bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adjuvant facilitates tolerance induction to factor VIII in hemophilic mice through a Foxp3-independent mechanism that relies on IL-10
Authors: Oliveira Vanessa G. , Agua-Doce Ana , Curotto de Lafaille Maria A. , Lafaille Juan J. , Graca Luis 
Published: March 2013

Key PointsAn adjuvant (alum), known to boost immune responses, can be used to facilitate a tolerogenic protocol. Nondepleting anti-CD4 can lead to Foxp3+ regulatory T-cell–independent tolerance that relies on IL-10.
Bovine HEXIM1 inhibits bovine immunodeficiency virus replication through regulating BTat-mediated transactivation
Authors: Guo Hong-yan , Ma Yong-gang , Gai Yuan-ming , Liang Zhi-bin , Ma Jing , Su Yang , Zhang Qi-cheng , Chen Qi-min , Tan Juan 
Published: March 2013

Abstract
The bovine immunodeficiency virus (BIV) transactivator (BTat) recruits the bovine cyclin T1 (B-cyclin T1) to the LTR to facilitate the transcription of BIV. Here, we demonstrate that bovine hexamethylene bisacetamide (HMBA)-induced protein 1 (BHEXIM1) inhibits BTat-mediated BIV LTR transcription. The results of in vivo and in vitro assays show direct binding of BHEXIM1 to the B-cyclin T1. These results suggest that the repression arises from BHEXIM1-BTat competition for B-cyclin T1, which allows BHEXIM1 to displace BTat from B-cyclin T1. Furthermore, we found that the C-terminal region and the centrally located region of BHEXIM1 are required for BHEXIM1 to associate with B-cyclin T1. Knockdown of BHEXIM1 enhances BIV replication. Taken together, our study provides the first clear evidence that BHEXIM1 is involved in BIV replication through regulating BTat-mediated transactivation.
TPMS: a set of utilities for querying collections of gene trees
Authors: Bigot Thomas , Daubin Vincent , Lassalle Florent , Perrière Guy 
Published: March 2013

Abstract

Background
The information in large collections of phylogenetic trees is useful for many comparative genomic studies. Therefore, there is a need for flexible tools that allow exploration of such collections in order to retrieve relevant data as quickly as possible.

Results
In this paper, we present TPMS (Tree Pattern-Matching Suite), a set of programs for handling and retrieving gene trees according to different criteria. The programs from the suite include utilities for tree collection building, specific tree-pattern search strategies and tree rooting. Use of TPMS is illustrated through three examples: systematic search for incongruencies in a large tree collection, a short study on the Coelomata/Ecdysozoa controversy and an evaluation of the level of support for a recently published Mammal phylogeny.

Conclusion
TPMS is a powerful suite allowing to quickly retrieve sets of trees matching complex patterns in large collection or to root trees using more rigorous approaches than the classical midpoint method. As it is made of a set of command-line programs, it can be easily integrated in any sequence analysis pipeline for an automated use.
Current manufactured cigarette smoking and roll-your-own cigarette smoking in Thailand: findings from the 2009 Global Adult Tobacco Survey
Authors: Benjakul Sarunya , Termsirikulchai Lakkhana , Hsia Jason , Kengganpanich Mondha , Puckcharern Hataichanok , Touchchai Chitrlada , Lohtongmongkol Areerat , Andes Linda , Asma Samira 
Published: March 2013

Abstract

Background
Current smoking prevalence in Thailand decreased from 1991 to 2004 and since that time the prevalence has remained flat. It has been suggested that one of the reasons that the prevalence of current smoking in Thailand has stopped decreasing is due to the use of RYO cigarettes. The aim of this study was to examine characteristics of users of manufactured and RYO cigarettes and dual users in Thailand, in order to determine whether there are differences in the characteristics of users of the different products.

Methods
The 2009 Global Adult Tobacco Survey (GATS Thailand) provides detailed information on current smoking patterns. GATS Thailand used a nationally and regionally representative probability sample of 20,566 adults (ages 15 years and above) who were chosen through stratified three-stage cluster sampling and then interviewed face-to-face.

Results
The prevalence of current smoking among Thai adults was 45.6% for men and 3.1% for women. In all, 18.4% of men and 1.0% of women were current users of manufactured cigarettes only, while 15.8% of men and 1.7% of women were current users of RYO cigarettes only. 11.2% of men and 0.1% of women used both RYO and manufactured cigarettes. Users of manufactured cigarettes were younger and users of RYO were older. RYO smokers were more likely to live in rural areas. Smokers of manufactured cigarettes appeared to be more knowledgeable about the health risks of tobacco use. However, the difference was confounded with age and education; when demographic variables were controlled, the knowledge differences no longer remained. Smokers of manufactured cigarettes were more likely than dual users and those who used only RYO to report that they were planning on quitting in the next month. Users of RYO only appeared to be more addicted than the other two groups as measured by time to first cigarette.

Conclusions
There appears to be a need for product targeted cessation and prevention efforts that are directed toward specific population subgroups in Thailand and include information on manufactured and RYO cigarettes.
Role of ROCK upregulation in endothelial and smooth muscle vascular functions in diabetic rat aorta
Authors: Cicek Figen Amber , Kandilci Hilmi B , Turan Belma 
Published: March 2013

Background
The RhoA/ROCK signaling pathway mediates vascular smooth muscle contraction while endogenous NO induces vasodilation through its inhibition. Since myosin light chain phosphatase (MLCP) and eNOS are targeted by RhoA/ROCK upregulation then turn to lead abnormalities in vasculature, we aimed to examine whether less endothelial NO-production and inhibited eNOS together with an upregulation of RhoA/ROCK signaling pathway in thoracic aorta can play an important role in vascular dysfunction under hyperglycemia.

Methods

We used streptozotocin-injected rats, as a model of type 1 diabetes, and their lean controls to investigate the role of ROCK upregulation in the function of toracic aorta by using electrophysiological and biochemical techniques.

Results

The protein level of ROCK isoform ROCK2 was found to be 2.5-fold higher in endothelium-intact aortic rings of the diabetic rats compared to those of the controls while its level in endothelium-denuded rings was similar among these two groups. Phosphorylation level of eNOS in endothelium-intact rings from the diabetics was 50% less compared to that of the control. ROCK inhibitors, either Y27632 or HA1077, induced concentration-dependent relaxation with a marked left-shift in phenylephrine pre-contracted endothelium-intact rings from either diabetics or high glucose incubated controls while pretreatment of these rings with L-NAME abolished this shift, fully. Moreover, phosphorylation levels of both MLCP and MLC in endothelium-denuded rings were markedly higher in the diabetics than the controls.

Conclusion

We demonstrated that diabetes-induced vascular dysfunction can arise due to either inbition of eNOS, thereby less endothelial NO-production, either directly or indirectly, in part, due to an upregulation of ROCK2 by hyperglycemia. Additionally, our data demonstrate that high phosphorylation levels of both MLC and MLCP in endothelium-denuded rings can be due to a less endothelial NO-production dependent ROCK upregulation in the smooth muscle cells under hyperglycemia, as well.
Genetic diversity and signatures of selection of drug resistance in Plasmodium populations from both human and mosquito hosts in continental Equatorial Guinea
Authors: Mendes Cristina , Salgueiro Patrícia , Gonzalez Vicenta , Berzosa Pedro , Benito Agustin , do Rosário Virgílio E , de Sousa Bruno , Cano Jorge , Arez Ana Paula 
Published: March 2013

Abstract

Background
In Plasmodium, the high level of genetic diversity and the interactions established by co-infecting parasite populations within the same host may be a source of selection on pathogen virulence and drug resistance. As different patterns have already been described in humans and mosquitoes, parasite diversity and population structure should be studied in both hosts to properly assess their effects on infection and transmission dynamics. This study aimed to characterize the circulating populations of Plasmodium spp and Plasmodium falciparum from a combined set of human blood and mosquito samples gathered in mainland Equatorial Guinea. Further, the origin and evolution of anti-malarial resistance in this area, where malaria remains a major public health problem were traced.

Methods

Plasmodium species infecting humans and mosquitoes were identified by nested-PCR of chelex-extracted DNA from dried blood spot samples and mosquitoes. Analysis of Pfmsp2 gene, anti-malarial-resistance associated genes, Pfdhps, Pfdhfr, Pfcrt and Pfmdr1, neutral microsatellites (STR) loci and Pfdhfr and Pfdhps flanking STR was undertaken to evaluate P. falciparum diversity.

Results
Prevalence of infection remains high in mainland Equatorial Guinea. No differences in parasite formula or significant genetic differentiation were seen in the parasite populations in both human and mosquito samples. Point mutations in all genes associated with anti-malarial resistance were highly prevalent. A high prevalence was observed for the Pfdhfr triple mutant in particular, associated with pyrimethamine resistance.
Analysis of Pfdhps and Pfdhfr flanking STR revealed a decrease in the genetic diversity. This finding along with multiple independent introductions of Pfdhps mutant haplotypes suggest a soft selective sweep and an increased differentiation at Pfdhfr flanking microsatellites hints a model of positive directional selection for this gene.

Conclusions
Chloroquine is no longer recommended for malaria treatment in Equatorial Guinea but sulphadoxine-pyrimethamine (SP) remains in use in combination with artesunate and is the only drug recommended in preventive chemotherapy in pregnancy. The high prevalence of point mutations in Pfdhfr and Pfdhps points to the danger of an eventual reduction in the efficacy of SP combined therapy in P. falciparum populations in Equatorial Guinea and to the essential continuous monitoring of these two genes.
Children’s physical activity and parents’ perception of the neighborhood environment: neighborhood impact on kids study
Authors: Tappe Karyn A , Glanz Karen , Sallis James F , Zhou Chuan , Saelens Brian E 
Published: March 2013

Abstract

Background
Physical activity is important to children’s physical health and well-being. Many factors contribute to children’s physical activity, and the built environment has garnered considerable interest recently, as many young children spend much of their time in and around their immediate neighborhood. Few studies have identified correlates of children’s activity in specific locations. This study examined associations between parent report of their home neighborhood environment and children’s overall and location-specific physical activity.

Methods
Parents and children ages 6 to 11 (n=724), living in neighborhoods identified through objective built environment factors as high or low in physical activity environments, were recruited from Seattle and San Diego metropolitan areas, 2007–2009. Parents completed a survey about their child’s activity and perceptions of home neighborhood environmental attributes. Children wore an accelerometer for 7 days. Multivariate regression models explored perceived environment correlates of parent-reported child’s recreational physical activity in their neighborhood, in parks, and in general, as well as accelerometry-based moderate-to-vigorous activity (MVPA) minutes.

Results
Parent-reported proximity to play areas correlated positively with both accelerometery MVPA and parent-reported total child physical activity. Lower street connectivity and higher neighborhood aesthetics correlated with higher reported child activity in the neighborhood, while reported safety from crime and walk and cycle facilities correlated positively with reported child activity in public recreation spaces.

Conclusions
Different aspects of parent’s perceptions of the neighborhood environment appear to correlate with different aspects of children’s activity. However, prioritizing closer proximity to safe play areas may best improve children’s physical activity and, in turn, reduce their risk of obesity and associated chronic diseases.
Maskless and low-destructive nanofabrication on quartz by friction-induced selective etching
Authors: Song Chenfei , Li Xiaoying , Cui Shuxun , Dong Hanshan , Yu Bingjun , Qian Linmao 
Published: March 2013

Abstract
A low-destructive friction-induced nanofabrication method is proposed to produce three-dimensional nanostructures on a quartz surface. Without any template, nanofabrication can be achieved by low-destructive scanning on a target area and post-etching in a KOH solution. Various nanostructures, such as slopes, hierarchical stages and chessboard-like patterns, can be fabricated on the quartz surface. Although the rise of etching temperature can improve fabrication efficiency, fabrication depth is dependent only upon contact pressure and scanning cycles. With the increase of contact pressure during scanning, selective etching thickness of the scanned area increases from 0 to 2.9 nm before the yield of the quartz surface and then tends to stabilise after the appearance of a wear. Refabrication on existing nanostructures can be realised to produce deeper structures on the quartz surface. Based on Arrhenius fitting of the etching rate and transmission electron microscopy characterization of the nanostructure, fabrication mechanism could be attributed to the selective etching of the friction-induced amorphous layer on the quartz surface. As a maskless and low-destructive technique, the proposed friction-induced method will open up new possibilities for further nanofabrication.
A joint design of security and quality-of-service (QoS) provisioning in vehicular ad hoc networks with cooperative communications
Authors: Zhu Li , Yu F Richard , Ning Bin , Tang Tao 
Published: March 2013

Abstract
In vehicular ad hoc networks (VANETs), some distinct characteristics, such as high node mobility, introduce new non-trivial challenges to quality-of-service (QoS) provisioning. Although some excellent works have been done on QoS issues in VANETs, security issues are largely ignored in these works. However, it is know that security always comes at a price in terms of QoS performance degradation. In this article, we consider security and QoS issues jointly for VANETs with cooperative communications. We take an integrated approach of optimizing both security and QoS parameters, and study the tradeoffs between them in VANETs. Specifically, we use recent advances in cooperative communication to enhance the QoS performance of VANETs. In addition, we present a prevention-based security technique that provides both hop-by-hop and end-to-end authentication and integrity protection. We derive the closed-form effective secure throughput considering both security and QoS provisioning in VANETs with cooperative communications. The system is formulated as a partially observable Markov decision process. Simulation results are presented to show that security schemes have significant impacts on the throughput QoS of VANETs, and our proposed scheme can substantially improve the effective secure throughput of VANETs with cooperative communications.
Paclitaxel and cisplatin combined with intensity-modulated radiotherapy for upper esophageal carcinoma
Authors: Tu Lingli , Sun Lan , Xu Yong , Wang Yongsheng , Zhou Lin , Liu Yongmei , Zhu Jiang , Peng Feng , Wei Yuquan , Gong Youling 
Published: March 2013

Abstract

Purpose
This study was conducted to evaluate the effectiveness and safety of intensity-modulated radiotherapy (IMRT) and concurrent paclitaxel plus cisplatin (TP regimen) for upper esophageal carcinoma.

Methods
36 patients of upper esophageal carcinoma were retrospectively analyzed. Patients were treated with IMRT (median 60 Gy) combined with concurrent TP regimen chemotherapy. The Kaplan-Meier analysis was performed in statistical analysis. Toxicities were recorded according to the NCI CTC version 3.0.

Results
36 patients aged 43–73 years (median 57 years). The median follow-up period was 14.0 months. The 1-year and 2-year survival rates were 83.3% and 42.8% respectively. The median progression-free survival (PFS) time and overall survival (OS) time were 12.0 (95% CI: 7.8–16.2 months) and 18.0 months (95% CI: 9.9–26.1 months), respectively. Grade 3 neutropenia, radiation-induced esophagitis and radiodermatitis were observed in 5 (13.9%), 3 (8.3%) and 8 (22.2%) patients respectively. There were two treatment-related deaths due to esophageal perforation and hemorrhea.

Conclusions
For those patients with upper esophageal carcinoma, IMRT combined with concurrent TP regimen chemotherapy was an effective treatment. However, more attention should be paid to the occurrence of perforation and hemorrhea.
Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes
Authors: Kourmpetis Yiannis AI , van Dijk Aalt DJ , ter Braak Cajo JF 
Published: March 2013

AbstractBackgroundGene Ontology (GO) is a hierarchical vocabulary for the description of biological functions and locations, often employed by computational methods for protein function prediction. Due to the structure of GO, function predictions can be self- contradictory. For example, a protein may be predicted to belong to a detailed functional class, but not in a broader class that, due to the vocabulary structure, includes the predicted one.We present a novel discrete optimization algorithm called Functional Annotation with Labeling CONsistency (FALCON) that resolves such contradictions. The GO is modeled as a discrete Bayesian Network. For any given input of GO term membership probabilities, the algorithm returns the most probable GO term assignments that are in accordance with the Gene Ontology structure. The optimization is done using the Differential Evolution algorithm. Performance is evaluated on simulated and also real data fromArabidopsis thalianashowing improvement compared to related approaches. We finally applied the FALCON algorithm to obtain genome-wide function predictions for six eukaryotic species based on data provided by the CAFA (Critical Assessment of Function Annotation) project.
Impact of enzyme replacement therapy on survival in adults with Pompe disease: results from a prospective international observational study
Authors: Güngör Deniz , Kruijshaar Michelle E , Plug Iris , D’Agostino Ralph B , Hagemans Marloes LC , van Doorn Pieter A , Reuser Arnold JJ , van der Ploeg Ans T 
Published: March 2013

Abstract

Background
Pompe disease is a rare metabolic myopathy for which disease-specific enzyme replacement therapy (ERT) has been available since 2006. ERT has shown efficacy concerning muscle strength and pulmonary function in adult patients. However, no data on the effect of ERT on the survival of adult patients are currently available. The aim of this study was to assess the effect of ERT on survival in adult patients with Pompe disease.

Methods
Data were collected as part of an international observational study conducted between 2002 and 2011, in which patients were followed on an annual basis. Time-dependent Cox’s proportional hazards models were used for univariable and multivariable analyses.

Results
Overall, 283 adult patients with a median age of 48 years (range, 19 to 81 years) were included in the study. Seventy-two percent of patients started ERT at some time during follow-up, and 28% never received ERT. During follow-up (median, 6 years; range, 0.04 to 9 years), 46 patients died, 28 (61%) of whom had never received ERT. After adjustment for age, sex, country of residence, and disease severity (based on wheelchair and ventilator use), ERT was positively associated with survival (hazard ratio, 0.41; 95% CI, 0.19 to 0.87).

Conclusion
This prospective study was the first to demonstrate the positive effect of ERT on survival in adults with Pompe disease. Given the relatively recent registration of ERT for Pompe disease, these findings further support its beneficial impact in adult patients.
Anthropometric differences among natives of Abuja living in urban and rural communities: correlations with other cardiovascular risk factors
Authors: Adediran Olufemi Sola , Adebayo Philip Babatunde , Akintunde Adeseye Abiodun 
Published: March 2013

Abstract

Background
There is an increase of obesity and other cardiovascular risk factors worldwide, but especially in developing countries where multifaceted transitions are occurring. There is need for more evidence for the cardio-metabolic effect of changing lifestyles and urbanization in Nigeria. This study aimed at defining rural–urban differences in anthropometric parameters in two Nigerian communities of the same ancestral origin and to determine the cardiovascular risk correlates of these anthropometric measurements. This was a cross-sectional epidemiological study using stratified cluster sampling method. We studied 335 and 332 urban and rural dwellers respectively. A complete cardiovascular profile as well as anthropometric measurements was compared between the two populations.

Results
All anthropometric indices considered in this study (weight, BMI, waist circumference, waist circumference/height ratio, abdominal height; biceps, triceps, sub-scapular, abdominal, superior iliac skinfold thicknesses) were significantly higher in urban than in the rural population (p = <0.001). Overweight, obesity and hypertension were significantly prevalent among the urban population (p = <0.001) while there was no significant difference in the prevalence of dyslipidaemia (p = 0.096) and diabetes (p = 0.083) between the two cohorts. Females tend to have a higher chance of obesity than males although there was no gender difference in waist circumference and central skin fold thickness in the rural population. Age was the significant predictor of systolic blood pressure among the rural (R2 = 0.157, β = 0.258, p = 0.016) and urban female population (R2 = 0.201, β = 0.351, p = <0.001) while Abdominal height (R2 = 0.16, β = 0.281, p = 0.001) and waist circumference (R2 = 0.064 β = 0.064, p = .003) were predictors of systolic blood pressure in urban and rural men respectively.

Conclusion
Anthropometric indices were significantly higher among the urban than the rural populations. Cardiovascular risks were equally more prevalent among the urban population. Appropriate health education and lifestyle modification strategies may reduce the increased burden of cardiovascular risk factors associated with rural–urban migration.