bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression pattern divergence of duplicated genes in rice
Authors: Li Zhe , Zhang He , Ge Song , Gu Xiaocheng , Gao Ge , Luo Jingchu 
Published: June 2009

Abstract

Background
Genome-wide duplication is ubiquitous during diversification of the angiosperms, and gene duplication is one of the most important mechanisms for evolutionary novelties. As an indicator of functional evolution, the divergence of expression patterns following duplication events has drawn great attention in recent years. Using large-scale whole-genome microarray data, we systematically analyzed expression divergence patterns of rice genes from block, tandem and dispersed duplications.

Results
We found a significant difference in expression divergence patterns for the three types of duplicated gene pairs. Expression correlation is significantly higher for gene pairs from block and tandem duplications than those from dispersed duplications. Furthermore, a significant correlation was observed between the expression divergence and the synonymous substitution rate which is an approximate proxy of divergence time. Thus, both duplication types and divergence time influence the difference in expression divergence. Using a linear model, we investigated the influence of these two variables and found that the difference in expression divergence between block and dispersed duplicates is attributed largely to their different divergence time. In addition, the difference in expression divergence between tandem and the other two types of duplicates is attributed to both divergence time and duplication type.

Conclusion
Consistent with previous studies on Arabidopsis, our results revealed a significant difference in expression divergence between the types of duplicated genes and a significant correlation between expression divergence and synonymous substitution rate. We found that the attribution of duplication mode to the expression divergence implies a different evolutionary course of duplicated genes.
Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus
Authors: Downing Tim , Lynn David J , Connell Sarah , Lloyd Andrew T , Bhuiyan A K , Silva Pradeepa , Naqvi A N , Sanfo Rahamame , Sow Racine-Samba , Podisi Baitsi , Hanotte Olivier , O'Farrelly Cliona , Bradley Daniel G 
Published: June 2009

Abstract

Background
The comparative analysis of genome sequences emerging for several avian species with the fully sequenced chicken genome enables the genome-wide investigation of selective processes in functionally important chicken genes. In particular, because of pathogenic challenges it is expected that genes involved in the chicken immune system are subject to particularly strong adaptive pressure. Signatures of selection detected by inter-species comparison may then be investigated at the population level in global chicken populations to highlight potentially relevant functional polymorphisms.

Results
Comparative evolutionary analysis of chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genes identified interleukin 4 receptor alpha-chain (IL-4Rα), a key cytokine receptor as a candidate with a significant excess of substitutions at nonsynonymous sites, suggestive of adaptive evolution. Resequencing and detailed population genetic analysis of this gene in diverse village chickens from Asia and Africa, commercial broilers, and in outgroup species red jungle fowl (JF), grey JF, Ceylon JF, green JF, grey francolin and bamboo partridge, suggested elevated and balanced diversity across all populations at this gene, acting to preserve different high-frequency alleles at two nonsynonymous sites.

Conclusion
Haplotype networks indicate that red JF is the primary contributor of diversity at chicken IL-4Rα: the signature of variation observed here may be due to the effects of domestication, admixture and introgression, which produce high diversity. However, this gene is a key cytokine-binding receptor in the immune system, so balancing selection related to the host response to pathogens cannot be excluded.
Comparison of Bayesian and classical methods in the analysis of cluster randomized controlled trials with a binary outcome: The Community Hypertension Assessment Trial (CHAT)
Authors: Ma Jinhui , Thabane Lehana , Kaczorowski Janusz , Chambers Larry , Dolovich Lisa , Karwalajtys Tina , Levitt Cheryl 
Published: June 2009

Abstract

Background
Cluster randomized trials (CRTs) are increasingly used to assess the effectiveness of interventions to improve health outcomes or prevent diseases. However, the efficiency and consistency of using different analytical methods in the analysis of binary outcome have received little attention. We described and compared various statistical approaches in the analysis of CRTs using the Community Hypertension Assessment Trial (CHAT) as an example. The CHAT study was a cluster randomized controlled trial aimed at investigating the effectiveness of pharmacy-based blood pressure clinics led by peer health educators, with feedback to family physicians (CHAT intervention) against Usual Practice model (Control), on the monitoring and management of BP among older adults.

Methods
We compared three cluster-level and six individual-level statistical analysis methods in the analysis of binary outcomes from the CHAT study. The three cluster-level analysis methods were: i) un-weighted linear regression, ii) weighted linear regression, and iii) random-effects meta-regression. The six individual level analysis methods were: i) standard logistic regression, ii) robust standard errors approach, iii) generalized estimating equations, iv) random-effects meta-analytic approach, v) random-effects logistic regression, and vi) Bayesian random-effects regression. We also investigated the robustness of the estimates after the adjustment for the cluster and individual level covariates.

Results
Among all the statistical methods assessed, the Bayesian random-effects logistic regression method yielded the widest 95% interval estimate for the odds ratio and consequently led to the most conservative conclusion. However, the results remained robust under all methods – showing sufficient evidence in support of the hypothesis of no effect for the CHAT intervention against Usual Practice control model for management of blood pressure among seniors in primary care. The individual-level standard logistic regression is the least appropriate method in the analysis of CRTs because it ignores the correlation of the outcomes for the individuals within the same cluster.

Conclusion
We used data from the CHAT trial to compare different methods for analysing data from CRTs. Using different methods to analyse CRTs provides a good approach to assess the sensitivity of the results to enhance interpretation.
Pontine infarction with pure motor hemiparesis or hemiplegia: A prospective study
Authors: Ling Li , Zhu Liangfu , Zeng Jinsheng , Liao Songjie , Zhang Suping , Yu Jian , Yang Zhiyun 
Published: June 2009

Abstract

Background
The study aimed to prospectively observe the clinical and neuroimaging features of pontine infarction with pure motor hemiparesis (PMH) or hemiplegia at early stage.

Methods
In 118 consecutive selected patients with the first-ever ischemic stroke within 6 hours after onset, fifty of them presented with PMH or hemiplegia and had negative acute computed tomography (CT) scans, then magnetic resonance imaging (MRI) confirmed the corresponding infarcts in pons or cerebrum. The clinical and neuroimaging features of the pontine infarctions were compared with those of cerebral infarctions.

Results
The pontine infarction with PMH or hemiplegia accounted for 10.2% (12/118) of all first-ever ischemic stroke patients and 24% (12/50) of the patients with both PMH or hemiplegia and acute negative CT scans. Compared to the patients with cerebral infarction, the patients with pontine infarction had more frequency of diabetes mellitus (50.0% vs 5.3%, P = 0.001), nonvertiginous dizziness at onset (58.3% vs 21.1%, P = 0.036) and a progressive course (33.3% vs 2.6%, P = 0.011).

Conclusion
The pontine infarction may present as PMH or hemiplegia with more frequency of nonvertiginous dizziness, a progressive course and diabetes mellitus. MRI can confirm the infarct location in the basal pons at early stage after stroke onset.
Colorectal carcinomas in MUTYH-associated polyposis display histopathological similarities to microsatellite unstable carcinomas
Authors: Nielsen Maartje , de Miranda Noel FCC , van Puijenbroek Marjo , Jordanova Ekaterina S , Middeldorp Anneke , van Wezel Tom , van Eijk Ronald , Tops Carli MJ , Vasen Hans FA , Hes Frederik J , Morreau Hans 
Published: June 2009

Abstract

Background
MUTYH-associated polyposis (MAP) is a recessively inherited disorder which predisposes biallelic carriers for a high risk of polyposis and colorectal carcinoma (CRC). Since about one third of the biallelic MAP patients in population based CRC series has no adenomas, this study aimed to identify specific clinicopathological characteristics of MAP CRCs and compare these with reported data on sporadic and Lynch CRCs.

Methods
From 44 MAP patients who developed ≥ 1 CRCs, 42 of 58 tumours were analyzed histologically and 35 immunohistochemically for p53 and beta-catenin. Cell densities of CD3, CD8, CD57, and granzyme B positive lymphocytes were determined. KRAS2, the mutation cluster region (MCR) of APC, p53, and SMAD4 were analyzed for somatic mutations.

Results
MAP CRCs frequently localized to the proximal colon (69%, 40/58), were mucinous in 21% (9/42), and had a conspicuous Crohn's like infiltrate reaction in 33% (13/40); all of these parameters occurred at a higher rate than reported for sporadic CRCs. Tumour infiltrating lymphocytes (TILs) were also highly prevalent in MAP CRCs. Somatic APC MCR mutations occurred in 14% (5/36) while 64% (23/36) had KRAS2 mutations (22/23 c.34G>T). G>T tranversions were found in p53 and SMAD4, although the relative frequency compared to other mutations was low.

Conclusion
MAP CRCs show some similarities to micro-satellite unstable cancers, with a preferential proximal location, a high rate of mucinous histotype and increased presence of TILs. These features should direct the practicing pathologist towards a MAP aetiology of CRC as an alternative for a mismatch repair deficient cause. High frequent G>T transversions in APC and KRAS2 (mutated in early tumour development) but not in P53 and SMAD4 (implicated in tumour progression) might indicate a predominant MUTYH effect in early carcinogenesis.
Population-based incidence of Type 2 diabetes and its associated risk factors: results from a six-year cohort study in Iran
Authors: Harati Hadi , Hadaegh Farzad , Saadat Navid , Azizi Fereidoun 
Published: June 2009

Abstract

Background
The Middle East is estimated to have the largest increase in prevalence of diabetes by 2030; yet there is lack of published data on the incidence of Type 2 diabetes in this region. This study aimed to estimate Type 2 diabetes incidence and its associated risk factors in an Iranian urban population.

Methods
Among 3307 non-diabetics ≥ 20 years (mean age 42 ± 13 years, 42% males), glucose tolerance test was performed at baseline in 1999–2001 and at two consecutive phases in 2001–2005 and 2005–2008. Diabetes and glucose tolerance status were defined according to the ADA 1997 criteria. Logistic regression was used to determine the independent variables associated with incident diabetes and their odds ratios (OR).

Results
After median follow-up of 6 years, 237 new cases of diabetes were ascertained corresponding to an age and sex standardized cumulative incidence of 6.4% (95%CI: 5.6–7.2) and incidence rate of 10.6 (9.2–12.1) per 1000 person years. Besides classical diabetes risk factors, female sex and low education level significantly increased risk of diabetes in age adjusted models. In full model, the independent predictors were age [OR, 95%CI: 1.2 (1.1–1.3)], family history of diabetes [1.8 (1.3–2.5)], body mass index ≥ 30 kg/m2 [2.3 (1.5–3.6)], abdominal obesity [1.9 (1.4–2.6)], high triglyceride [1.4 (1.1–1.9)], Isolated impaired fasting glucose (IFG) [7.4 (3.6–15.0)], Isolated impaired glucose tolerance (IGT) [5.9 (4.2–8.4)] and combined IFG and IGT [42.2 (23.8–74.9)].

Conclusion
More than 1% of the Iranian urban population older than 20 years develops Type 2 diabetes each year. Combination of IFG and IGT was the strongest predictor of incident diabetes among the modifiable risk factors.
Approach to the diagnosis and management of suspected exercise-induced bronchoconstriction by primary care physicians
Authors: Hull James H , Hull Peter J , Parsons Jonathan P , Dickinson John W , Ansley Les 
Published: June 2009

Abstract

Background
Exercise-related respiratory symptoms in the diagnosis of exercise-induced bronchoconstriction (EIB) have poor predictive value. The aim of this study was to evaluate how athletes presenting with these symptoms are diagnosed and managed in primary care.

Methods
An electronic survey was distributed to a random selection of family practitioners in England. The survey was designed to assess the frequency with which family practitioners encounter adults with exercise-related respiratory symptoms and how they would approach diagnostic work-up and management. The survey also evaluated awareness of and access to diagnostic tests in this setting and general knowledge of prescribing asthma treatments to competitive athletes.

Results
257 family practitioners completed the online survey. One-third of respondents indicated they encountered individuals with this problem at a frequency of more than one case per month. Over two-thirds of family practitioners chose investigation as an initial management strategy, while one-quarter would initiate treatment based on clinical information alone. PEFR pre- and post-exercise was the most commonly selected test for investigation (44%), followed by resting spirometry pre- and post-bronchodilator (35%). Short-acting β2-agonists were the most frequently selected choice of treatment indicated by respondents (90%).

Conclusion
Family practitioners encounter individuals with exercise-related respiratory symptoms commonly and although objective testing is often employed in diagnostic work-up, the tests most frequently utilised are not the most accurate for diagnosis of EIB. This diagnostic approach may be dictated by the reported lack of access to more precise testing methods, or may reflect a lack of dissemination or awareness of current evidence. Overall the findings have implications both for the management and hence welfare of athletes presenting with this problem to family practitioners and also for the competitive athletes requiring therapeutic use exemption.
Expression of endo-1, 4-beta-xylanase from Trichoderma reesei in Pichia pastorisand functional characterization of the produced enzyme
Authors: He Jun , Yu Bing , Zhang Keying , Ding Xuemei , Chen Daiwen 
Published: June 2009

AbstractBackgroundIn recent years, xylanases have attracted considerable research interest because of their potential in various industrial applications. The yeastPichia pastoriscan neither utilize nor degrade xylan, but it possesses many attributes that render it an attractive host for the expression and production of industrial enzymes.ResultsThe Xyn2 gene, which encodes the mainTrichoderma reeseiRut C-30 endo-β-1, 4-xylanase was cloned into the pPICZαA vector and expressed inPichia pastoris. The selectedP. pastorisstrains produced as 4,350 nkat/ml β-xylanase under the control of the methanol inducible alcohol oxidase 1 (AOX1) promoter. The secreted recombinant Xyn2 was estimated by SDS-PAGE to be 21 kDa. The activity of the recombinant Xyn2 was highest at 60°C and it was active over a broad range of pH (3.0–8.0) with maximal activity at pH 6.0. The enzyme was quite stable at 50°C and retained more than 94% of its activity after 30 mins incubation at this temperature. Using Birchwood xylan, the determined apparentKmand kcatvalues were 2.1 mg/ml and 219.2 S-1, respectively. The enzyme was highly specific towards xylan and analysis of xylan hydrolysis products confirmed as expected that the enzyme functions as endo-xylanase with xylotriose as the main hydrolysis products. The produced xylanase was practically free of cellulolytic activity.ConclusionTheP. pastorisexpression system allows a high level expression of xylanases. Xylanase was the main protein species in the culture supernatant, and the functional tests indicated that even the non-purified enzyme shows highly specific xylanase activity that is free of cellulolytic side acitivities. Therefore,P pastorisis a very useful expression system when the goal is highly specific and large scale production of glycosyl hydrolases.
Risk factors for malaria deaths in Jalpaiguri district, West Bengal, India: evidence for further action
Authors: Sarkar Jagannath , Murhekar Manoj V , Shah Naman K , van Hutin Y 
Published: June 2009

Abstract

Background
In 2006, a cluster of malaria deaths in the highly endemic Jalpaiguri district, West Bengal, India, led to assignment of additional resources. Malaria deaths decreased, but continued to occur. A study was conducted to identify the risk factors for residual malaria deaths.

Methods
Malaria death was defined as a death from fever with microscopically confirmed Plasmodium falciparum among residents of Jalpaiguri during 2007–2008. For each case, three age-, sex- and locality-matched controls were recruited among microscopically confirmed falciparum malaria patients cured during the same period. Clinical and treatment information was abstracted from records. Information about knowledge about malaria, presence of bed nets and DDT spraying was collected through interviews of the close relatives of study subjects. Odds ratio (OR) were calculated using multivariate methods.

Results
51 malaria deaths were matched with 153 controls, which did not differ by age (median: 35 versus 36 years) and proportion of males (63% versus 63%). On multiple logistic regression analysis, compared with survivors, malaria deaths were more likely to have been admitted with already existing complications [OR = 4.1, 95% confidence interval (CI) = 1.6–10)], treated at a private facility (OR = 3.7, 95% CI = 1.2–12), received treatment after 48 hours of fever onset (OR = 14, 95% CI = 2.9–64), received chloroquine (OR = 13.3, 95% CI = 3.7–47). Households of the deceased were also more likely to miss bed nets (OR = 6.3, 95% CI = 1.9–24) and DDT spraying (OR = 9.2, 95% CI = 2.8–31).

Conclusion
Elimination of malaria deaths will require education of providers for prompt referral before complications, engagement of the private sector, community awareness for early treatment as well as scaled-up use of bed nets use and DDT. Use of newer generation anti-malarials must to be generalized.
Increases in norepinephrine release and ovarian cyst formation during ageing in the rat
Authors: Acuña Eric , Fornes Romina , Fernandois Daniela , Garrido Maritza P , Greiner Monika , Lara Hernan E , Paredes Alfonso H 
Published: June 2009

Abstract

Background
Depletion of ovarian follicles is associated with the end of reproductive function in ageing females. Recently, it has been described that this process parallels increases in the concentration of norepinephrine (NE) in the rat ovary. In sexually mature rats, experimentally-induced increases in the sympathetic tone of the ovary is causally related to ovarian cyst formation and deranged follicular development. Thus, there is a possibility that increased ovarian NE concentrations represent changes in the activity of sympathetic nerves, which consequently participate in the process of ovarian cyst formation observed during ageing in the human and experimental animal models.

Methods
Sprague-Dawley rats between 6 and 14 months old were used to analyse the capacity of the ovary to release 3H-NE recently incorporated under transmural depolarisation in relation to changes in the ovarian follicular population. Morphometric analysis of ovarian follicles and real time PCR for Bcl2 and Bax mRNA were used to assess follicular atresia.

Results
From 8 months old, the induced release of recently incorporated 3H-norepinephrine (3H-NE) from the ovary and ovarian NE concentrations increased, reaching their peak values at 12 months old and remained elevated up to 14 months old. Increases in sympathetic nerve activity paralleled changes in the follicular population, as well as disappearance of the corpus luteum. In contrast, luteinised follicles, precystic follicles, and cystic follicles increased. During this period, the relationship between Bax and Bcl2 mRNAs (the proapoptotic/antiapoptotic signals) increased, suggesting atresia as the principal mechanism contributing to the decreased follicular population. When NE tone was increased, the mRNA ratio favoured Bcl2 to Bax and antiapoptotic signals dominated this period of development. Thus, these changing ratios could be responsible for the increase in luteinised follicles, as well as precystic and cystic follicles.

Conclusion
These data suggest that the ageing process in the ovary of the Sprague-Dawley rat is accompanied by an increased sympathetic tone of the ovary. Consequently, this sympathetic change could be related to a neuroendocrine-driven formation of a polycystic condition similar to that observed in the sympathetic-activated adult ovary.
Effectiveness of antiretroviral therapy and development of drug resistance in HIV-1 infected patients in Mombasa, Kenya
Authors: Steegen Kim , Luchters Stanley , Dauwe Kenny , Reynaerts Jacqueline , Mandaliya Kishor , Jaoko Walter , Plum Jean , Temmerman Marleen , Verhofstede Chris 
Published: June 2009

AbstractAccess to antiretroviral therapy (ART) is increasing in resource-limited settings (RLS) and can successfully reduce HIV-related morbidity and mortality. However, virologic failure and development of viral drug resistance can result in reduced treatment options and disease progression. Additionally, transmission of resistant virus, and particularly multi-drug resistance, could become a public health concern. This study evaluated treatment success and development of ART drug resistance after short-term treatment among patients attending the Comprehensive HIV Care Centre (CCC) of Coast Province General Hospital, Mombasa, Kenya. One hundred and fifty HIV-infected individuals receiving ART were consecutively recruited to participate in the study. After determination of plasma viral load, patients with detectable viral load levels were subjected to genotypic drug resistance testing. At the time of sampling, 132 of the 150 participants were on ART for more than 6 months (median 21 months, IQR = 12–26). An efficient viral load reduction to below 50 copies/ml was observed in 113 (85.6%) of them. Of the 19 patients with a detectable viral load, sequencing of the protease (PR) and reverse transcriptase (RT) gene was successful in 16. Eleven (11) of these 16 patients were infected with a subtype A1 virus. Major PR mutations were absent, but mutations associated with drug resistance in RT were detected in 14 of the 16 patients (87.5%). High-level resistance against at least 2 drugs of the ART regimen was observed in 9/14 (64.3%). The 3TC mutation M184V and the NNRTI mutation K103N were most frequent but also the multi-drug resistance Q151M and the broad NRTI cross-resistance K65R were observed. The results of this study revealed a high rate of treatment success after short term ART in patients treated at a public provincial hospital in a RLS. Nevertheless, the observed high risk of accumulation of resistance mutations among patients failing treatment and the selection of multi-drug resistance mutations in some, remains of great concern for future treatment options and potential transmission to partners.