bluuebunny/crossref_metadata_2025_split huggingface dataset:
KMUP‐1 inhibits hypertension‐induced left ventricular hypertrophy through regulation of nitric oxide synthases, ERK1/2, and calcineurin
Authors: Yeh Jwu‐Lai , Liu Chung‐Pin , Hsu Jong‐Hau , Tseng Ching‐Jiunn , Wu Ping‐Ju , Wang Yi‐Ya , Wu Jiunn‐Ren , Chen Ing‐Jun 
Published: July 2012

AbstractHypertension can induce left ventricular hypertrophy (LVH), and the nitric oxide (NO) pathway plays an important role in the pathogenesis of cardiac hypertrophy. This study aimed to examine whether KMUP‐1, a novel xanthine‐based derivative, could inhibit LVH in spontaneously hypertensive rats (SHRs) and to investigate potential mechanisms underlying its antihypertrophic effects. Two groups of animals with chronic or subacute LVH were treated. In the chronic LVH group, KMUP‐1 (10 or 30 mg/kg/d orally) was administered for 28 days to both normotensive rats and SHRs. In the subacute LVH group, KMUP‐1 (0.5 mg/kg/d intraperitoneally) or sildenafil (0.7 mg/kg/d intraperitoneally) was administered for 10 days with or without co‐treatment with the nitric oxide synthase (NOS) inhibitor N‐omega‐nitro‐l‐arginine (L‐NNA; 20 mg/L orally). After treatment, the effects of KMUP‐1 or sildenafil on hypertension, cardiac hypertrophy, survival, expression of the NO/soluble guanylate cyclase (sGC)/protein kinase G (NO/sGC/PKG) pathway in the aorta andleft ventricle, and calcineurin A/extracellular signal‐regulated kinase 1/2 (ERK1/2) signaling in the left ventricle were examined. In the chronic LVH group, the SHRs developed hypertension with LVH over the 28 days. KMUP‐1 attenuated the hypertension and LVH, increased survival rate, enhanced endothelial NOS/cyclic guanosine monophosphate/PKG (eNOS/cGMP/PKG) and decreased inducible NOS (iNOS) expression in the aorta and left ventricle of the SHRs. In the subacute LVH group, both KMUP‐1 and sildenafil administered for 10 days attenuated the LVH in SHRs, with enhanced eNOS/cGMP/PKG and suppressed iNOS/calcineurin A/ERK1/2 expression in the left ventricle. In addition, both KMUP‐1 and sildenafil attenuated L‐NNA‐induced LVH. KMUP‐1 inhibition of hypertension‐induced LVH with associated upregulation of eNOS, downregulation of iNOS in both the aorta and left ventricle, and attenuation of calcineurin A and ERK1/2 signaling in the left ventricle.
Prevalence of Mitral Valve Prolapse in Residents Living at Moderately High Altitude
Authors: Güvenç Tolga Sinan , Çanga Yiğit , Karabağ Yavuz , Özen Kaya , Balcı Bahattin 
Published: July 2012

Objective Prolapse of mitral valve leaflets is a frequent disorder and the most common cause of severe mitral regurgitation in western countries. However, little is known about the effects of altitude on mitral valve prolapse. We studied the prevalence and echocardiographic characteristics of mitral valve prolapse at moderately high altitude and sea level. Methods A total of 936 consecutive subjects who were admitted to 2 study institutions at Kars, Turkey (1750 m) and Istanbul, Turkey (7 m) were enrolled in this study to determine prevalence of mitral valve prolapse. Demographic and 2-dimensional echocardiographic characteristics of participants were recorded. Results Prevalance of mitral valve prolapse was found to be significantly higher in people living at moderate altitude compared with those living at sea level (6.2% vs 2.0%; P = .007). Overall echocardiographic features regarding valve thickness (4.1 ± 0.80 mm vs 3.6 ± 0.66 mm; P = 0.169), maximal valve prolapse (4.6 ± 2.08 mm vs 3.9 ± 0.91 mm; P = .093), and frequency of mitral regurgitation (89% vs 73%; P = .65) were similar between groups, although anterior valve prolapse was seen more frequently at moderate altitude (50% vs 11%; P = .056) and posterior leaflet prolapse was significantly more frequent at sea level (66% vs 10%; P = .002). Conclusions Mitral valve prolapse is more frequently observed at moderately high altitudes. Further studies are needed to determine clinical importance of our findings.
Neuropsychological evidence for abnormal neurodevelopment associated with early-onset psychoses
Authors: Bombin I. , Mayoral M. , Castro-Fornieles J. , Gonzalez-Pinto A. , de la Serna E. , Rapado-Castro M. , Barbeito S. , Parellada M. , Baeza I. , Graell M. , Payá B. , Arango C. 
Published: July 2012

BackgroundThe longitudinal neuropsychological study of first-episode early-onset psychosis (EOP) patients, whose brain maturation is still in progress at the time of illness onset, provides a unique opportunity to compare their cognitive development with that of healthy subjects, in search of specific patterns resulting from the interaction between neurodevelopmental processes and the presence of psychotic disorders.MethodSeventy-five first-episode EOP patients (schizophrenian = 35; bipolar disordern = 17; other forms of psychosisn = 23) with a mean age of 15.53 years were assessed with a neuropsychological battery that included measures of attention, working memory, memory and executive functions within 6 months following the onset of the first psychotic symptom (baseline) and 2 years later. Psychotic symptoms were assessed at both times with the Positive and Negative Symptom Scale (PANSS). Seventy-nine healthy subjects matched for age and education served as controls.ResultsEOP patients showed significant cognitive impairment at both baseline and the 2-year follow-up, with no significant differences between diagnostic groups at either time. Both healthy controls and EOP patients improved in all cognitive measures, except for patient working memory. Improvement in patient attention lost significance after controlling for psychotic symptom reduction. No significant time/diagnosis interaction was found among patients (p > 0.405).ConclusionsCognitive impairment in EOP is already present at the first episode, and cognitive development seems to be arrested early in EOP patients compared to their healthy peers, at least for some cognitive functions. These and previous similar results support the neurodevelopmental hypothesis of psychosis.
Characteristics and contributions of non-kin carers of older people: a closer look at friends and neighbours
Authors: LAPIERRE TRACEY A. , KEATING NORAH 
Published: July 2012

ABSTRACTResearch on informal care-giving has largely neglected the contributions of non-kin carers. This paper investigated the characteristics and contributions of non-kin who care for older adults with a long-term health problem, and investigated friends and neighbours as distinct categories of care providers. Using data from 324 non-kin carers in the 1996 General Social Survey of Canada, this study compared individual and relationship characteristics, care tasks and amount of care provided for the two groups. Interpersonal and socio-demographic characteristics were investigated as mediators of potential differences between friends and neighbours in patterns of care. Results demonstrate that friend and neighbour carers differed on age, marital status, geographical proximity and relationship closeness. Friends were more likely than neighbours to assist with personal care, bills and banking, and transportation. Neighbours were more likely to assist with home maintenance. Friends provided assistance with a greater number of tasks and provided more hours of care per week, suggesting a more prominent role in the care of non-kin than neighbours. Age, income, a minor child in the household, proximity and relationship closeness significantly predicted amount of care provided, and relationship closeness largely explained differences between friends and neighbours. Future research on informal care-giving can build on the findings that distinguish friend and neighbour carers to further discriminate the dynamics of non-kin care.
Neuregulin 3 is associated with attention deficits in schizophrenia and bipolar disorder
Authors: Meier Sandra , Strohmaier Jana , Breuer Rene , Mattheisen Manuel , Degenhardt Franziska , Mühleisen Thomas W. , Schulze Thomas G. , Nöthen Markus M. , Cichon Sven , Rietschel Marcella , Wüst Stefan 
Published: July 2012

Abstract
Linkage and fine mapping studies have established that the neuregulin 3 gene (NRG3) is a susceptibility locus for schizophrenia. Association studies of this disorder have implicated NRG3 variants in both psychotic symptoms and attention performance. Psychotic symptoms and cognitive deficits are also frequent features of bipolar disorder. The aims of the present study were to extend analysis of the association between NRG3 and psychotic symptoms and attention in schizophrenia and to determine whether these associations also apply to bipolar disorder. A total of 358 patients with schizophrenia and 111 patients with bipolar disorder were included. Psychotic symptoms were evaluated using the Operational Criteria Checklist for Psychotic Illness (OPCRIT) and attention performance was assessed using the Trail Making Test (TMT). Symptoms and performance scores were then tested for association with the NRG3 variant rs6584400. A significant association was found between the number of rs6584400 minor alleles and the total OPCRIT score for psychotic symptoms in patients with schizophrenia. Moreover, in both schizophrenia and bipolar disorder patients, minor allele carriers of rs6584400 outperformed homozygous major allele carriers in the TMT. The results suggest that rs6584400 is associated with psychotic symptoms and attention performance in schizophrenia. The finding of a significant association between rs6584400 and attention performance in bipolar disorder supports the hypothesis that this NRG3 variant confers genetic susceptibility to cognitive deficits in both schizophrenia and bipolar disorder.
A global evaluation of temperature and carbonate ion control on Mg/Ca ratios of ostracoda genus Krithe
Authors: Elmore A. C. , Sosdian S. , Rosenthal Y. , Wright J. D. 
Published: July 2012

Improving estimates of past ocean temperatures is paramount to our understanding of ocean circulation and its role in climate change. Magnesium/calcium (Mg/Ca) ratios of carapaces of the benthic ostracod genus Krithe were determined from new, globally distributed core top samples from the Norwegian Sea, Cape Hatteras shelf, Gulf of Mexico, Sulawesi Margin (Indonesia), New Zealand shelf, Ceara Rise, and the North Atlantic. A linear regression of the Krithe Mg/Ca ratios and bottom water temperature (BWT) reveals a significant correlation for locations where temperature during carapace calcification was above ∼3°C, which can be described by the equation Mg/Ca = (0.972 ± 0.152) * BWT + (7.948 ± 1.103) consistent with previous North Atlantic calibrations. Deviations from the global calibration line below ∼3°C follow the same pattern observed for benthic foraminifera, suggesting that the incorporation of magnesium into ostracodal calcite may be secondarily controlled by changes in carbonate ion concentration. Therefore, we propose a linear regression that describes the relationship between magnesium incorporation, temperature, and carbonate saturation for low temperatures (<3°C); Mg/Ca = (0.972 ± 0.152) * BWT + (0.100 ± 0.030) * Δ[CO32−]) + (4.440 ± 1.103) (1 SE = ± 0.3°C). While the standard error of the calibration is small, it requires an accurate knowledge of past Δ[CO32−] concentration, which necessitates additional proxy data. Applying the calibration to glacial samples from the deep North Atlantic Ocean we show that estimates of bottom water temperatures generated from the new Δ[CO32−]‐ corrected equations are more consistent with results from oxygen isotopes and pore water studies.
Iron isotope and trace metal records of iron cycling in the proto‐North Atlantic during the Cenomanian‐Turonian oceanic anoxic event (OAE‐2)
Authors: Owens Jeremy D. , Lyons Timothy W. , Li Xiaona , Macleod Kenneth G. , Gordon Gwenyth , Kuypers Marcel M. M. , Anbar Ariel , Kuhnt Wolfgang , Severmann Silke 
Published: July 2012

The global carbon cycle during the mid‐Cretaceous (∼125–88 million years ago, Ma) experienced numerous major perturbations linked to increased organic carbon burial under widespread, possibly basin‐scale oxygen deficiency and episodes of euxinia (anoxic and H2S‐containing). The largest of these episodes, the Cenomanian‐Turonian boundary event (ca. 93.5 Ma), or oceanic anoxic event (OAE) 2, was marked by pervasive deposition of organic‐rich, laminated black shales in deep waters and in some cases across continental shelves. This deposition is recorded in a pronounced positive carbon isotope excursion seen ubiquitously in carbonates and organic matter. Enrichments of redox‐sensitive, often bioessential trace metals, including Fe and Mo, indicate major shifts in their biogeochemical cycles under reducing conditions that may be linked to changes in primary production. Iron enrichments and bulk Fe isotope compositions track the sources and sinks of Fe in the proto‐North Atlantic at seven localities marked by diverse depositional conditions. Included are an ancestral mid‐ocean ridge and euxinic, intermittently euxinic, and oxic settings across varying paleodepths throughout the basin. These data yield evidence for a reactive Fe shuttle that likely delivered Fe from the shallow shelf to the deep ocean basin, as well as (1) hydrothermal sources enhanced by accelerated seafloor spreading or emplacement of large igneous province(s) and (2) local‐scale Fe remobilization within the sediment column. This study, the first to explore Fe cycling and enrichment patterns on an ocean scale using iron isotope data, demonstrates the complex processes operating on this scale that can mask simple source‐sink relationships. The data imply that the proto‐North Atlantic received elevated Fe inputs from several sources (e.g., hydrothermal, shuttle and detrital inputs) and that the redox state of the basin was not exclusively euxinic, suggesting previously unknown heterogeneity in depositional conditions and biogeochemical cycling within those settings during OAE‐2.
MOJAVE: Monitoring of Jets in Active galactic nuclei with VLBA Experiments
Authors: Pushkarev A. B. , Hovatta T. , Kovalev Y. Y. , Lister M. L. , Lobanov A. P. , Savolainen T. , Zensus J. A. 
Published: July 2012

Aims. We have investigated a frequency-dependent shift in the absolute
position of the optically thick apparent origin of parsec-scale jets (“core shift” effect)
to probe physical conditions in ultra-compact relativistic outflows in active galactic
nuclei.
Methods. We used multi-frequency Very Long Baseline Array (VLBA)
observations of 191 sources carried out in 12 epochs in 2006 within the Monitoring Of Jets
in Active galactic nuclei with VLBA Experiments (MOJAVE) program. The observations were
performed at 8.1, 8.4, 12.1, and 15.4 GHz. We implemented a method of determining the core
shift vector based on (i) image registration by two-dimensional normalized
cross-correlation and (ii) model-fitting the source brightness distribution to take into
account a non-zero core component offset from the phase center.
Results. The 15.4−8.1, 15.4−8.4, and 15.4−12.1 GHz core shift vectors
are derived for 163 sources, and have median values of 128, 125, and
88 μas, respectively, compared to the typical measured errors of 50, 51,
35 μas. The effect occurs predominantly along the jet direction, with
departures smaller than 45° from the median jet position angle in over 80% of the cases.
Despite the moderate ratio of the observed frequencies (<2), core shifts significantly
different from zero (>2σ) are detected for about 55% of the sources.
These shifts are even better aligned with the jet direction, deviating from the latter by
less than 30° in over 90% of the cases. There is an indication that the core shift
decreases with increasing redshift. Magnetic fields in the jet at a distance of 1 parsec
from the central black hole, calculated from the obtained core shifts, are found to be
systematically stronger in quasars (median B1 ≈ 0.9 G) than
those in BL Lacs (median B1 ≈ 0.4 G). We also constrained the
absolute distance of the core from the apex of the jet at 15 GHz as well as the magnetic
field strength in the 15 GHz core region.
Peak acceleration during impact with helmet materials: Effects of impactor mass and speed
Authors: Hutchinson Timothy Paul 
Published: July 2012

AbstractThe impact properties of six foam materials used for energy absorption as the liner of children's helmets, reported by Gimbel and Hoshizaki are considered further. In high‐energy impacts, almost complete compression of the energy‐absorbing material (bottoming out) may occur, and the severity of the impact increases greatly. Too soft a material means bottoming out occurs at low speeds, but if it is too stiff, the material itself is injurious. The fitting of equations to results in ‘no bottoming out’ and ‘bottoming out’ conditions may help assessment of what compromise is appropriate. The equations in this article correspond to peak acceleration being proportional to power functions of impactor speed and mass. 1. When there was no bottoming out, peak acceleration was found to be proportional to m ∧(c−1).v ∧(2c), with c being approximately 0.25. 2. For bottoming out, peak acceleration was found to be proportional to m ∧(p).v ∧(q), with p and q being approximately 2 and approximately 3. 3. The constants of proportionality were related to material density in a regular way.
YAHA: fast and flexible long-read alignment with optimal breakpoint detection
Authors: Faust Gregory G. , Hall Ira M. 
Published: July 2012

Abstract
Motivation: With improved short-read assembly algorithms and the recent development of long-read sequencers, split mapping will soon be the preferred method for structural variant (SV) detection. Yet, current alignment tools are not well suited for this.
Results: We present YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints.
Availability: YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from http://faculty.virginia.edu/irahall/YAHA.
Contact: imh4y@virginia.edu
Nebula—a web-server for advanced ChIP-seq data analysis
Authors: Boeva Valentina , Lermine Alban , Barette Camille , Guillouf Christel , Barillot Emmanuel 
Published: July 2012

Abstract
Motivation: ChIP-seq consists of chromatin immunoprecipitation and deep sequencing of the extracted DNA fragments. It is the technique of choice for accurate characterization of the binding sites of transcription factors and other DNA-associated proteins. We present a web service, Nebula, which allows inexperienced users to perform a complete bioinformatics analysis of ChIP-seq data.
Results: Nebula was designed for both bioinformaticians and biologists. It is based on the Galaxy open source framework. Galaxy already includes a large number of functionalities for mapping reads and peak calling. We added the following to Galaxy: (i) peak calling with FindPeaks and a module for immunoprecipitation quality control, (ii) de novo motif discovery with ChIPMunk, (iii) calculation of the density and the cumulative distribution of peak locations relative to gene transcription start sites, (iv) annotation of peaks with genomic features and (v) annotation of genes with peak information. Nebula generates the graphs and the enrichment statistics at each step of the process. During Steps 3–5, Nebula optionally repeats the analysis on a control dataset and compares these results with those from the main dataset. Nebula can also incorporate gene expression (or gene modulation) data during these steps. In summary, Nebula is an innovative web service that provides an advanced ChIP-seq analysis pipeline providing ready-to-publish results.
Availability: Nebula is available at http://nebula.curie.fr/
Supplementary Information: Supplementary data are available at Bioinformatics online.
Folding RNA/DNA hybrid duplexes
Authors: Lorenz Ronny , Hofacker Ivo L. , Bernhart Stephan H. 
Published: July 2012

Abstract
Motivation: While there are numerous programs that can predict RNA or DNA secondary structures, a program that predicts RNA/DNA hetero-dimers is still missing. The lack of easy to use tools for predicting their structure may be in part responsible for the small number of reports of biologically relevant RNA/DNA hetero-dimers.
Results: We present here an extension to the widely used ViennaRNAPackage (Lorenz et al., 2011) for the prediction of the structure of RNA/DNA hetero-dimers.
Availability: http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html
Contact: ronny@tbi.univie.ac.at, berni@bioinf.uni-leipzig.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Photosynthetic Adaptation to Length of Day Is Dependent on S-Sulfocysteine Synthase Activity in the Thylakoid Lumen
Authors: Bermúdez María Ángeles , Galmés Jeroni , Moreno Inmaculada , Mullineaux Philip M. , Gotor Cecilia , Romero Luis C. 
Published: July 2012

Abstract
Arabidopsis (Arabidopsis thaliana) chloroplasts contain two O-acetyl-serine(thiol)lyase (OASTL) homologs, OAS-B, which is an authentic OASTL, and CS26, which has S-sulfocysteine synthase activity. In contrast with OAS-B, the loss of CS26 function resulted in dramatic phenotypic changes, which were dependent on the light treatment. We have performed a detailed characterization of the photosynthetic and chlorophyll fluorescence parameters in cs26 plants compared with those of wild-type plants under short-day growth conditions (SD) and long-day growth conditions (LD). Under LD, the photosynthetic characterization, which was based on substomatal CO2 concentrations and CO2 concentration in the chloroplast curves, revealed significant reductions in most of the photosynthetic parameters for cs26, which were unchanged under SD. These parameters included net CO2 assimilation rate, mesophyll conductance, and mitochondrial respiration at darkness. The analysis also showed that cs26 under LD required more absorbed quanta per driven electron flux and fixed CO2. The nonphotochemical quenching values suggested that in cs26 plants, the excess electrons that are not used in photochemical reactions may form reactive oxygen species. A photoinhibitory effect was confirmed by the background fluorescence signal values under LD and SD, which were higher in young leaves compared with mature ones under SD. To hypothesize the role of CS26 in relation to the photosynthetic machinery, we addressed its location inside of the chloroplast. The activity determination and localization analyses that were performed using immunoblotting indicated the presence of an active CS26 enzyme exclusively in the thylakoid lumen. This finding was reinforced by the observation of marked alterations in many lumenal proteins in the cs26 mutant compared with the wild type.