estimation of poverty‐related variables is an increasingly important analytical tool in targeting the delivery of food and other aid in developing countries. We compare two methods for the estimation of small‐area means and proportions, namely empirical Bayes and composite estimation, with what has become the international standard method of Elbers, Lanjouw & Lanjouw (2003). In addition to differences among the sets of estimates and associated estimated standard errors, we discuss data requirements, design and model selection issues and computational complexity. The Elbers, Lanjouw and Lanjouw (ELL) method is found to produce broadly similar estimates but to have much smaller estimated standard errors than the other methods. The question of whether these standard error estimates are downwardly biased is discussed. Although the question cannot yet be answered in full, as a precautionary measure it is strongly recommended that the ELL model be modified to include a small‐area‐level error component in addition to the cluster‐level and household‐level errors it currently contains. This recommendation is particularly important because the allocation of billions of dollars of aid funding is being determined and monitored via ELL. Under current aid distribution mechanisms, any downward bias in estimates of standard error may lead to allocations that are suboptimal because distinctions are made between estimated poverty levels at the small‐area level that are not significantly different statistically.
THE MATHEMATICS OF TIME IN HISTORY1
Authors: BONNEUIL NOËL 
Published: December 2010

ABSTRACTThe themes of connectedness and continuity, which are also mathematical properties, have run like a red thread through the last fifty years of History and Theory, notably in the theory of the narration of action in history. In this essay I review various answers to the question of the driving force that motivates action and that propels a sequence, continuous or discontinuous. These answers underpin narrative strategies intended to solve the problem of human agency and thereby to provide the basis for historical narratives. I argue that both continuous and discontinuous conceptions of history have to do with the restrictive concept of trajectory. Most of our familiar concepts such as trajectory, equilibrium, optimum, probability, and sensitivity to initial conditions are taken from mathematics and physics, but how well adapted are they to dealing with the time of actors, whose actions are intermingled with uncertainty? I shall present alternative concepts of dynamics, ones that no longer lead toward just one particular future or that reflect a single past. On this basis I suggest reorganizing our view of historical time along the principles of maintenance, acquisition, and victory. Historical sources trace back not to one story or one process that is plausible or that appeals to common sense, but to a whole family of processes. From the past, we can obtain sets of constraints that circumscribe sets of stories rather than a single scenario. I shall then propose a topology of the time of action based on my alternative conception of dynamics, a topology made of what I call viability kernels, capture basins, and victory domains.
WHERE DO WE GO FROM HERE? JUBILEE REPORT ON HISTORY AND THEORY
Authors: TUCKER AVIEZER 
Published: December 2010

ABSTRACTProgress in understanding, clarifying, forming, and devising methods for analyzing, eliminating, or resolving the problems of the philosophies of history and historiography requires integration with other branches of philosophy such as metaphysics, epistemology, the philosophy of science, the philosophy of mind, and ethics. Conversely, mainstream philosophical theories would benefit from confronting the problems of the philosophies of history and historiography. Solving the problems of the philosophies of historiography and history requires considering historiography as continuous with philosophy.This approach is exemplified by examining metaphysical issues in the philosophy of history—historical contingency, necessity, determination, causation, over‐determination, and under‐determination—as well as investigating the epistemology of testimony for its relevance to the epistemology of our knowledge of the past.Inference from multiple testimonies is a particular case of a general model of inference, one in which scientists infer a common cause from multiple sources of evidence that preserve similar information about their common causes. The historical sciences—history, phylogeny, evolutionary biology, comparative historical linguistics, and cosmology—all infer common causes or origins. The theoretical sciences are not interested in any particular token event, but in types of events, whereas, in contrast, the historical sciences attempt to infer common‐cause tokens.The main reasons for the absence of decisive progress in the philosophy of historiography along the promising directions the article outlines are external: random, adverse institutional and market conditions that block the professionalization of the field.
WHEN THE MONOGRAPH IS NO LONGER THE MEDIUM: HISTORICAL NARRATIVE IN THE ONLINE AGE1
Authors: RIGNEY ANN 
Published: December 2010

ABSTRACTOver the last fifty years there has been much discussion about the value of narrative in the production of historical knowledge whereby it is generally assumed that “narrative” is a given and that the only thing at issue is its epistemological value. This article critically examines this assumption. It shows how conceptions of “narrative” have mutated in response to changes in cultural practice and, as importantly, how they have been implicitly modeled on the particular medium envisaged for telling stories: the stand‐alone monograph. The belief that history's natural form is a book written by an individual historian has thus informed most discussions of narrative in the twentieth century, meaning that the primacy of language, the autonomy of the author, and the finished, self‐contained character of the work have been taken for granted. The “naturalness” of the stand‐alone monograph can no longer be taken as a given, however, in the new media ecologies. Digitization and the internet offer new technologies for producing and disseminating historical knowledge and, in the process, present both opportunities and challenges to professional historians. Beyond their practical implications, the digital media also provide a new theoretical model for viewing historical narrative in terms of its social production by multiple agents across different platforms, and this changes our understanding both of past and of future practices.