bluuebunny/crossref_metadata_2025_split huggingface dataset:
Encephalitis temporally associated with live attenuated Japanese encephalitis vaccine: four case reports
Authors: Jia Na , Zhao Qiu-Min , Guo Xiao-Fang , Cheng Jing-Xia , Wu Chao , Zuo Shu-Qing , Dai Pei-Fang , Zhao Jun-Ying , Zhang Jiu-Song 
Published: December 2011

Abstract

Background
Japanese encephalitis (JE) vaccination is the most effective measure for preventing JE disease. The live attenuated JE vaccine, which has shown good efficacy and safety, has been widely used in China.

Case presentations
We report four laboratory-confirmed JE cases detected in JE-endemic areas during the JE virus (JEV) transmission season, who all received a first dose of live attenuated JE vaccine within 2 weeks prior to the onset of illness. All cases presented with acute encephalitis and rapidly reduced consciousness. All cerebrospinal fluid (CSF) samples from the patients were positive for JEV-specific immunoglobulin M (IgM) antibodies, but viral isolation and polymerase chain reaction (PCR) detection of JEV were both negative.

Conclusions
It is difficult to identify a causal link between the disease and the vaccination, as the source of positive CSF JEV IgM antibodies might be natural JEV infection or possibly due to a traumatic lumbar puncture. Our observations highlight the need for public health officers and doctors to consider reasonable vaccination policies during the JE season. In addition, continued surveillance as well as thorough investigation of any events that occur after JE vaccination is necessary.
Enhanced upper genital tract pathologies by blocking Tim-3 and PD-L1 signaling pathways in mice intravaginally infected with Chlamydia muridarum
Authors: Peng Bo , Lu Chunxue , Tang Lingli , Yeh I-Tien , He Zhimin , Wu Yimou , Zhong Guangming 
Published: December 2011

Abstract

Background
Although Tim-3 & PD-L1 signaling pathways play important roles in negatively regulating immune responses, their roles in chlamydial infection have not been evaluated.

Methods
Neutralization antibodies targeting Tim-3 and PD-L1 were used to treat mice. Following an intravaginal infection with C. muridarum organisms, mice with or without the dual antibody treatment were compared for live chlamydial organism shedding from the lower genital tract and inflammatory pathology in the upper genital tract.

Results
Mice treated with anti-Tim-3 and anti-PD-L1 antibodies displayed a time course of live organism shedding similar to that of mice treated with equivalent amounts of isotype-matched IgG molecules. The combined antibody blocking failed to alter either the lower genital tract cytokine or systemic humoral and cellular adaptive responses to C. muridarum infection. However, the antibody blocking significantly enhanced C. muridarum-induced pathologies in the upper genital tract, including more significant hydrosalpinx and inflammatory infiltration in uterine horn and oviduct tissues.

Conclusions
The Tim-3 and PD-L1-mediated signaling can significantly reduce pathologies in the upper genital tract without suppressing immunity against chlamydial infection, suggesting that Tim-3 and PD-L1-mediated negative regulation may be manipulated to attenuate tubal pathologies in women persistently infected with C. trachomatis organisms.
Incidence of maternal Toxoplasma infections in pregnancy in Upper Austria, 2000-2007
Authors: Sagel Ulrich , Krämer Alexander , Mikolajczyk Rafael T 
Published: December 2011

Abstract

Background
Despite three decades of prenatal screening program for toxoplasmosis in Austria, population-based estimates for the incidence of maternal infections with Toxoplasma gondii during pregnancy are lacking. We studied the incidence of primary maternal infections during pregnancy in the Federal State of Upper Austria.

Methods
Screening tests for 63,416 women and over 90,000 pregnancies (more than 84.5% of pregnancies in the studied region) in the time period between 01.01.2000 and 31.12.2007 were analysed. The incidence of toxoplasmosis was estimated indirectly by binomial and directly by interval censored regression.

Results
During the studied period, 66 acute infections (risk of 0.07% per pregnancy) were detected, but only 29.8% of seronegative women were tested at least three times during their pregnancies. The seroprevalence of Toxoplasma antibodies among all tested women was 31%. Indirectly estimated incidence (from differences in prevalence by age) was 0.5% per pregnancy, while directly estimated incidence (interval censored regression) was 0.17% per pregnancy (95% confidence interval: 0.13-0.21%).

Conclusions
Calculating incidence from observed infections results in severe underreporting due to many missed tests and potential diagnostic problems. Using statistical modelling, we estimated primary toxoplasmosis to occur in 0.17% (0.13-0.21%) of all pregnancies in Upper Austria.
Measurement of gender inequality in neighbourhoods of Québec, Canada
Authors: Tamambang Lum , Auger Nathalie , Lo Ernest , Raynault Marie-France 
Published: December 2011

Abstract

Introduction
Few studies have measured gender inequality at levels lower than the country. We sought to develop neighbourhood indicators of gender inequality, and assess their ability to capture variability in gender inequality across Québec, Canada.

Methods
Aggregate 2001 census data for 11,564 neighbourhoods were obtained for men and women. Twelve indicators of gender inequality representing demographic/household characteristics, education, income, work/leisure, and political participation were selected. Neighbourhood-level gender inequality scores were computed for each indicator, and examined across parts of Québec (metropolitan areas, mid-sized cities, rural areas). Monte Carlo simulations were used to assess the ability of indicators to capture heterogeneity in gender inequality across neighbourhoods.

Results
Male-dominant neighbourhood-level gender inequality tended to be present for average employment income, labour force participation, employment rate, and employment in managerial positions. Female-dominant gender inequality tended to be present for divorce, single-headed households, and participation in unpaid housework, child and elderly care. Neighbourhood-level gender inequality tended to vary across metropolitan areas, mid-sized cities, and rural areas. Gender inequality scores also varied within these geographic areas. For example, there was greater income-related gender inequality in high than low income neighbourhoods. Monte Carlo simulations suggested that the variation in gender inequality across neighbourhoods was greater than expected with chance alone.

Conclusion
Neighbourhood-level gender inequality tended to be present in Québec, and varied across parts of the province. Greater awareness of and research on neighbourhood-level gender inequality may be warranted to inform gender policies in Québec and other nations.
Mucosal exposure to cockroach extract induces allergic sensitization and allergic airway inflammation
Authors: Arizmendi Narcy G , Abel Melanie , Puttagunta Lakshmi , Asaduzzaman Muhammad , Davidson Courtney , Karimi Khalil , Forsythe Paul , Vliagoftis Harissios 
Published: December 2011

AbstractBackgroundAllergic sensitization to aeroallergens develops in response to mucosal exposure to these allergens. Allergic sensitization may lead to the development of asthma, which is characterized by chronic airway inflammation. The objective of this study is to describe in detail a model of mucosal exposure to cockroach allergens in the absence of an exogenous adjuvant.MethodsCockroach extract (CE) was administered to mice intranasally (i.n.) daily for 5 days, and 5 days later mice were challenged with CE for 4 consecutive days. A second group received CE i.n. for 3 weeks. Airway hyperresponsiveness (AHR) was assessed 24 h after the last allergen exposure. Allergic airway inflammation was assessed by BAL and lung histology 48 h after the last allergen exposure. Antigen-specific antibodies were assessed in serum. Lungs were excised from mice from measurement of cytokines and chemokines in whole lung lysate.ResultsMucosal exposure of Balb/c mice to cockroach extract induced airway eosinophilic inflammation, AHR and cockroach-specific IgG1; however, AHR to methacholine was absent in the long term group. Lung histology showed patchy, multicentric damage with inflammatory infiltrates at the airways in both groups. Lungs from mice from the short term group showed increased IL-4, CCL11, CXCL1 and CCL2 protein levels. IL4 and CXCL1 were also increased in the BAL of cockroach-sensitized mice in the short-term protocol.ConclusionsMucosal exposure to cockroach extract in the absence of adjuvant induces allergic airway sensitization characterized by AHR, the presence of Th2 cytokines in the lung and eosinophils in the airways.
The infectivity and pathogenicity of a foot-and-mouth disease virus persistent infection strain from oesophageal-pharyngeal fluid of a Chinese cattle in 2010
Authors: Bao Hui-Fang , Li Dong , Sun Pu , Zhou Qiang , Hu Jun , Bai Xing-Wen , Fu Yuan-Fang , Lu Zeng-Jun , Liu Zai-Xin 
Published: December 2011

Abstract

Background
Foot-and mouth disease (FMD) is an acute, febrile, and contagious vesicular disease affecting cloven-hoofed animals. Some animals may become persistent infected carriers when they contact FMD virus (FMDV), and persistent infected animals are a dangerous factor to cause FMD outbreak.

Findings
300 OP (oesophageal-pharyngeal) fluid samples were collected from cattle without clinic symptom after one month FMD circulated in 2010 in China. A FMDV strain was isolated when a positive OP sample was passed in BHK21 cell line. The strain, named O/CHN/2010/33-OP, was detected to be O/Myanmar/1998 lineage with VP1 DNA sequence comparison. In order to testify its infectivity, two cattle were challenged with OP fluid and three pigs were put into the same pen for direct contact infection. The result showed that one of the cattle and one of the pigs appeared FMD clinic symptoms respectively. Furthermore, two cattle (three pigs were also put into the same pen for direct contact infection) and three pigs were inoculated with O/CHN/2010/33-OP cell passaged strain. The result showed that one of the challenged pigs appeared FMD clinic symptoms. Two cattle and three pigs in the same pen did not appeared FMD clinic symptoms, but the sera antibody and their OP fluid of two cattle were positive. Meanwhile, the spinal cords of three pigs in the same pen with two cattle were positive detected with multiplex- RT-PCR.

Conclusion
The persistent infection strain O/CHN/2010/33-OP has infectivity and pathogenicity to cattle and pigs, and infected cattle may transmit the virus to pigs although its virulence was lower than the circulated strain O/CHN/Mya98/2010.
SigCS base: an integrated genetic information resource for human cerebral stroke
Authors: Park Young-Kyu , Bang Ok Sun , Cha Min-Ho , Kim Jaeheup , Cole John W , Lee Doheon , Kim Young Joo 
Published: December 2011

Abstract

Background
To understand how stroke risk factors mechanistically contribute to stroke, the genetic components regulating each risk factor need to be integrated and evaluated with respect to biological function and through pathway-based algorithms. This resource will provide information to researchers studying the molecular and genetic causes of stroke in terms of genomic variants, genes, and pathways.

Methods
Reported genetic variants, gene structure, phenotypes, and literature information regarding stroke were collected and extracted from publicly available databases describing variants, genome, proteome, functional annotation, and disease subtypes. Stroke related candidate pathways and etiologic genes that participate significantly in risk were analyzed in terms of canonical pathways in public biological pathway databases. These efforts resulted in a relational database of genetic signals of cerebral stroke, SigCS base, which implements an effective web retrieval system.

Results
The current version of SigCS base documents 1943 non-redundant genes with 11472 genetic variants and 165 non-redundant pathways. The web retrieval system of SigCS base consists of two principal search flows, including: 1) a gene-based variant search using gene table browsing or a keyword search, and, 2) a pathway-based variant search using pathway table browsing. SigCS base is freely accessible at http://sysbio.kribb.re.kr/sigcs.

Conclusions
SigCS base is an effective tool that can assist researchers in the identification of the genetic factors associated with stroke by utilizing existing literature information, selecting candidate genes and variants for experimental studies, and examining the pathways that contribute to the pathophysiological mechanisms of stroke.
SNP-PRAGE: SNP-based parametric robust analysis of gene set enrichment
Authors: Lee Jaehoon , Ahn Soyeon , Oh Sohee , Weir Bruce , Park Taesung 
Published: December 2011

Abstract

Background
The current genome-wide association (GWA) analysis mainly focuses on the single genetic variant, which may not reveal some the genetic variants that have small individual effects but large joint effects. Considering the multiple SNPs jointly in Genome-wide association (GWA) analysis can increase power. When multiple SNPs are jointly considered, the corresponding SNP-level association measures are likely to be correlated due to the linkage disequilibrium (LD) among SNPs.

Methods
We propose SNP-based parametric robust analysis of gene-set enrichment (SNP-PRAGE) method which handles correlation adequately among association measures of SNPs, and minimizes computing effort by the parametric assumption. SNP-PRAGE first obtains gene-level association measures from SNP-level association measures by incorporating the size of corresponding (or nearby) genes and the LD structure among SNPs. Afterward, SNP-PRAGE acquires the gene-set level summary of genes that undergo the same biological knowledge. This two-step summarization makes the within-set association measures to be independent from each other, and therefore the central limit theorem can be adequately applied for the parametric model.

Results & conclusions
We applied SNP-PRAGE to two GWA data sets: hypertension data of 8,842 samples from the Korean population and bipolar disorder data of 4,806 samples from the Wellcome Trust Case Control Consortium (WTCCC). We found two enriched gene sets for hypertension and three enriched gene sets for bipolar disorder. By a simulation study, we compared our method to other gene set methods, and we found SNP-PRAGE reduced many false positives notably while requiring much less computational efforts than other permutation-based gene set approaches.
Ryanodine receptors, a family of intracellular calcium ion channels, are expressed throughout early vertebrate development
Authors: Wu Houdini HT , Brennan Caroline , Ashworth Rachel 
Published: December 2011

Abstract

Background
Calcium signals ([Ca2+]i) direct many aspects of embryo development but their regulation is not well characterised. Ryanodine receptors (RyRs) are a family of intracellular Ca2+ release channels that control the flux of Ca2+ from internal stores into the cytosol. RyRs are primarily known for their role in excitation-contraction coupling in adult striated muscle and ryr gene mutations are implicated in several human diseases. Current evidence suggests that RyRs do not have a major role to play prior to organogenesis but regulate tissue differentiation.

Findings
The sequences of the five zebrafish ryr genes were confirmed, their evolutionary relationship established and the primary sequences compared to other vertebrates, including humans. RyRs are differentially expressed in slow (ryr1a), fast (ryr3) and both types (ryr1b) of developing skeletal muscle. There are two ryr2 genes (ryr2a and ryr2b) which are expressed exclusively in developing CNS and cardiac tissue, respectively. In addition, ryr3 and ryr2a mRNA is detectable in the initial stages of development, prior to embryonic axis formation.

Conclusions
Our work reveals that zebrafish ryr genes are differentially expressed throughout the developing embryo from cleavage onwards. The data suggests that RyR-regulated Ca2+ signals are associated with several aspects of embryonic development, from organogenesis through to the differentiation of the musculoskeletal, cardiovascular and nervous system. These studies will facilitate further work to explore the developmental function of RyRs in each of these tissue types.
Advanced glycation endproducts are increased in rheumatoid arthritis patients with controlled disease
Authors: de Groot Lodewijk , Hinkema Helmy , Westra Johanna , Smit Andries J , Kallenberg Cees GM , Bijl Marc , Posthumus Marcel D 
Published: December 2011

Abstract

Introduction

Advanced glycation end products (AGEs) are produced and can accumulate during chronic inflammation, as might be present in patients with rheumatoid arthritis (RA). AGEs are involved in the development of cardiovascular disease. The aim of this study is to evaluate whether AGEs are increased in patients with long-standing RA and whether AGE accumulation is related to disease activity, disease severity and measures of (premature) atherosclerosis, such as endothelial activation, endothelial dysfunction and intima media thickness (IMT).

Methods

In a cross-sectional study, 49 consecutive RA patients with longstanding disease (median disease duration of 12.3 years (range 9.3 to 15.1)), receiving standard of care, were included and compared with 49 age- and sex-matched healthy controls (HC). AGEs were determined by skin autofluorescence. Disease activity was evaluated by the Disease Activity Score of 28 joints (DAS-28) score and joint damage by modified Sharp-v.d. Heijde score. Endothelial activation (soluble vascular cellular adhesion molecule-1) sVCAM-1, von Willebrand factor (vWF), thrombomodulin), endothelial dysfunction (determined by small artery elasticity (SAE)) and IMT were measured and related to AGE accumulation.

Results

AGEs were increased in RA patients (median 2.4 arbitrary units (a.u.), range 1.6 to 4.2) compared to HC (2.2, 1.3 to 3.8). RA patients had a DAS-28 score of 2.9 (0.8 to 6.9) and a modified Sharp-v.d. Heijde score of 19 (0 to 103). sVCAM-1 and vWF levels were higher in RA patients. SAE was significantly decreased in RA (3.9 ml/mmHg (1.4 to 12.2) vs. 6.1 in HC (1.7 to 12.9). IMT did not differ between the two groups. Combining both groups' AGEs correlated with vWF, sVCAM-1 and IMT, and was inversely related to SAE. In RA, AGEs had an inverse relation with SAE, but did not relate to disease activity or radiological damage. In multivariate analysis for both groups, smoking, glucose levels, vWF, SAE and male gender were significantly related to the formation of AGEs.

Conclusions

AGEs were increased in RA patients with long-standing disease and without signs of premature atherosclerosis. AGEs were related to endothelial activation and endothelial dysfunction. This supports the hypothesis that in RA AGEs may be an early marker of cardiovascular disease.
High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing
Authors: Sims David , Mendes-Pereira Ana M , Frankum Jessica , Burgess Darren , Cerone Maria-Antonietta , Lombardelli Cristina , Mitsopoulos Costas , Hakas Jarle , Murugaesu Nirupa , Isacke Clare M , Fenwick Kerry , Assiotis Ioannis , Kozarewa Iwanka , Zvelebil Marketa , Ashworth Alan , Lord Christopher J 
Published: December 2011

AbstractRNA interference (RNAi) screening is a state-of-the-art technology that enables the dissection of biological processes and disease-related phenotypes. The commercial availability of genome-wide, short hairpin RNA (shRNA) libraries has fueled interest in this area but the generation and analysis of these complex data remain a challenge. Here, we describe complete experimental protocols and novel open source computational methodologies, shALIGN and shRNAseq, that allow RNAi screens to be rapidly deconvoluted using next generation sequencing. Our computational pipeline offers efficient screen analysis and the flexibility and scalability to quickly incorporate future developments in shRNA library technology.
MicroRNA profiling reveals age-dependent differential expression of nuclear factor κB and mitogen-activated protein kinase in adipose and bone marrow-derived human mesenchymal stem cells
Authors: Pandey Amitabh C , Semon Julie A , Kaushal Deepak , O'Sullivan Regina P , Glowacki Julie , Gimble Jeffery M , Bunnell Bruce A 
Published: December 2011

Abstract
Introduction
Mesenchymal stem cells (MSCs) play a central role in mediating endogenous repair of cell and tissue damage. Biologic aging is a universal process that results in changes at the cellular and molecular levels. In the present study, the role of microRNA (miRNA) in age-induced molecular changes in MSCs derived from adipose tissue (ASCs) and bone marrow (BMSCs) from young and old human donors were investigated by using an unbiased genome-wide approach.

Methods
Human ASCs and BMSCs from young and old donors were cultured, and total RNA was isolated. The miRNA fraction was enriched and used to determine the expression profile of miRNA in young and old donor MSCs. Based on miRNA expression, differences in donor MSCs were further investigated by using differentiation assays, Western blot, immunocytochemistry, and bioinformatics.

Results
Biologic aging demonstrated reduced osteogenic and adipogenic potential in ASCs isolated from older donors, whereas cell size, complexity, and cell-surface markers remained intact with aging. Analysis of miRNA profiles revealed that small subsets of active miRNAs changed secondary to aging. Evaluation of miRNA showed significantly decreased levels of gene expression of inhibitory kappa B kinase (IκB), interleukin-1α, inducible nitric oxide synthase (iNOS), mitogen-activated protein kinase/p38, ERK1/2, c-fos, and c-jun in MSCs from older donors by both bioinformatics and Western blot analysis. Nuclear factor kappa B (NF-κB), myc, and interleukin-4 receptor mRNA levels were significantly elevated in aged cells from both the adipose and bone marrow depots. Immunocytochemistry showed nuclear localization in young donors, but a cytosolic predominance of phosphorylated NF-κB in ASCs from older donors. Western blot demonstrated significantly elevated levels of NF-κB subunits, p65 and p50, and AKT.

Conclusions
These findings suggest that differential expression of miRNA is an integral component of biologic aging in MSCs.
M-ficolin and leukosialin (CD43): new partners in neutrophil adhesion
Authors: Moreno-Amaral Andrea N , Gout Evelyne , Danella-Polli Claudia , Tabarin Fanny , Lesavre Philippe , Pereira-da-Silva Gabriela , Thielens Nicole M , Halbwachs-Mecarelli Lise 
Published: December 2011

ABSTRACT
M-ficolin specificity for sialylated ligands prompted us to investigate its interactions with the main membrane sialoprotein of human neutrophils, CD43. rM-ficolin bound CD43 and prevented the access of anti-CD43 mAb. Moreover, rM-ficolin reacted exclusively with CD43 on Western blots of neutrophil lysate. We confirmed that M-ficolin is secreted by fMLP-activated neutrophils, and this endogenous M-ficolin also binds to CD43 and competes with anti-CD43 mAb. Anti-CD43 antibody cross-linking or fMLP resulted in M-ficolin and CD43 colocalization on polarized neutrophils. The binding of rM-ficolin to resting neutrophils induced cell polarization, adhesion, and homotypic aggregation as anti-CD43 mAb. The M-ficolin Y271F mutant, unable to bind sialic acid, neither reacted with neutrophils nor modulated their functions. Finally, rM-ficolin activated the lectin complement pathway on neutrophils. These results emphasize a new function of M-ficolin, different from ficolin pathogen recognition, i.e., a participation to neutrophil adhesion potentially important in early inflammation, as nanomolar agonist concentrations are sufficient to mobilize M-ficolin to the neutrophil surface. This multivalent lectin could then endow the antiadhesive CD43, essentially designed to prevent leukocyte aggregation in the blood flow, with new adhesive properties and explain, at least in part, dual-adhesive/antiadhesive roles of CD43 in neutrophil recruitment.