bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of HRH2 promoter polymorphism on aberrant DNA methylation of DAPK and CDH1in the gastric epithelium
Authors: Nomura Tomoe , Tahara Tomomitsu , Shiroeda Hisakazu , Minato Takahiro , Matsue Yasuhiro , Hayashi Ranji , Matsunaga Kazuhiro , Otsuka Toshimi , Nakamura Masakatsu , Toshikuni Nobuyuki , Shibata Tomoyuki , Arisawa Tomiyasu 
Published: January 2013

Abstract

Background
Aberrant methylation patterns in CpG island are known to be influential in gene silencing. Histamine plays important physiological roles in the upper gastrointestinal tract and acts via the H2 receptor. We report an investigation into the effect of HRH2 promoter polymorphism (rs2607474 G > A) on the methylation of DAPK and CDH1.

Methods
Non cancerous gastric mucosa samples were obtained from 115 subjects with gastric cancer (GC) and 412 non-cancer subjects (non-GC). Methylation status of genes was determined by MSP. The genotyping of rs2607474 was performed by PCR-SSCP.

Results
Methylation of DAPK and CDH1 was observed in 296 and 246 subjects, respectively. The frequency of CDH1 methylation in the subjects with GC was significantly lower in cancer lesion than in non cancerous mucosa, whereas that of DAPK methylation was not different. The allelic distribution of rs2607474 was 401GG, 119GA and 7AA. The GG homozygote was associated with a significantly increased risk for methylation of both DAPK and CDH1 (p < 0.0001 and p = 0.0009, respectively). In the non-GC subjects or more than 60 years of age, GG homozygote was more closely associated with both DAPK and CDH1 methylation. However, this genotype did not show an increased risk for the development of methylation of both genes in patients with GC. In H. pylori negative subjects, GG homozygote showed an increased risk for the methylation of both DAPK and CDH1 (p = 0.0074 and p = 0.0016, respectively), whereas this genotype was associated with an increased risk for the development of DAPK methylation in H. pylori positive subjects (p = 0.0018). In addition, in subjects older than 60 years of age, atrophy and metaplasia scores were significantly higher in the GG homozygote (p = 0.011 and p = 0.039, respectively) and a significant correlation was observed between age and atrophy or metaplasia.

Conclusions
Our results suggest that rs2607474 GG homozygote confers a significantly increased risk for age- and inflammation-related DAPK and CDH1 methylation.
Factors associated with the use of home-visit nursing services covered by the long-term care insurance in rural Japan: a cross-sectional study
Authors: Kashiwagi Masayo , Tamiya Nanako , Sato Mikiya , Yano Eiji 
Published: January 2013

Abstract

Background
In Japan, there is a large increase in the number of elderly persons who potentially need home-visit nursing services (VNS). However, the number of persons using the VNS has increased only little in comparison to the number of individuals who use home social services, which are also covered by the Long-Term Care Insurance (LTCI) system. This cross-sectional study investigated the predictors of the VNS used under the LTCI system in Japan.

Methods
We used 1,580 claim data from all the users of community-based services and 1,574 interview survey data collected in 2001 from the six municipal bodies in Japan. After we merged the two datasets, 1,276 users of community-based services under the LTCI were analyzed. Multiple logistic regression models stratified by care needs levels were used for analysis.

Results
Only 8.3% of the study subjects were VNS users. Even among study participants within the higher care-needs level, only 22.0% were VNS users. In the lower care level group, people with a higher care level (OR: 3.50, 95% CI: 1.50–8.93), those whose condition needed long term care due to respiratory or heart disease (OR: 4.31, 95% CI: 1.88–89.20), those whose period of needing care was two years or more (OR: 2.01, 95% CI: 1.14–3.48), those whose service plan was created by a medical care management agency (OR: 2.39, 95% CI: 1.31–4.33), those living with family (OR: 1.86, 95% CI: 1.00–3.42), and those who use home-help services (OR: 2.12, 95% CI: 1.17–3.83) were more likely to use the VNS. In the higher care level group, individuals with higher care level (OR: 3.63, 95% CI: 1.56–8.66), those with higher income (OR: 3.79, 95% CI: 1.01–14.25), and those who had regular hospital visits before entering the LTCI (OR: 2.36, 95% CI: 1.11–5.38) were more likely to use the VNS.

Conclusions
Our results suggested that VNS use is limited due to management by non-medical care management agencies, due to no caregivers being around or a low income household. The findings of this study provide valuable insight for LTCI policy makers: the present provision of VNS should be reconsidered.
A new tool for the paediatric HIV research: general data from the Cohort of the Spanish Paediatric HIV Network (CoRISpe)
Authors: de Jose Ma Isabel , Jiménez de Ory Santiago , Espiau Maria , Fortuny Claudia , Navarro Ma Luisa , Soler-Palacín Pere , Muñoz-Fernandez Ma Angeles ,   from the working groups of CoRISpe and HIV HGM BioBank
Published: January 2013

Abstract
There are approximately from 1,100 to 1,200 HIV-infected children in a follow-up in Spain. In 2008 an open, multicentral, retrospective and prospective Cohort of the Spanish Paediatric HIV Network (CoRISpe) was founded. The CoRISpe is divided into the node 1 and node 2 representing geographically almost the whole territory of Spain. Since 2008 seventy-five hospitals have been participating in the CoRISpe. All the retrospective data of the HIV-infected children have been kept in the CoRISpe since 1995 and prospective data since 2008. In this article we are going to present the notion of CoRISpe, its role, the structure, how the CoRISpe works and the process how a child is transferred from Paediatric to Adults Units.
The main objective of the CoRISpe is to contribute to furthering scientific knowledge on paediatric HIV infection by providing demographic, sociopsychological, clinical and laboratory data from HIV-infected paediatric patients. Its aim is to enable high-quality research studies on HIV-infected children.
Aging is associated with increased activities of matrix metalloproteinase-2 and -9 in tenocytes
Authors: Yu Tung-Yang , Pang Jong-Hwei S , Wu Katie Pei-Hsuan , Chen Max J-L , Chen Chien-Hung , Tsai Wen-Chung 
Published: January 2013

Abstract

Background
Most tendon pathology is associated with degeneration, which is thought to involve cyclic loading and cumulative age-related changes in tissue architecture. However, the association between aging and degeneration of the extracellular matrix (ECM) in tendons has not been investigated extensively.

Methods
We examined tenocytes from Achilles tendons taken from rats of three different ages (2, 12, and 24 months). Tenocyte viability was assessed using the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) assay. Quantitative real-time polymerase chain reaction (PCR) was used to determine the levels of mRNAs that encode type-I collagen, matrix metalloproteinase (MMP)-2 and −9, tissue inhibitor of metalloproteinase (TIMP)-1 and −2 and transforming growth factor (TGF)-β1. Gelatin zymography was used to evaluate the enzymatic activities of MMP-2 and −9. Furthermore, the concentration of TGF-β1 in conditioned medium was evaluated using enzyme-linked immunosorbent assay (ELISA).

Results
The results of the MTT assay showed that the number of viable tenocytes decreased with age. No differences were observed in the levels of mRNAs that encode type-I collagen and TGF-β1 among the three age groups, and the TGF-β1 concentration did not change with age. However, mRNAs that encode MMP-2 and −9 were significantly more abundant in tenocytes from the aging group, and gelatin zymography revealed that the enzymatic activities of MMP-2 and −9 also increased significantly with age. Furthermore, as compared with young group, mRNAs that encode TIMP-1 and −2 were significantly decreased in tenocytes from the aging group.

Conclusions
Activities of MMP-2 and MMP-9 in tenocytes increase with age. This might provide a mechanistic explanation of how aging contributes to tendinopathy or tendon rupture with age.
The study of leachate treatment by using three advanced oxidation process based wet air oxidation
Authors: Karimi Behroz , Ehrampoush Mohammad Hassan , Ebrahimi Asghar , Mokhtari Mehdi 
Published: January 2013

Abstract
Wet air oxidation is regarded as appropriate options for wastewater treatment with average organic compounds. The general purpose of this research is to determine the efficiency of three wet air oxidation methods, wet oxidation with hydrogen peroxide and absorption with activated carbon in removing organic matter and nitrogenous compounds from Isfahan's urban leachate. A leachate sample with the volume of 1.5 liters entered into a steel reactor with the volume of three liters and was put under a 10-bar pressure, at temperatures of 100, 200, and 300° as well as three retention times of 30, 60, and 90 minutes. The sample was placed at 18 stages of leachate storage ponds in Isfahan Compost Plant with the volume of 20 liters, using three WPO, WAO methods and a combination of WAO/GAC for leachate pre-treatment. Thirty percent of pure oxygen and hydrogen peroxide were applied as oxidation agents. The COD removal efficiency in WAO method is 7.8-33.3%, in BOD is 14.7-50.6%, the maximum removal percentage (efficiency) for NH4-N is 53.3% and for NO3-N is 56.4-73.9%. The removal efficiency of COD and BOD5 is 4.6%-34 and 24%-50 respectively in WPO method. Adding GAC to the reactor, the removal efficiency of all parameters was improved. The maximum removal efficiency was increased 48% for COD, 31%-43.6 for BOD5 by a combinational method, and the ratio of BOD5/COD was also increased to 90%. In this paper, WAO and WPO process was used for Leachate pre-treatment and WAO/GAC combinational process was applied for improving the organic matter removal and leachate treatment; it was also determined that the recent process is much more efficient in removing resistant organic matter.
Plasminogen activator inhibitor-1 4G/5G polymorphism and retinopathy risk in type 2 diabetes: a meta-analysis
Authors: Zhang Tengyue , Pang Chong , Li Ningdong , Zhou Elaine , Zhao Kanxing 
Published: January 2013

Abstract

Background
Mounting evidence has suggested that plasminogen activator inhibitor-1 (PAI-1) is a candidate for increased risk of diabetic retinopathy. Studies have reported that insertion/deletion polymorphism in the PAI-1 gene may influence the risk of this disease. To comprehensively address this issue, we performed a meta-analysis to evaluate the association of PAI-1 4G/5G polymorphism with diabetic retinopathy in type 2 diabetes.

Methods
Data were retrieved in a systematic manner and analyzed using Review Manager and STATA Statistical Software. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of associations.

Results
Nine studies with 1, 217 cases and 1, 459 controls were included. Allelic and genotypic comparisons between cases and controls were evaluated. Overall analysis suggests a marginal association of the 4G/5G polymorphism with diabetic retinopathy (for 4G versus 5G: OR 1.13, 95%CI 1.01 to 1.26; for 4G/4G versus 5G/5G: OR 1.30, 95%CI 1.04 to 1.64; for 4G/4G versus 5G/5G + 4G/5G: OR 1.26, 95%CI 1.05 to 1.52). In subgroup analysis by ethnicity, we found an association among the Caucasian population (for 4G versus 5G: OR 1.14, 95% CI 1.00 to 1.30; for 4G/4G versus 5G/5G: OR 1.33, 95%CI 1.02 to 1.74; for 4G/4G versus 5G/5G + 4G/5G: OR 1.41, 95%CI 1.13 to 1.77). When stratified by the average duration of diabetes, patients with diabetes histories longer than 10 years have an elevated susceptibility to diabetic retinopathy than those with shorter histories (for 4G/4G versus 5G/5G: OR 1.47, 95%CI 1.08 to 2.00). We also detected a higher risk in hospital-based studies (for 4G/4G versus 5G/5G+4G/5G: OR 1.27, 95%CI 1.02 to 1.57).

Conclusions
The present meta-analysis suggested that 4G/5G polymorphism in the PAI-1 gene potentially increased the risk of diabetic retinopathy in type 2 diabetes and showed a discrepancy in different ethnicities. A higher susceptibility in patients with longer duration of diabetes (more than 10 years) indicated a gene-environment interaction in determining the risk of diabetic retinopathy.
Examination of soluble integrin resistant mutants of foot-and-mouth disease virus
Authors: Lawrence Paul , LaRocco Michael , Baxt Barry , Rieder Elizabeth 
Published: January 2013

Abstract

Background
Foot-and-mouth disease virus (FMDV) initiates infection via recognition of one of at least four cell-surface integrin molecules αvβ1, αvβ3, αvβ6, or αvβ8 by a highly conserved Arg-Gly-Asp (RGD) amino acid sequence motif located in the G-H loop of VP1. Within the animal host, the αvβ6 interaction is believed to be the most relevant. Sub-neutralizing levels of soluble secreted αvβ6 (ssαvβ6) was used as a selective pressure during passages in vitro to explore the plasticity of that interaction.

Results
Genetically stable soluble integrin resistant (SIR) FMDV mutants derived from A24 Cruzeiro were selected after just 3 passages in cell culture in the presence of sub-neutralizing levels of ssαvβ6. SIR mutants were characterized by: replication on selective cell lines, plaque morphology, relative sensitivity to ssαvβ6 neutralization, relative ability to utilize αvβ6 for infection, as well as sequence and structural changes. All SIR mutants maintained an affinity for αvβ6. Some developed the ability to attach to cells expressing heparan sulfate (HS) proteoglycan, while others appear to have developed affinity for a still unknown third receptor. Two classes of SIR mutants were selected that were highly or moderately resistant to neutralization by ssαvβ6. Highly resistant mutants displayed a G145D substitution (RGD to RDD), while moderately resistant viruses exhibited a L150P/R substitution at the conserved RGD + 4 position. VP1 G-H loop homology models for the A-type SIR mutants illustrated potential structural changes within the integrin-binding motif by these 2 groups of mutations. Treatment of O1 Campos with ssαvβ6 resulted in 3 SIR mutants with a positively charged VP3 mutation allowing for HS binding.

Conclusions
These findings illustrate how FMDV particles rapidly gain resistance to soluble receptor prophylactic measures in vitro. Two different serotypes developed distinct capsid mutations to circumvent the presence of sub-neutralizing levels of the soluble cognate receptor, all of which resulted in a modified receptor tropism that expanded the cell types susceptible to FMDV. The identification of some of these adaptive mutations in known FMDV isolates suggests these findings have implications beyond the cell culture system explored in these studies.
Tool for evaluating research implementation challenges: A sense-making protocol for addressing implementation challenges in complex research settings
Authors: Simpson Kelly M , Porter Kristie , McConnell Eleanor S , Colón-Emeric Cathleen , Daily Kathryn A , Stalzer Alyson , Anderson Ruth A 
Published: January 2013

AbstractBackgroundMany challenges arise in complex organizational interventions that threaten research integrity. This article describes aTool forEvaluating Research ImplementationChallenges (TECH), developed using a complexity science framework to assist research teams in assessing and managing these challenges.MethodsDuring the implementation of a multi-site, randomized controlled trial (RCT) of organizational interventions to reduce resident falls in eight nursing homes, we inductively developed, and later codified the TECH. The TECH was developed through processes that emerged from interactions among research team members and nursing home staff participants, including a purposive use of complexity science principles.ResultsThe TECH provided a structure to assess challenges systematically, consider their potential impact on intervention feasibility and fidelity, and determine actions to take. We codified the process into an algorithm that can be adopted or adapted for other research projects. We present selected examples of the use of the TECH that are relevant to many complex interventions.ConclusionsComplexity theory provides a useful lens through which research procedures can be developed to address implementation challenges that emerge from complex organizations and research designs. Sense-making is a group process in which diverse members interpret challenges when available information is ambiguous; the groups’ interpretations provide cues for taking action. Sense-making facilitates the creation of safe environments for generating innovative solutions that balance research integrity and practical issues. The challenges encountered during implementation of complex interventions are often unpredictable; however, adoption of a systematic process will allow investigators to address them in a consistent yet flexible manner, protecting fidelity. Research integrity is also protected by allowing for appropriate adaptations to intervention protocols that preserve the feasibility of ‘real world’ interventions.
Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0
Authors: Weber Michael , Henkel Sebastian G , Vlaic Sebastian , Guthke Reinhard , van Zoelen Everardus J , Driesch Dominik 
Published: January 2013

AbstractBackgroundInference of gene-regulatory networks (GRNs) is important for understanding behaviour and potential treatment of biological systems. Knowledge about GRNs gained from transcriptome analysis can be increased by multiple experiments and/or multiple stimuli. Since GRNs are complex and dynamical, appropriate methods and algorithms are needed for constructing models describing these dynamics. Algorithms based on heuristic approaches reduce the effort in parameter identification and computation time.ResultsThe NetGenerator V2.0 algorithm, a heuristic for network inference, is proposed and described. It automatically generates a system of differential equations modelling structure and dynamics of the network based on time-resolved gene expression data. In contrast to a previous version, the inference considers multi-stimuli multi-experiment data and contains different methods for integrating prior knowledge. The resulting significant changes in the algorithmic procedures are explained in detail. NetGenerator is applied to relevant benchmark examples evaluating the inference for data from experiments with different stimuli. Also, the underlying GRN of chondrogenic differentiation, a real-world multi-stimulus problem, is inferred and analysed.ConclusionsNetGenerator is able to determine the structure and parameters of GRNs and their dynamics. The new features of the algorithm extend the range of possible experimental set-ups, results and biological interpretations. Based upon benchmarks, the algorithm provides good results in terms of specificity, sensitivity, efficiency and model fit.
Interactions of commonly used dietary supplements with cardiovascular drugs: a systematic review
Authors: Kanji Salmaan , Seely Dugald , Yazdi Fatemeh , Tetzlaff Jennifer , Singh Kavita , Tsertsvadze Alexander , Tricco Andrea C , Sears Margaret E , Ooi Teik C , Turek Michele A , Skidmore Becky , Ansari Mohammed T 
Published: January 2013

Abstract

Background
The objective of this systematic review was to examine the benefits, harms and pharmacokinetic interactions arising from the co-administration of commonly used dietary supplements with cardiovascular drugs. Many patients on cardiovascular drugs take dietary supplements for presumed benefits and may be at risk for adverse supplement-drug interactions.

Methods
The Allied and Complementary Medicine Database, the Cochrane Library, EMBASE, International Bibliographic Information on Dietary Supplements and MEDLINE were searched from the inception of the review to October 2011. Grey literature was also reviewed.
Two reviewers independently screened records to identify studies comparing a supplement plus cardiovascular drug(s) with the drug(s) alone. Reviewers extracted data using standardized forms, assessed the study risk of bias, graded the strength of evidence and reported applicability.

Results
Evidence was obtained from 65 randomized clinical trials, 2 controlled clinical trials and 1 observational study. With only a few small studies available per supplement, evidence was insufficient for all predefined gradable clinical efficacy and harms outcomes, such as mortality and serious adverse events. One long-term pragmatic trial showed no benefit from co-administering vitamin E with aspirin on a composite cardiovascular outcome. Evidence for most intermediate outcomes was insufficient or of low strength, suggesting no effect. Incremental benefits were noted for triglyceridemia with omega-3 fatty acid added to statins; and there was an improvement in levels of high-density lipoprotein cholesterol with garlic supplementation when people also consumed nitrates

Conclusions
Evidence of low-strength indicates benefits of omega-3 fatty acids (plus statin, or calcium channel blockers and antiplatelets) and garlic (plus nitrates or warfarin) on triglycerides and HDL-C, respectively. Safety concerns, however, persist.
Microwave-assisted polystyrene sulfonate-catalyzed synthesis of novel pyrroles
Authors: Cárdenas Rosario Astrid Vargas , Leal Blanca Olinda Quintanilla , Reddy Ashwini , Bandyopadhyay Debasish , Banik Bimal K 
Published: January 2013

Abstract

Background
Pyrroles are widely distributed in nature and important biologically active molecules. The reaction of amines with 2,5-dimethoxytetrahydrofuran is a promising pathway for the synthesis of pharmacologically active pyrroles under microwave irradiation.

Results
Microwave-induced polystyrenesulfonate-catalyzed synthesis of pyrroles from amines and 2,5-diemthoxytetrahydrofuran has been accomplished with excellent yield. This method produces pyrroles with polyaromatic amines.

Conclusion
The present procedure for the synthesis of N-aromatic substituted pyrroles will find useful application in the area of pharmacologically active molecules.