bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep divergences and extensive phylogeographic structure in a clade of lowland tropical salamanders
Authors: Rovito Sean M , Parra-Olea Gabriela , Vásquez-Almazán Carlos R , Luna-Reyes Roberto , Wake David B 
Published: December 2012

AbstractBackgroundThe complex geological history of Mesoamerica provides the opportunity to study the impact of multiple biogeographic barriers on population differentiation. We examine phylogeographic patterns in a clade of lowland salamanders (BolitoglossasubgenusNanotriton) using two mitochondrial genes and one nuclear gene. We use several phylogeographic analyses to infer the history of this clade and test hypotheses regarding the geographic origin of species and location of genetic breaks within species. We compare our results to those for other taxa to determine if historical events impacted different species in a similar manner.ResultsDeep genetic divergence between species indicates that they are relatively old, and two of the three widespread species show strong phylogeographic structure. Comparison of mtDNA and nuclear gene trees shows no evidence of hybridization or introgression between species. Isolated populations ofBolitoglossa rufescensfrom Los Tuxtlas region constitute a separate lineage based on molecular data and morphology, and divergence between Los Tuxtlas and other areas appears to predate the arrival ofB. rufescensin other areas west of the Isthmus of Tehuantepec. The Isthmus appears responsible for Pliocene vicariance withinB. rufescens, as has been shown for other taxa. The Motagua-Polochic fault system does not appear to have caused population vicariance, unlike in other systems.ConclusionsSpecies ofNanotritonhave responded to some major geological events in the same manner as other taxa, particularly in the case of the Isthmus of Tehuantepec. The deep divergence of the Los Tuxtlas populations ofB. rufescensfrom other populations highlights the contribution of this volcanic system to patterns of regional endemism, and morphological differences observed in the Los Tuxtlas populations suggests that they may represent an undescribed species ofBolitoglossa. The absence of phylogeographic structure inB. nympha, in contrast to the other widespread species in the subgenus, may be due to historical forest contraction and more recent range expansion in the region. Phylogeographic data provide substantial insight into the evolutionary history of these morphologically similar species of salamanders, and contribute to our understanding of factors that have generated the high biodiversity of Mesoamerica.
Diversification of the expanded teleost-specific toll-like receptor family in Atlantic cod, Gadus morhua
Authors: Sundaram Arvind YM , Kiron Viswanath , Dopazo Joaquín , Fernandes Jorge MO 
Published: December 2012

AbstractBackgroundToll-like receptors (Tlrs) are major molecular pattern recognition receptors of the innate immune system. Atlantic cod (Gadus morhua) is the first vertebrate known to have lost most of the mammalian Tlr orthologues, particularly all bacterial recognising and other cell surface Tlrs. On the other hand, its genome encodes a unique repertoire of teleost-specific Tlrs. The aim of this study was to investigate if these duplicate Tlrs have been retained through adaptive evolution to compensate for the lack of other cell surface Tlrs in the cod genome.ResultsIn this study, onetlr21, 12tlr22and twotlr23genes representing the teleost-specific Tlr family have been cloned and characterised in cod. Phylogenetic analysis grouped alltlr22genes under a single clade, indicating that the multiple cod paralogues have arisen through lineage-specific duplications. Alltlrs examined were transcribed in immune-related tissues as well as in stomach, gut and gonads of adult cod and were differentially expressed during early development. Thesetlrs were also differentially regulated following immune challenge by immersion withVibrio anguillarum, indicating their role in the immune response. An increase in water temperature from 4 to 12°C was associated with a 5.5-fold down-regulation oftlr22dtranscript levels in spleen. Maximum likelihood analysis with different evolution models revealed thattlr22genes are under positive selection. A total of 24 codons were found to be positively selected, of which 19 are in the ligand binding region of ectodomain.ConclusionPositive selection pressure coupled with experimental evidence of differential expression strongly support the hypothesis that teleost-specifictlrparalogues in cod are undergoing neofunctionalisation and can recognise bacterial pathogen-associated molecular patterns to compensate for the lack of other cell surface Tlrs.
Functional α7β2 nicotinic acetylcholine receptors expressed in hippocampal interneurons exhibit high sensitivity to pathological level of amyloid β peptides
Authors: Liu Qiang , Huang Yao , Shen Jianxin , Steffensen Scott , Wu Jie 
Published: December 2012

Abstract

Background
β-amyloid (Aβ) accumulation is described as a hallmark of Alzheimer’s disease (AD). Aβ perturbs a number of synaptic components including nicotinic acetylcholine receptors containing α7 subunits (α7-nAChRs), which are abundantly expressed in the hippocampus and found on GABAergic interneurons. We have previously demonstrated the existence of a novel, heteromeric α7β2-nAChR in basal forebrain cholinergic neurons that exhibits high sensitivity to acute Aβ exposure. To extend our previous work, we evaluated the expression and pharmacology of α7β2-nAChRs in hippocampal interneurons and their sensitivity to Aβ.

Results
GABAergic interneurons in the CA1 subregion of the hippocampus expressed functional α7β2-nAChRs, which were characterized by relatively slow whole-cell current kinetics, pharmacological sensitivity to dihydro-β-erythroidine (DHβE), a nAChR β2* subunit selective blocker, and α7 and β2 subunit interaction using immunoprecipitation assay. In addition, α7β2-nAChRs were sensitive to 1 nM oligomeric Aβ. Similar effects were observed in identified hippocampal interneurons prepared from GFP-GAD mice.

Conclusion
These findings suggest that Aβ modulation of cholinergic signaling in hippocampal GABAergic interneurons via α7β2-nAChRs could be an early and critical event in Aβ-induced functional abnormalities of hippocampal function, which may be relevant to learning and memory deficits in AD.
OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize
Authors: Colmsee Christian , Mascher Martin , Czauderna Tobias , Hartmann Anja , Schlüter Urte , Zellerhoff Nina , Schmitz Jessica , Bräutigam Andrea , Pick Thea R , Alter Philipp , Gahrtz Manfred , Witt Sandra , Fernie Alisdair R , Börnke Frederik , Fahnenstich Holger , Bucher Marcel , Dresselhaus Thomas , Weber Andreas PM , Schreiber Falk , Scholz Uwe , Sonnewald Uwe 
Published: December 2012

Abstract

Background
Maize is a major crop plant, grown for human and animal nutrition, as well as a renewable resource for bioenergy. When looking at the problems of limited fossil fuels, the growth of the world’s population or the world’s climate change, it is important to find ways to increase the yield and biomass of maize and to study how it reacts to specific abiotic and biotic stress situations. Within the OPTIMAS systems biology project maize plants were grown under a large set of controlled stress conditions, phenotypically characterised and plant material was harvested to analyse the effect of specific environmental conditions or developmental stages. Transcriptomic, metabolomic, ionomic and proteomic parameters were measured from the same plant material allowing the comparison of results across different omics domains. A data warehouse was developed to store experimental data as well as analysis results of the performed experiments.

Description
The OPTIMAS Data Warehouse (OPTIMAS-DW) is a comprehensive data collection for maize and integrates data from different data domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. Within the OPTIMAS project, a 44K oligo chip was designed and annotated to describe the functions of the selected unigenes. Several treatment- and plant growth stage experiments were performed and measured data were filled into data templates and imported into the data warehouse by a Java based import tool. A web interface allows users to browse through all stored experiment data in OPTIMAS-DW including all data domains. Furthermore, the user can filter the data to extract information of particular interest. All data can be exported into different file formats for further data analysis and visualisation. The data analysis integrates data from different data domains and enables the user to find answers to different systems biology questions. Finally, maize specific pathway information is provided.

Conclusions
With OPTIMAS-DW a data warehouse for maize was established, which is able to handle different data domains, comprises several analysis results that will support researchers within their work and supports systems biological research in particular. The system is available at http://www.optimas-bioenergy.org/optimas_dw.
Search strategies to identify reports on “off-label” drug use in EMBASE
Authors: Mesgarpour Bita , Müller Markus , Herkner Harald 
Published: December 2012

Abstract

Background
Medications are frequently prescribed outside their regulatory approval (off-label) by physicians particularly where appropriate therapies are not available. However, the risk/benefit ratio of drugs in off-label use needs to be critically appraised because it may differ from approved on-label usage. Therefore, an extensive exploration of current evidence on clinical data is well-advised. The objective of this study was to develop a search strategy that facilitates detection of the off-label drug use documents in EMBASE via OvidSP.

Methods
We constructed two sets of gold standards from relevant records to off-label drug use by a sensitive search of MEDLINE and EMBASE. Search queries, including search words and strings, were conceived based on definition of off-label use of medications as well as text analysis of 500 randomly selected relevant documents. The selected terms were searched in EMBASE (from 1988 to 2011) and their retrieval performance was compared with the gold standards. We developed a sensitivity-maximizing, and a sensitivity- and precision-maximizing search strategy.

Results
From 4067 records relevant to off-label drug use in our full gold standard set, 3846 records were retrievable from EMBASE. “off label*.af.” was the most sensitive single term (overall sensitivity 77.5%, sensitivity within EMBASE 81.9%, precision 88.1%). The highest sensitive search strategy was achieved by combining 36 search queries with overall sensitivity of 94.0% and precision of 69.5%. An optimal sensitive and precise search strategy was yielded precision 87.4% at the expense of decreasing overall sensitivity to 89.4%.

Conclusion
We developed highly sensitive search strategies to enhance the retrieval of studies on off-label drug use in OvidSP EMBASE.
Additional corpus biopsy enhances the detection of Helicobacter pylori infection in a background of gastritis with atrophy
Authors: Lan Hung-Chieh , Chen Tseng-Shing , Li Anna Fen-Yau , Chang Full-Young , Lin Han-Chieh 
Published: December 2012

AbstractBackgroundThe best sites for biopsy-based tests to evaluateH. pyloriinfection in gastritis with atrophy are not well known. This study aimed to evaluate the site and sensitivity of biopsy-based tests in terms of degree of gastritis with atrophy.MethodsOne hundred and sixty-four (164) uninvestigated dyspepsia patients were enrolled. Biopsy-based tests (i.e., culture, histology Giemsa stain and rapid urease test) and non-invasive tests (anti-H. pyloriIgG) were performed. The gold standard ofH. pyloriinfection was defined according to previous criteria. The sensitivity, specificity, positive predictive rate and negative predictive rate of biopsy-based tests at the gastric antrum and body were calculated in terms of degree of gastritis with atrophy.ResultsThe prevalence rate ofH. pyloriinfection in the 164 patients was 63.4%. Gastritis with atrophy was significantly higher at the antrum than at the body (76% vs. 31%;p<0.001). The sensitivity of biopsy-based test decreased when the degree of gastritis with atrophy increased regardless of biopsy site (for normal, mild, moderate, and severe gastritis with atrophy, the sensitivity of histology Giemsa stain was 100%, 100%, 88%, and 66%, respectively, and 100%, 97%, 91%, and 66%, respectively, for rapid urease test). In moderate to severe antrum or body gastritis with atrophy, additional corpus biopsy resulted in increased sensitivity to 16.67% compare to single antrum biopsy.ConclusionsIn moderate to severe gastritis with atrophy, biopsy-based test should include the corpus for avoiding false negative results.
Culture-negative subacute bacterial endocarditis masquerades as granulomatosis with polyangiitis (Wegener’s granulomatosis) involving both the kidney and lung
Authors: Peng Hui , Chen Wen-fang , Wu Chao , Chen Yan-ru , Peng Bo , Paudel Sujay Dutta , Lou Tan-qi 
Published: December 2012

Abstract

Background
Subacute bacterial endocarditis (SBE) occasionally exhibits positive cytoplasmic anti-neutrophil cytoplasmic antibody (c-ANCA) of the anti-proteinase-3 (PR-3) type. Clinically, it mimics ANCA-associated vasculitis, such as Wegener's disease with glomerulonephritis. Lung abscesses are the most common manifestation of lung involvement. We herein report a case of culture-negative SBE strongly c-ANCA/PR3-positive accompanied by pulmonary involvement and glomerulonephritis. In this case, we took biopsies of both the lung and kidney, although renal biopsy is usually preferred over lung biopsy. The lung biopsy showed severe alveolar capillaritis, suggesting vasculitis consistent with polyangiitis. The renal biopsy revealed glomerulonephritis with a membranoproliferative pattern. To our knowledge, this is the first such reported case.

Case presentation
A 68-year-old Chinese male patient presented to our hospital with a fever, cough, chest pain, and recurrent peripheral edema. He had a past medical history significant for treated schistosomiasis 20 years previously. Physical examination revealed palpable purpura, mild hypertension, hepatosplenomegaly, and a holosystolic cardiac murmur (Levine 2/6). Echocardiography showed tricuspid valve vegetations with moderate to severe regurgitation. Serum c-ANCA/PR3 and cryoglobulin were strongly positive. Renal biopsy results indicated membranoproliferative glomerulonephritis with several crescents. Chest CT revealed multiple intraparenchymal and subpleural nodules, and lung biopsy showed polyangiitis. The patient’s ANCA titers, glomerulonephritis, and pulmonary injury all resolved after antibiotic therapy.

Conclusion
SBE may present with positive c-ANCA/PR3, multiple pulmonary nodules, pulmonary polyangiitis, and glomerulonephritis clinically mimicking granulomatosis with polyangiitis (Wegener's granulomatosis).
Signal alterations of the basal ganglia in the differential diagnosis of Parkinson’s disease: a retrospective case-controlled MRI data bank analysis
Authors: Jesse Sarah , Kassubek Jan , Müller Hans-Peter , Ludolph Albert C , Unrath Alexander 
Published: December 2012

Abstract

Background
Based upon the acquainted loss of dopaminergic neurons in the substantia nigra in Parkinson’s disease (PD), we hypothesised changes in magnetic resonance imaging signal intensities of the basal ganglia to be useful as an additional technical tool in the diagnostic work-up.

Methods
Region-of-interest analyses (substantia nigra and globus pallidus internus) of T2-weighted scans were performed in seventy subjects with PD, 170 age- and gender-matched controls and 38 patients with an atypical form of neurodegenerative Parkinsonian syndrome (N = 11 multisystem atrophy, N = 22 progressive supranuclear palsy, N = 5 corticobasal syndrome).

Results
In patients with PD, significant changes in signal intensities within the substantia nigra were observed compared to controls at p < 0.001. For the globus pallidus internus, signal alterations in PD and progressive supranuclear palsy were found to be significant (p < 0.001) if compared to controls. Furthermore, signal changes of substantia nigra correlated with signal intensities of globus pallidus internus in the ipsilateral hemisphere in both groups. Sensitivity was 86% and specificity was 90% for the combined analysis of substantia nigra and globus pallidus internus in the complete patient sample versus controls.

Conclusions
Signal alterations of substantia nigra and globus pallidus internus in routine magnetic resonance imaging were useful to distinguish patients with PD from controls. In addition, signal changes in globus pallidus internus could be used to differentiate progressive supranuclear palsy patients from controls. These analyses have the potential to serve as an additional non-invasive technical tool to support the individual differential diagnosis of PD.
Low level maternal smoking and infant birthweight reduction: genetic contributions of GSTT1 and GSTM1polymorphisms
Authors: Danileviciute Asta , Grazuleviciene Regina , Paulauskas Algimantas , Nadisauskiene Ruta , Nieuwenhuijsen Mark J 
Published: December 2012

Abstract

Background
Genetic susceptibility to tobacco smoke might modify the effect of smoking on pregnancy outcomes.

Methods
We conducted a case–control study of 543 women who delivered singleton live births in Kaunas (Lithuania), examining the association between low-level tobacco smoke exposure (mean: 4.8 cigarettes/day) during pregnancy, GSTT1 and GSTM1 polymorphisms and birthweight of the infant. Multiple linear-regression analysis was performed adjusting for gestational age, maternal education, family status, body mass index, blood pressure, and parity. Subsequently, we tested for the interaction effect of maternal smoking, GSTT1 and GSTM1 genes polymorphisms with birthweight by adding all the product terms in the regression models.

Results
The findings suggested a birthweight reduction among light-smoking with the GSTT1–null genotype (−162.9 g, P = 0.041) and those with the GSTM1–null genotype (−118.7 g, P = 0.069). When a combination of these genotypes was considered, birthweight was significantly lower for infants of smoking women the carriers of the double-null genotypes (−311.2 g, P = 0.008). The interaction effect of maternal smoking, GSTM1 and GSTT1 genotypes was marginally significant on birthweight (−234.5 g, P = 0.078). Among non-smokers, genotype did not independently confer an adverse effect on infant birthweight.

Conclusions
The study shows the GSTT1–null genotype, either presents only one or both with GSTM1–null genotype in a single subject, have a modifying effect on birthweight among smoking women even though their smoking is low level. Our data also indicate that identification of the group of susceptible subjects should be based on both environmental exposure and gene polymorphism. Findings of this study add additional evidence on the interplay among two key GST genes and maternal smoking on birth weight of newborns.
Internalized stigma among patients with schizophrenia in Ethiopia: a cross-sectional facility-based study
Authors: Assefa Dereje , Shibre Teshome , Asher Laura , Fekadu Abebaw 
Published: December 2012

Abstract

Background
Despite the potential impact on treatment adherence and recovery, there is a dearth of data on the extent and correlates of internalized stigma in patients with schizophrenia in low income countries. We conducted a study to determine the extent, domains and correlates of internalized stigma amongst outpatients with schizophrenia in Ethiopia.

Methods
The study was a cross-sectional facility-based survey conducted at a specialist psychiatric hospital in Addis Ababa, Ethiopia. Consecutive consenting individuals with a diagnosis of schizophrenia were recruited and assessed using an Amharic version of the Internalized Stigma of Mental Illness (ISMI) scale.

Results
Data were collected from 212 individuals, who were mostly single (71.2%), unemployed (70.3%) and male (65.1%). Nearly all participants (97.4%) expressed agreement to at least one stigma item contained in the ISMI; 46.7% had a moderate to high mean stigma score. Rural residence (OR = 5.67; 95% CI = 2.30, 13.00; p < 0.001), single marital status (OR = 3.39; 95% CI = 1.40, 8.22; p = 0.019) and having prominent psychotic symptoms (OR = 2.33; 95% CI = 1.17, 4.61; p = 0.016) were associated independently with a higher stigma score. Almost half of those who discontinued their treatment reported that they had done so because of perceived stigma. Those who had attempted suicide (45.3%) were more likely to have a high stigma score (OR = 2.29; 95% CI = 1.27, 4.11; p = 0.006). Over 60% of the variation in the experience of stigma was explained by four factors: social withdrawal (16.7%), perceived discrimination (14.1%), alienation (13.9%) and stereotype endorsement (12.7%).

Conclusion
Internalized stigma is a major problem among persons with schizophrenia in this outpatient setting in Ethiopia. Internalized stigma has the potential to substantially affect adherence to medication and is likely to affect the recovery process.
Risk of death in crashes on Ontario’s highways
Authors: Rzeznikiewiz Damian , Tamim Hala , Macpherson Alison K 
Published: December 2012

Abstract

Background
Motor vehicle collisions (MVCs) that result in one or more fatalities on the 400-series Highways represent a serious public health problem in Ontario, and were estimated to have cost $11 billion in 2004. To date, no studies have examined risk factors for fatal MVCs on Ontario’s 400 series highways.
The investigate how demographic and environmental risk factors are associated with fatal MVCs on Ontario’s 400-Series Highways.

Methods
Data were provided from the Ontario Ministry of Transport database, and included driver demographics, vehicle information, environmental descriptors, structural descriptors, as well as collision information (date and time), and severity of the collision. Multivariate analysis was used to identify factors significantly associated with the odds of dying in a collision.

Results
There were 53,526 vehicles involved in collisions from 2001 to 2006 included in our analysis. Results from the multivariate analysis suggest that collisions with older age and male drivers were associated with an increased risk of involving a fatality. Highway 405 and an undivided 2-way design proved to be the most fatal structural configurations. Collisions in the summer, Fridays, between 12 am-4 am, and in drifting snow conditions during the wintertime were also shown to have a significantly increased risk of fatality.

Conclusion
Our results suggest that interventions to reduce deaths as a result of MVCs should focus on both driver-related and road-related modifications.