bluuebunny/crossref_metadata_2025_split huggingface dataset:
SOCIAL SUPPORT AND HEALTH AMONG ELDERLY KUWAITIS
Authors: AL-KANDARI YAGOUB Y. , CREWS DOUGLAS E. 
Published: November 2013

SummaryThe aim of this study was to examine differences in several aspects of health between Kuwaiti men and women aged 60 years and over across three age categories (60–69, 70–79, 80+ years). The relationships between several social support variables, somatic symptoms and systolic and diastolic blood pressures were examined. A total of 1427 adult men (472) and women (955) aged 60 years and over representing all six governorates were selected. Data were collected during 2008–2009 by interview and completion of a questionnaire by participants in their own homes, after obtaining their informed consent. The Social Support Scale (SSS), Frequency of Contact Scale (FOC), Strength of Relations (SOR), Somatic Symptoms Inventory (SSI) and self-rated scales of general health were included. Systolic and diastolic blood pressures were measured. The data show that self-rated health and health in the last year differ significantly across age groups. Glycaemia differed significantly across the three age groups for the total sample. Systolic and diastolic blood pressure were higher in older respondents than younger ones, but no significant differences were observed between men and women. No significant differences in somatic symptoms were observed across the three age groups. Strength of relationship, frequency of contact, social support and children living with an elderly adult were all associated with fewer somatic symptoms, and all, except social support, were associated with lower systolic and diastolic blood pressure. Having children, the perception of social support, frequency of contact with, and strength of, relationships with kin are important modulators of somatic symptoms and blood pressure among elderly Kuwaitis.
Double Bent Crystal Monochromator for High Resolution Neutron Powder Diffraction
Authors: Mikula P. , Vrána M. , Šaroun J. , Seong B.S. , Woo W. 
Published: November 2013

Recent results of focusing and reflectivity properties of the dispersive double-bent-crystal monochromator have shown that it could be succesfully used in high resolution neutron diffraction experiment. By using a standard polycrystalline sample of α-Fe, the resolution of the diffraction performance in the vicinity of the scattering angle 2θS = 90o for the neutron wavelength λ= 0.162 nm was tested in detail. It has been found that for thin (1.3 mm) bent second crystal the angular resolution represented by FWHM of diffraction profiles was 1x10−3 rad for 211 and 200 reflections and about 3x10−3 rad for 220 reflection.
Using X-ray diffraction for studying the effect of modulation and machining parameters on deformation level in brass particulate produced by modulation assisted machining
Authors: Joshi Ravinder Singh , Singh Harpreet 
Published: November 2013

In present investigation, effect of modulation and machining parameters on deformation level of the chips produced during modulation assisted machining (MAM) has been studied. It is shown that disruption in tool-chip contact during modulation assisted machining helps in the formation of discrete chips. Size and shape of the particles produced in MAM can be controlled by varying modulation and machining conditions. Particulates of different shapes and sizes ranging from 100 µm to 5 mm with an aspect ratio of ~10 were produced using MAM. The morphology of the particulates produced was characterized by scanning electron microscope (SEM). Deformation in chip particulates was investigated using X-Ray diffraction. The crystallite size and internal strain in particulates were evaluated using Scherrer and Williamson-Hall methods respectively. The crystallite size of the particulates was found to decrease with decrease in their size, whereas internal strain in particulates was observed to increase with decrease in their size. Furthermore, the length of particulates was observed to decrease with an increase in the ratio of frequency of modulation (fm) to frequency of workpiece rotation (fw). However, the corresponding change in microstrain and crystallite size was insignificant with change in this ratio.
Neutron diffraction study of the crystallographic preferential orientation of metagabro mylonite
Authors: Kučeráková M. , Vratislav S. , Kalvoda L. , Machek M. 
Published: November 2013

Neutron diffraction (ND) was used to investigate the crystallographic preferential orientation (CPO, texture) and structure parameters of four samples of metagabro mylonite collected from the eastern part of the metagabbro sheet at the Stare Mesto belt, Bohemia Massif, Czech Republic. The samples were selected to form a deformation-ordered series with the microstructure varying from non-deformed metagabbro protolith to strongly sheared ultramylonite and amphibole-rich ulramylonite. The specimens used in ND measurements were polished in form of an exact sphere with diameter 50 ± 0.1 mm. The obtained ND patterns were corrected for non-linear background and then evaluated using the Rietveld method implemented in the software package GSAS. Data recorded from powder preparded by milling material from the sampled rocks were used to refine the structure parameters of plagioclase (labradorite structure, triclinic space group C-1) and amphibole (monoclinic space group C2/m). The experiments were performed on the KSN-2 neutron diffractometer situated at the research reactor LVR-15 of the Nuclear Research Institute, plc. Rez, Czech Republic. The data sets of ND patterns measured on each of the four spherical specimens consisted of 90 diagrams collected for different diffraction vectors covering uniformly one orientation hemisphere of the specimen. Based on the collected data, the orientation distribution function (ODF) of crystalline grains was determined by Rietveld harmonic method (coefficients C(l,m,n) of the spherical harmonics expansion determined up to the order L = 8) for the two principal mineral phases - amphibole and plagioclase. The ODF was used to reconstruct (001), (020), (021), (110), (111) (plagioclase) and (001), (11-1), (020), (110), (200) (amphibole) pole figures (PFs). Direct method of ODF calculation implemented in ResMat software package was then used to calculate inverted pole figures (IPFs) of the plagioclase phase. CPO of the amphibole and plagioclase is then discussed in terms of the obtained texture indices and calculated PFs and IPFs and compared with data measured by other methods or available in literature.
The development of web-based surveillance provides new insights into the burden of norovirus outbreaks in hospitals in England
Authors: HARRIS J. P. , ADAMS N. L. , LOPMAN B. A. , ALLEN D. J. , ADAK G. K. 
Published: November 2013

SUMMARYA new surveillance system for outbreaks of norovirus in English hospitals, the hospital norovirus outbreak reporting system (HNORS), was launched in January 2009. On site investigators were enabled to enter data on outbreaks of norovirus directly onto a tailored system via an internet-based front end. A standard dataset was designed to collect information describing the key epidemiological characteristics of each outbreak. In the period 1992–2008, 1817 suspected and confirmed outbreaks of norovirus in English hospitals were reported to national surveillance. After introduction of the new system there were 3980 reports of outbreaks of suspected and confirmed norovirus received in the years 2009–2011. Data from the new reporting system demonstrates that transmission of norovirus levies a heavy burden on English hospitals. On average, reported outbreaks are associated with 13 000 patients and 3400 staff becoming ill, 8900 days of ward closure and the loss of over 15 500 bed-days annually.
Introduction to the special issue: ‘Negation and Clitics in French: Interaction and Variation’
Authors: STARK ELISABETH , MEISNER CHARLOTTE , VÖLKER HARALD 
Published: November 2013

ABSTRACTThis introduction presents very briefly some of the main issues currently discussed around negation particles and clitics in contemporary French and taken up by the six contributions it assembles, namely language change (grammaticalisation of clitics into agreement markers, completion of the Jespersen Cycle) vs. stable variation, and external (sociolinguistic) or internal (phonotactic, prosodic, or syntactic) factors triggering variation in both cases; the hypothesis of a potential diglossia in French opposing two grammars with considerable syntactic differences. Five out of six contributions focus on modern standard and non-standard varieties of French, with a formal theoretical background, while one shows a more philological-descriptive approach and is dedicated to Old French manuscripts.
Factors behind the administrative fees of private pension systems: an international analysis
Authors: TUESTA DAVID 
Published: November 2013

AbstractThis work has three objectives: first, to provide a comprehensive review of administrative fees; second, to construct a comparative data set for 53 countries; and third, to perform an empirical analysis that highlights the main determinants of pension fees from a world-wide perspective. The paper provides an econometric analysis by using panel data techniques. It finds the greater statistical significance of market size, result that is reinforced by mandatory pension schemes. Other factors, such as structural country conditions, market's vertical integration and the presence of an occupational pension scheme, seem to be less relevant.
Effective mechanical weed control in processing tomato: Seven years of results
Authors: Cirujeda A. , Aibar J. , Moreno M.M. , Zaragoza C. 
Published: November 2013

AbstractOpen-air crops are important in Spanish horticulture. The limited number of herbicide active ingredients in minor crops, the waste problem of polyethylene (PE) plastic mulch and the high prices of biodegradable plastics leave hand-weeding and mechanical weed control as the most viable weed control methods. Different tools have been tested in northern European countries but their performance remains unknown in the edaphoclimatic situation of southern Europe. The objective of this work was to test novel physical weed control methods on processing tomato in northeastern Spain compared with other effective control methods, i.e., plastic and paper mulches. A first sequence of field trials was established from 2005 to 2008 at Zaragoza (Spain) to select the best physical control methods out of flamer, torsion weeder, finger weeder, flex-tine harrow and brush hoe used alone or in combination. The best method was the brush hoe which was then compared from 2009 to 2011 with PE mulch, biodegradable plastic mulch and paper mulch. Flamer, flex-tine harrow, torsion weeder and finger weeder performed quite irregularly due to crusty soil conditions and needed additional tools or repeated treatments to increase weed control efficacy. The brush hoe performed best in this soil situation working at about 5 cm depth. Weed biomass reduction was higher than 80% in 6 out of 7 years and similar yield was obtained in the brushed plots compared to the yield obtained with PE, biodegradable plastic and paper mulch. The brush hoe is thus a suitable option for weed control in processing tomato while the other tools were too weak to control aggressive summer weeds in the tested conditions.
Jun dimerization protein 2 is a critical component of the Nrf2/MafK complex regulating the response to ROS homeostasis
Authors: Tanigawa S , Lee C H , Lin C S , Ku C C , Hasegawa H , Qin S , Kawahara A , Korenori Y , Miyamori K , Noguchi M , Lee L H , Lin Y C , Steve Lin C L , Nakamura Y , Jin C , Yamaguchi N , Eckner R , Hou D-X , Yokoyama K K 
Published: November 2013

AbstractOxidative stress and reactive oxygen species (ROS) are associated with diseases such as cancer, cardiovascular complications, inflammation and neurodegeneration. Cellular defense systems must work constantly to control ROS levels and to prevent their accumulation. We report here that the Jun dimerization protein 2 (JDP2) has a critical role as a cofactor for transcription factors nuclear factor-erythroid 2-related factor 2 (Nrf2) and small Maf protein family K (MafK) in the regulation of the antioxidant-responsive element (ARE) and production of ROS. Chromatin immunoprecipitation–quantitative PCR (qPCR), electrophoresis mobility shift and ARE-driven reporter assays were carried out to examine the role of JDP2 in ROS production. JDP2 bound directly to the ARE core sequence, associated with Nrf2 and MafK (Nrf2–MafK) via basic leucine zipper domains, and increased DNA-binding activity of the Nrf2–MafK complex to the ARE and the transcription of ARE-dependent genes. In mouse embryonic fibroblasts from Jdp2-knockout (Jdp2 KO) mice, the coordinate transcriptional activation of several ARE-containing genes and the ability of Nrf2 to activate expression of target genes were impaired. Moreover, intracellular accumulation of ROS and increased thickness of the epidermis were detected in Jdp2 KO mice in response to oxidative stress-inducing reagents. These data suggest that JDP2 is required to protect against intracellular oxidation, ROS activation and DNA oxidation. qPCR demonstrated that several Nrf2 target genes such as heme oxygenase-1, glutamate–cysteine ligase catalytic and modifier subunits, the notch receptor ligand jagged 1 and NAD(P)H dehydrogenase quinone 1 are also dependent on JDP2 for full expression. Taken together, these results suggest that JDP2 is an integral component of the Nrf2–MafK complex and that it modulates antioxidant and detoxification programs by acting via the ARE.
Ecological succession among iron-oxidizing bacteria
Authors: Fleming Emily J , Cetinić Ivona , Chan Clara S , King D Whitney , Emerson David 
Published: November 2013

Abstract
Despite over 125 years of study, the factors that dictate species dominance in neutrophilic iron-oxidizing bacterial (FeOB) communities remain unknown. In a freshwater wetland, we documented a clear ecological succession coupled with niche separation between the helical stalk-forming Gallionellales (for example, Gallionella ferruginea) and tubular sheath-forming Leptothrix ochracea. Changes in the iron-seep community were documented using microscopy and cultivation-independent methods. Quantification of Fe-oxyhydroxide morphotypes by light microscopy was coupled with species-specific fluorescent in situ hybridization (FISH) probes using a protocol that minimized background fluorescence caused by the Fe-oxyhydroxides. Together with scanning electron microscopy, these techniques all indicated that Gallionellales dominated during early spring, with L. ochracea becoming more abundant for the remainder of the year. Analysis of tagged pyrosequencing reads of the small subunit ribosomal RNA gene (SSU rRNA) collected during seasonal progression supported a clear Gallionellales to L. ochracea transition, and community structure grouped according to observed dominant FeOB forms. Axis of redundancy analysis of physicochemical parameters collected from iron mats during the season, plotted with FeOB abundance, corroborated several field and microscopy-based observations and uncovered several unanticipated relationships. On the basis of these relationships, we conclude that the ecological niche of the stalk-forming Gallionellales is in waters with low organic carbon and steep redoxclines, and the sheath-forming L. ochracea is abundant in waters that contain high concentrations of complex organic carbon, high Fe and Mn content and gentle redoxclines. Finally, these findings identify a largely unexplored relationship between FeOB and organic carbon.
Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms
Authors: Goffredi Shana K , Yi Hana , Zhang Qingpeng , Klann Jane E , Struve Isabelle A , Vrijenhoek Robert C , Brown C Titus 
Published: November 2013

Abstract
An unusual symbiosis, first observed at ∼3000 m depth in the Monterey Submarine Canyon, involves gutless marine polychaetes of the genus Osedax and intracellular endosymbionts belonging to the order Oceanospirillales. Ecologically, these worms and their microbial symbionts have a substantial role in the cycling of carbon from deep-sea whale fall carcasses. Microheterogeneity exists among the Osedax symbionts examined so far, and in the present study the genomes of the two dominant symbionts, Rs1 and Rs2, were sequenced. The genomes revealed heterotrophic versatility in carbon, phosphate and iron uptake, strategies for intracellular survival, evidence for an independent existence, and numerous potential virulence capabilities. The presence of specific permeases and peptidases (of glycine, proline and hydroxyproline), and numerous peptide transporters, suggests the use of degraded proteins, likely originating from collagenous bone matter, by the Osedax symbionts. 13C tracer experiments confirmed the assimilation of glycine/proline, as well as monosaccharides, by Osedax. The Rs1 and Rs2 symbionts are genomically distinct in carbon and sulfur metabolism, respiration, and cell wall composition, among others. Differences between Rs1 and Rs2 and phylogenetic analysis of chemotaxis-related genes within individuals of symbiont Rs1 revealed the influence of the relative age of the whale fall environment and support possible local niche adaptation of ‘free-living’ lifestages. Future genomic examinations of other horizontally-propogated intracellular symbionts will likely enhance our understanding of the contribution of intraspecific symbiont diversity to the ecological diversification of the intact association, as well as the maintenance of host diversity.
к Opioids inhibit tumor angiogenesis by suppressing VEGF signaling
Authors: Yamamizu Kohei , Furuta Sadayoshi , Hamada Yusuke , Yamashita Akira , Kuzumaki Naoko , Narita Michiko , Doi Kento , Katayama Shiori , Nagase Hiroshi , Yamashita Jun K. , Narita Minoru 
Published: November 2013

AbstractOpioids are effective analgesics for the management of moderate to severe cancer pain. Here we show that κ opioid receptor (KOR) agonists act as anti-angiogenic factors in tumors. Treatment with KOR agonists, U50,488H and TRK820, significantly inhibited human umbilical vein endothelial cell (HUVEC) migration and tube formation by suppressing VEGFR2 expression. In contrast, treatment with a μ opioid receptor agonist, DAMGO, or a δ opioid receptor agonist, SNC80, did not prevent angiogenesis in HUVECs. Lewis lung carcinoma (LLC) or B16 melanoma grafted in KOR knockout mice showed increased proliferation and remarkably enhanced tumor angiogenesis compared with those in wild type mice. On the other hand, repeated intraperitoneal injection of TRK820 (0.1–10 μg/kg, b.i.d.) significantly inhibited tumor growth by suppressing tumor angiogenesis. These findings indicate that KOR agonists play an important role in tumor angiogenesis and this knowledge could lead to a novel strategy for cancer therapy.
Pathogen selection drives nonoverlapping associations between HLA loci
Authors: Penman Bridget S. , Ashby Ben , Buckee Caroline O. , Gupta Sunetra 
Published: November 2013

SignificanceHuman leukocyte antigens (HLA), first identified in tissue-matching for transplantation, play a critical role in immunity. HLAs are extraordinarily diverse, but certain sets of HLA genes are more likely to be found together than others. Here, we show that associations between HLA genes can arise through their coevolutionary interaction with pathogens. Technological advances are making it easier to determine HLA types, but DNA sequence alone cannot fully predict an HLA’s functional properties. Our work offers a new evolutionary approach to tackling this problem.
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
Authors: Raney Brian J. , Dreszer Timothy R. , Barber Galt P. , Clawson Hiram , Fujita Pauline A. , Wang Ting , Nguyen Ngan , Paten Benedict , Zweig Ann S. , Karolchik Donna , Kent W. James 
Published: November 2013

Abstract
Summary: Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror.
Availability and implementation: Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu.
Contact: donnak@soe.ucsc.edu
MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
Authors: Lienhard Matthias , Grimm Christina , Morkel Markus , Herwig Ralf , Chavez Lukas 
Published: November 2013

Abstract
Motivation: DNA enrichment followed by sequencing is a versatile tool in molecular biology, with a wide variety of applications including genome-wide analysis of epigenetic marks and mechanisms. A common requirement of these diverse applications is a comparison of read coverage between experimental conditions. The amount of samples generated for such comparisons ranges from few replicates to hundreds of samples per condition for epigenome-wide association studies. Consequently, there is an urgent need for software that allows for fast and simple processing and comparison of sequencing data derived from enriched DNA.
Results: Here, we present a major update of the R/Bioconductor package MEDIPS, which allows for an arbitrary number of replicates per group and integrates sophisticated statistical methods for the detection of differential coverage between experimental conditions. Our approach can be applied to a diversity of quantitative sequencing data. In addition, our update adds novel functionality to MEDIPS, including correlation analysis between samples, and takes advantage of Bioconductor’s annotation databases to facilitate annotation of specific genomic regions.
Availability and implementation: The latest version of MEDIPS is available as version 1.12.0 and part of Bioconductor 2.13. The package comes with a manual containing detailed description of its functionality and is available at http://www.bioconductor.org.
Contact: lienhard@molgen.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.