bluuebunny/crossref_metadata_2025_split huggingface dataset:
SIS: a program to generate draft genome sequence scaffolds for prokaryotes
Authors: Dias Zanoni , Dias Ulisses , Setubal João C 
Published: May 2012

Abstract

Background
Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome.

Results
We present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversion signature pair is present in contigs and no inversion signatures have been overwritten in evolution. The algorithm is also capable of generating scaffolds in the presence of any kind of inversion, even though in this general case there is no guarantee that all scaffolds in the scaffold set will be correct. We compare the performance of sis, the program that implements the algorithm, to seven other scaffold-generating programs. The results of our tests show that sis has overall better performance.

Conclusions

sis is a new easy-to-use tool to generate contig scaffolds, available both as stand-alone and as a web server. The good performance of sis in our tests adds evidence that large-scale inversions are widespread in prokaryotic genomes.
Regulation of ROCK1 via Notch1 during breast cancer cell migration into dense matrices
Authors: Raviraj Vanisri , Fok Sandra , Zhao Jifei , Chien Hsin-Ya , Lyons J Guy , Thompson Erik W , Soon Lilian 
Published: May 2012

AbstractBackgroundThe behaviour of tumour cells depends on factors such as genetics and the tumour microenvironment. The latter plays a crucial role in normal mammary gland development and also in breast cancer initiation and progression. Breast cancer tissues tend to be highly desmoplastic and dense matrix as a pre-existing condition poses one of the highest risk factors for cancer development. However, matrix influence on tumour cell gene expression and behaviour such as cell migration is not fully elucidated.ResultsWe generated high-density (HD) matrices that mimicked tumour collagen content of 20 mg/cm3that were ~14-fold stiffer than low-density (LD) matrix of 1 mg/cm3. Live-cell imaging showed breast cancer cells utilizing cytoplasmic streaming and cell body contractility for migration within HD matrix. Cell migration was blocked in the presence of both the ROCK inhibitor, Y-27632, and the MMP inhibitor, GM6001, but not by the drugs individually. This suggests roles for ROCK1 and MMP in cell migration are complicated by compensatory mechanisms. ROCK1 expression and protein activity, were significantly upregulated in HD matrix but these were blocked by treatment with a histone deacetylase (HDAC) inhibitor, MS-275. In HD matrix, the inhibition of ROCK1 by MS-275 was indirect and relied upon protein synthesis and Notch1. Inhibition of Notch1 using pooled siRNA or DAPT abrogated the inhibition of ROCK1 by MS-275.ConclusionIncreased matrix density elevates ROCK1 activity, which aids in cell migration via cell contractility. The upregulation of ROCK1 is epigenetically regulated in an indirect manner involving the repression of Notch1. This is demonstrated from inhibition of HDACs by MS-275, which caused an upregulation of Notch1 levels leading to blockade of ROCK1 expression.
Artificial neural networks modeling gene-environment interaction
Authors: Günther Frauke , Pigeot Iris , Bammann Karin 
Published: May 2012

AbstractBackgroundGene-environment interactions play an important role in the etiological pathway of complex diseases. An appropriate statistical method for handling a wide variety of complex situations involving interactions between variables is still lacking, especially when continuous variables are involved. The aim of this paper is to explore the ability of neural networks to model different structures of gene-environment interactions. A simulation study is set up to compare neural networks with standard logistic regression models. Eight different structures of gene-environment interactions are investigated. These structures are characterized by penetrance functions that are based on sigmoid functions or on combinations of linear and non-linear effects of a continuous environmental factor and a genetic factor with main effect or with a masking effect only.ResultsIn our simulation study, neural networks are more successful in modeling gene-environment interactions than logistic regression models. This outperfomance is especially pronounced when modeling sigmoid penetrance functions, when distinguishing between linear and nonlinear components, and when modeling masking effects of the genetic factor.ConclusionOur study shows that neural networks are a promising approach for analyzing gene-environment interactions. Especially, if no prior knowledge of the correct nature of the relationship between co-variables and response variable is present, neural networks provide a valuable alternative to regression methods that are limited to the analysis of linearly separable data.
Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit
Authors: Lima-Silva Viviana , Rosado Abel , Amorim-Silva Vitor , Muñoz-Mérida Antonio , Pons Clara , Bombarely Aureliano , Trelles Oswaldo , Fernández-Muñoz Rafael , Granell Antonio , Valpuesta Victoriano , Botella Miguel Ángel 
Published: May 2012

AbstractBackgroundL-ascorbic acid (AsA; vitamin C) is essential for all living plants where it functions as the main hydrosoluble antioxidant. It has diverse roles in the regulation of plant cell growth and expansion, photosynthesis, and hormone-regulated processes. AsA is also an essential component of the human diet, being tomato fruit one of the main sources of this vitamin. To identify genes responsible for AsA content in tomato fruit, transcriptomic studies followed by clustering analysis were applied to two groups of fruits with contrasting AsA content. These fruits were identified after AsA profiling of an F8 Recombinant Inbred Line (RIL) population generated from a cross between the domesticated speciesSolanum lycopersicumand the wild relativeSolanum pimpinellifollium.ResultsWe found large variability in AsA content within the RIL population with individual RILs with up to 4-fold difference in AsA content. Transcriptomic analysis identified genes whose expression correlated either positively (PVCgenes) or negatively (NVCgenes) with the AsA content of the fruits. Cluster analysis using SOTA allowed the identification of subsets of co-regulated genes mainly involved in hormones signaling, such as ethylene, ABA, gibberellin and auxin, rather than any of the known AsA biosynthetic genes. Data mining of the correspondingPVCandNVCorthologs in Arabidopis databases identified flagellin and other ROS-producing processes as cues resulting in differential regulation of a high percentage of the genes from both groups of co-regulated genes; more specifically, 26.6% of the orthologous PVC genes, and 15.5% of the orthologous NVC genes were induced and repressed, respectively, under flagellin22 treatment inArabidopsis thaliana.ConclusionResults here reported indicate that the content of AsA in red tomato fruit from our selected RILs are not correlated with the expression of genes involved in its biosynthesis. On the contrary, the data presented here supports that AsA content in tomato fruit co-regulates with genes involved in hormone signaling and they are dependent on the oxidative status of the fruit.
The prevalence of Chlamydia trachomatis infection in Australia: a systematic review and meta-analysis
Authors: Lewis Dyani , Newton Danielle C , Guy Rebecca J , Ali Hammad , Chen Marcus Y , Fairley Christopher K , Hocking Jane S 
Published: May 2012

AbstractBackgroundChlamydia trachomatisis a common sexually transmitted infection in Australia. This report aims to measure the burden of chlamydia infection by systematically reviewing reports on prevalence in Australian populations.MethodsElectronic databases and conference websites were searched from 1997–2011 using the terms ‘Chlamydia trachomatis’ OR ‘chlamydia’ AND ‘prevalence’ OR ‘epidemiology’ AND ‘Australia’. Reference lists were checked and researchers contacted for additional literature. Studies were categorised by setting and participants, and meta-analysis conducted to determine pooled prevalence estimates for each category.ResultsSeventy-six studies met the inclusion criteria for the review. There was a high level of heterogeneity between studies; however, there was a trend towards higher chlamydia prevalence in younger populations, Indigenous Australians, and those attending sexual health centres. In community or general practice settings, pooled prevalence for women <25 years in studies conducted post-2005 was 5.0% (95% CI: 3.1, 6.9; five studies), and for men <30 years over the entire review period was 3.9% (95% CI: 2.7, 5.1; six studies). For young Australians aged <25 years attending sexual health, family planning or youth clinics, estimated prevalence was 6.2% (95% CI: 5.1, 7.4; 10 studies) for women and 10.2% (95% CI: 9.5, 10.9; five studies) for men. Other key findings include pooled prevalence estimates of 22.1% (95% CI: 19.0, 25.3; three studies) for Indigenous women <25 years, 14.6% (95% CI: 11.5, 17.8; three studies) for Indigenous men <25 years, and 5.6% (95% CI: 4.8, 6.3; 11 studies) for rectal infection in men who have sex with men. Several studies failed to report basic demographic details such as sex and age, and were therefore excluded from the analysis.ConclusionsChlamydia trachomatisinfections are a significant health burden in Australia; however, accurate estimation of chlamydia prevalence in Australian sub-populations is limited by heterogeneity within surveyed populations, and variations in sampling methodologies and data reporting. There is a need for more large, population-based studies and prospective cohort studies to compliment mandatory notification data.
Prevention and treatment of surgical site infection in HIV-infected patients
Authors: Zhang Lei , Liu Bao-Chi , Zhang Xiao-Yan , Li Lei , Xia Xian-Jun , Guo Rui-Zhang 
Published: May 2012

Abstract

Background
Surgical site infection (SSI) are the third most frequently reported nosocomial infection, and the most common on surgical wards. HIV-infected patients may increase the possibility of developing SSI after surgery. There are few reported date on incidence and the preventive measures of SSI in HIV-infected patients. This study was to determine the incidence and the associated risk factors for SSI in HIV-infected patients. And we also explored the preventive measures.

Methods
A retrospective study of SSI was conducted in 242 HIV-infected patients including 17 patients who combined with hemophilia from October 2008 to September 2011 in Shanghai Public Health Clinical Center. SSI were classified according to Centers for Disease Control and Prevention (CDC) criteria and identified by bedside surveillance and post-discharge follow-up. Data were analyzed using SPSS 16.0 statistical software (SPSS Inc., Chicago, IL).

Results
The SSI incidence rate was 47.5% (115 of 242); 38.4% incisional SSIs, 5.4% deep incisional SSIs and 3.7% organ/space SSIs. The SSI incidence rate was 37.9% in HIV-infected patients undergoing abdominal operation. Patients undergoing abdominal surgery with lower preoperative CD4 counts were more likely to develop SSIs. The incidence increased from 2.6% in clean wounds to 100% in dirty wounds. In the HIV-infected patients combined with hemophilia, the mean preoperative albumin and postoperative hemoglobin were found significantly lower than those in no-SSIs group (P<0.05).

Conclusions
SSI is frequent in HIV-infected patients. And suitable perioperative management may decrease the SSIs incidence rate of HIV-infected patients.
The genetic variants at the HLA-DRB1 gene are associated with primary IgA nephropathy in Han Chinese
Authors: Jiyun Yang , Guisen Li , Li Zhu , Yi Shi , Jicheng Lv , Fang Lu , Xiaoqi Liu , Shi Ma , Cheng Jing , Ying Lin , Haiyan Wang , Li Wang , Hong Zhang , Zhenglin Yang 
Published: May 2012

Abstract

Background
Immunoglobulin A nephropathy (IgAN), an immune-complex-mediated glomerulonephritis defined immunohistologically by the presence of glomerular IgA deposits, is the most common primary glomerular disease worldwide and a significant cause of end-stage renal disease. Familial clustering of patients with IgAN suggests a genetic predisposition.

Methods
In this study, 192 patients with IgAN and 192 normal controls in the Sichuan cohort and 935 patients with IgAN and 2,103 normal controls in the Beijing cohort were investigated. HLA-DRB1*01–DRB1*10 specificities were genotyped by the PCR–SSP technique in both cohorts. Based on the HLA-DRB1*04-positive results, the subtypes of HLA-DRB1*04 were analyzed using sequencing-based typing (SBT) in 291 IgAN cases and 420 matched controls.

Results
The frequency of HLA-DRB1*04 in the IgAN group was significantly higher than that in the control group (0.129 vs. 0.092, P = 8.29 × 10-5, odds ratio (OR) =1.381, 95% confidence interval (CI) 1.178–1.619). Other alleles at the HLA-DRB1 locus were observed with no significant differences between the case and control groups. The dominant alleles of the HLA-DRB1*04 subtypes were DRB1*0405 in both cohorts. The frequencies of HLA-DRB1*0405 and 0403 were significantly increased in the patients compared to healthy subjects.

Conclusion
HLA-DRB1*04 was significantly associated with primary IgAN in Chinese population. This result implies that HLA-DRB1 gene plays a major role in primary IgAN.
Cost-effectiveness of family psychoeducation to prevent relapse in major depression: Results from a randomized controlled trial
Authors: Shimodera Shinji , Furukawa Toshi A , Mino Yoshio , Shimazu Kae , Nishida Atsushi , Inoue Shimpei 
Published: May 2012

Abstract

Background
Family psychoeducation is a relatively simple and straightforward intervention whose prophylactic effectiveness and cost-effectiveness is well-established for schizophrenia. We have recently demonstrated its effectiveness for unipolar depression, but its cost-effectiveness has never been examined. We hereby report a cost-effectiveness analysis alongside a randomized controlled trial in order to assess its cost-effectiveness for preventing relapse/recurrence in depression.

Methods
Fifty-seven patients diagnosed with major depression and undergoing its maintenance treatment, and their primary family members were randomized to treatment as usual (TAU) only or to TAU plus family psychoeducation, which consisted of four 2-hour multiple-family sessions consisting of didactic lectures about depression (30 minutes) and group discussion and problem solving (60–90 minutes). The economic analyses were undertaken from the perspective of the National Health Insurance (NHI), assuming the most reasonable price of US$50 per psychoeducation session per patient. The main outcome measures included relapse-free days and direct costs to the NHI.

Results
The intervention group enjoyed 272 (SD: 7.1) relapse-free days, while the control group spent 214 (SD: 90.8) relapse-free days (Cox proportional hazard ratio = 0.17, 95%CI: 0.04 to 0.75, p = 0.002). Cost-effectiveness acceptability curves suggested that the family psychoeducation has 90% or more chances of being cost-effective if the decision-maker is prepared to pay US$20 for one additional relapse-free day. This cost-effectiveness finding was robust when the price for family psychoeducation ranged between 50% to 150% of the baseline scenario in sensitivity analyses. If a relapse-free day is considered to be worth $30 or more, all the pricing scenarios have a close to 100% probability of being cost-effective.

Conclusion
Family psychoeducation is effective in the relapse prevention of depression and is highly likely to be cost-effective if a relapse-free day is valued as US$20 or more.

Trial registration
UMIN-CTR (UMIN000005555)
Use of glucometer and fasting blood glucose as screening tools for diabetes mellitus type 2 and glycated haemoglobin as clinical reference in rural community primary care settings of a middle income country
Authors: Muktabhant Benja , Sanchaisuriya Pattara , Sarakarn Pongdech , Tawityanon Worawitaya , Trakulwong Mantana , Worawat Songsri , Schelp Frank P 
Published: May 2012

Abstract

Background
Thailand is considered to be a middle income country, and to control and prevent type 2 diabetes mellitus (T2DM) is one of the main concerns of the Thai Ministry of Public Health (MoPH). Screening for T2DM and care for T2DM patients has been integrated into the primary health care system, especially in rural areas. The intention of this investigation is to link public health research at the academic level with the local health authorities of a district of a north-eastern province of the country.

Methods
Epidemiological methods were applied to validate the screening tools fasting capillary blood glucose (CBG), measured by glucometer and venous blood for the determination of plasma glucose (VPG), used for screening for T2DM among asymptomatic villagers. For assessing the validity of these two methods glycated haemoglobin (HbA1c) values were determined and used as the ‘clinical reference’.

Results
All together 669 villagers were investigated. Determinations of CBG and VPG resulted in suspected T2DM cases, with 7.3% when assessed by CBG and 6.4% by VPG using a cutoff point of 7 mmol/L (126 mg/dl). Taking HbA1c determinations with a cutoff point of 7% into account, the proportion of T2DM suspected participants increased to 10.4%. By estimating sensitivity, specificity and the positive predictive value of CBG and VPG against the ‘clinical reference’ of HbA1c, sensitivity below 50% for both screening methods has been observed. The positive predictive value was determined to be 58.5% for CBG and 56.8% for VPG. The specificity of the two screening tests was over 96%.

Conclusions
The low sensitivity indicates that using fasting CBG or VPG as a screening tool in the field results in a high proportion of diseased individuals remaining undetected. The equally low positive predictive values (below 60%) indicate a high working load for the curative sector in investigating suspected T2DM cases to determine whether they are truly diseased or false positive cases according to the screening method. Further implications of the results and the controversial discussion related to the use of HbA1c as clinical evidence for suffering from T2DM are also discussed.
Children eat their school lunch too quickly: an exploratory study of the effect on food intake
Authors: Zandian Modjtaba , Ioakimidis Ioannis , Bergström Jakob , Brodin Ulf , Bergh Cecilia , Leon Michael , Shield Julian , Södersten Per 
Published: May 2012

Abstract

Background
Speed of eating, an important aspect of eating behaviour, has recently been related to loss of control of food intake and obesity. Very little time is allocated for lunch at school and thus children may consume food more quickly and food intake may therefore be affected. Study 1 measured the time spent eating lunch in a large group of students eating together for school meals. Study 2 measured the speed of eating and the amount of food eaten in individual school children during normal school lunches and then examined the effect of experimentally increasing or decreasing the speed of eating on total food intake.

Methods
The time spent eating lunch was measured with a stop watch in 100 children in secondary school. A more detailed study of eating behaviour was then undertaken in 30 secondary school children (18 girls). The amount of food eaten at lunch was recorded by a hidden scale when the children ate amongst their peers and by a scale connected to a computer when they ate individually. When eating individually, feedback on how quickly to eat was visible on the computer screen. The speed of eating could therefore be increased or decreased experimentally using this visual feedback and the total amount of food eaten measured.

Results
In general, the children spent very little time eating their lunch. The 100 children in Study 1 spent on average (SD) just 7 (0.8) minutes eating lunch. The girls in Study 2 consumed their lunch in 5.6 (1.2) minutes and the boys ate theirs in only 6.8 (1.3) minutes. Eating with peers markedly distorted the amount of food eaten for lunch; only two girls and one boy maintained their food intake at the level observed when the children ate individually without external influences (258 (38) g in girls and 289 (73) g in boys). Nine girls ate on average 33% less food and seven girls ate 23% more food whilst the remaining boys ate 26% more food. The average speed of eating during school lunches amongst groups increased to 183 (53)% in the girls and to 166 (47)% in the boys compared to the speed of eating in the unrestricted condition. These apparent changes in food intake during school lunches could be replicated by experimentally increasing the speed of eating when the children were eating individually.

Conclusions
If insufficient time is allocated for consuming school lunches, compensatory increased speed of eating puts children at risk of losing control over food intake and in many cases over-eating. Public health initiatives to increase the time available for school meals might prove a relatively easy way to reduce excess food intake at school and enable children to eat more healthily.
Gender difference in carotid intima-media thickness in type 2 diabetic patients: a 4-year follow-up study
Authors: Zhao Bo , Liu Yanping , Zhang Yifei , Chen Yuhong , Yang Zhifang , Zhu Ying , Zhan Weiwei 
Published: May 2012

Abstract

Background
Different population studies have reported gender difference in carotid intima-media thickness (CIMT), which is proved to be a risk factor of cardiovascular diseases. However, few longitudinal researches examine this gender difference in type 2 diabetes mellitus (T2DM) patients. Therefore, we prospectively analyzed CIMT in T2DM patients over a 4-year follow-up period.

Methods
355 T2DM patients (mean age 59 years; 54.9% women) were included in the present study. CIMT were measured using Color Doppler ultrasound. CIMT was measured at baseline (CIMT) in 2006 and at follow-up in 2010. Biochemical and clinical measurements were collected at baseline.

Results
Mean value of CIMT1 and CIMT2 were 0.740 ± 0.148 mm and 0.842 ± 0.179 mm, respectively. Men had higher CIMT than women both at baseline and at follow-up (CIMT1: 0.762 ± 0.149 vs 0.723 ± 0.146 mm, P = 0.0149; CIMT2: 0.880 ± 0.189 vs 0.810 ± 0.164 mm, P = 0.0002). Mean annual progression of CIMT (dCIMT) was 0.025 ± 0.022 mm/year. dCIMT was larger in men than in women (0.030 ± 0.025 vs 0.022 ± 0.019 mm, P = 0.0006). In multiple regression analyses, age was an independent risk factor of CIMT in both genders, while dCIMT was associated with age only in men.

Conclusions
Gender difference in CIMT was confirmed in T2DM patients. Moreover, impact of ageing on CIMT progression only existed in men, which might be the reason that gender difference in CIMT increased with age.