bluuebunny/crossref_metadata_2025 huggingface dataset:
Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements
Authors: Creanza Teresa M , Horner David S , D'Addabbo Annarita , Maglietta Rosalia , Mignone Flavio , Ancona Nicola , Pesole Graziano
Published: June 2009

Background

The identification of protein coding elements in sets of mammalian conserved elements is one of the major challenges in the current molecular biology research. Many features have been proposed for automatically distinguishing coding and non coding conserved sequences, making so necessary a systematic statistical assessment of their differences. A comprehensive study should be composed of an association study, i.e. a comparison of the distributions of the features in the two classes, and a prediction study in which the prediction accuracies of classifiers trained on single and groups of features are analyzed, conditionally to the compared species and to the sequence lengths.

Results

In this paper we compared distributions of a set of comparative and non comparative features and evaluated the prediction accuracy of classifiers trained for discriminating sequence elements conserved among human, mouse and rat species. The association study showed that the analyzed features are statistically different in the two classes. In order to study the influence of the sequence lengths on the feature performances, a predictive study was performed on different data sets composed of coding and non coding alignments in equal number and equally long with an ascending average length. We found that the most discriminant feature was a comparative measure indicating the proportion of synonymous nucleotide substitutions per synonymous sites. Moreover, linear discriminant classifiers trained by using comparative features in general outperformed classifiers based on intrinsic ones. Finally, the prediction accuracy of classifiers trained on comparative features increased significantly by adding intrinsic features to the set of input variables, independently on sequence length (Kolmogorov-Smirnov P-value ≤ 0.05).

Conclusion

We observed distinct and consistent patterns for individual and combined use of comparative and intrinsic classifiers, both with respect to different lengths of sequences/alignments and with respect to error rates in the classification of coding and non-coding elements. In particular, we noted that comparative features tend to be more accurate in the classification of coding sequences – this is likely related to the fact that such features capture deviations from strictly neutral evolution expected as a consequence of the characteristics of the genetic code.
Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application
Authors: Roubelakis Maria G , Zotos Pantelis , Papachristoudis Georgios , Michalopoulos Ioannis , Pappa Kalliopi I , Anagnou Nicholas P , Kossida Sophia
Published: June 2009

Background

microRNAs (miRNAs) are single-stranded RNA molecules of about 20–23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit translation. Predicting or verifying mRNA targets of specific miRNAs is a difficult process of great importance.

Results

GOmir is a novel stand-alone application consisting of two separate tools: JTarget and TAGGO. JTarget integrates miRNA target prediction and functional analysis by combining the predicted target genes from TargetScan, miRanda, RNAhybrid and PicTar computational tools as well as the experimentally supported targets from TarBase and also providing a full gene description and functional analysis for each target gene. On the other hand, TAGGO application is designed to automatically group gene ontology annotations, taking advantage of the Gene Ontology (GO), in order to extract the main attributes of sets of proteins. GOmir represents a new tool incorporating two separate Java applications integrated into one stand-alone Java application.

Conclusion

GOmir (by using up to five different databases) introduces miRNA predicted targets accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology clustering. Additionally, a reverse search initiated by a potential target can also be conducted. GOmir can freely be downloaded BRFAA.
Massive non-natural proteins structure prediction using grid technologies
Authors: Minervini Giovanni , Evangelista Giuseppe , Villanova Laura , Slanzi Debora , De Lucrezia Davide , Poli Irene , Luisi Pier Luigi , Polticelli Fabio
Published: June 2009

Background

The number of natural proteins represents a small fraction of all the possible protein sequences and there is an enormous number of proteins never sampled by nature, the so called "never born proteins" (NBPs). A fundamental question in this regard is if the ensemble of natural proteins possesses peculiar chemical and physical properties or if it is just the product of contingency coupled to functional selection. A key feature of natural proteins is their ability to form a well defined three-dimensional structure. Thus, the structural study of NBPs can help to understand if natural protein sequences were selected for their peculiar properties or if they are just one of the possible stable and functional ensembles.

Methods

The structural characterization of a huge number of random proteins cannot be approached experimentally, thus the problem has been tackled using a computational approach. A large random protein sequences library (2 × 104 sequences) was generated, discarding amino acid sequences with significant similarity to natural proteins, and the corresponding structures were predicted using Rosetta. Given the highly computational demanding problem, Rosetta was ported in grid and a user friendly job submission environment was developed within the GENIUS Grid Portal. Protein structures generated were analysed in terms of net charge, secondary structure content, surface/volume ratio, hydrophobic core composition, etc.

Results

The vast majority of NBPs, according to the Rosetta model, are characterized by a compact three-dimensional structure with a high secondary structure content. Structure compactness and surface polarity are comparable to those of natural proteins, suggesting similar stability and solubility. Deviations are observed in α helix-β strands relative content and in hydrophobic core composition, as NBPs appear to be richer in helical structure and aromatic amino acids with respect to natural proteins.

Conclusion

The results obtained suggest that the ability to form a compact, ordered and water-soluble structure is an intrinsic property of polypeptides. The tendency of random sequences to adopt α helical folds indicate that all-α proteins may have emerged early in pre-biotic evolution. Further, the lower percentage of aromatic residues observed in natural proteins has important evolutionary implications as far as tolerance to mutations is concerned.
Expression pattern divergence of duplicated genes in rice
Authors: Li Zhe , Zhang He , Ge Song , Gu Xiaocheng , Gao Ge , Luo Jingchu
Published: June 2009

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

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

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

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

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

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

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

Background

In 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.

Results

The 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.

Conclusion

TheP. 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

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

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

Access 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.
Enhanced anti-HCV activity of interferon alpha 17 subtype
Authors: Dubois Aurelie , François Catherine , Descamps Veronique , Fournier Carole , Wychowski Czeslaw , Dubuisson Jean , Castelain Sandrine , Duverlie Gilles
Published: June 2009

Background

Pegylated interferon alpha 2 (a or b) plus ribavirin is the most effective treatment of chronic hepatitis C but a large proportion of patients do not respond to therapy. So, it is interesting to improve the treatment efficacy. Interferon alpha is a type I interferon composed of 12 different subtypes. Each subtype signals by the Jak-Stat pathway but modulations in the antiviral activity was previously described.

Methods

Using the hepatitis C virus (HCV) culture system, we have tested the anti-HCV activity of each interferon alpha subtypes. We have analyzed the effect of each subtype on the HCV multiplication and the cell-signaling pathway for some subtypes.

Results

There were divergent effects of IFN alpha subtypes against HCV. We have found that IFN alpha 17 was three times more efficient than IFN alpha 2a on HCV. This efficiency was related to a stronger stimulation of the Jak-Stat pathway.

Conclusion

We suggest that IFN α17 should be tested therapeutically with a view to improving treatment efficacy.
Genetic predisposition to chikungunya – a blood group study in chikungunya affected families
Authors: Lokireddy Sudarsanareddy , Sarojamma Vemula , Ramakrishna Vadde
Published: June 2009

Chikungunya fever is a viral disease transmitted to humans by the bite of CHIKV virus infected Aedes mosquitoes. During monsoon outbreak of chikungunya fever, we carried out the genetic predisposition to chikungunya in disease affected 100 families by doing blood group (ABO) tests by focusing on individuals who were likely to have a risk of chikungunya and identified the blood group involved in susceptibility/resistance to chikungunya. In the present study, based on blood group antigens, the individuals were kept in four groups – A (108), B (98), AB (20) and O (243). The result obtained was showed all Rh positive blood group individuals are susceptible to chikungunya fever. Among ABO group, the blood group O +ve individuals are more susceptible to chikungunya than other blood groups. No blood group with Rh negative was affected with chikungunya, it indicates Rh -ve more resistance to chikungunya.
γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates
Authors: Wang Da-Peng , Wan Hao-Lei , Zhang Song , Yu Jun
Published: June 2009

Background

Over the past two decades, there have been several approximate methods that adopt different mutation models and used for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) based on protein-coding sequences across species or even different evolutionary lineages. Among them, MYN method (a Modified version of Yang-Nielsen method) considers three major dynamic features of evolving DNA sequences–bias in transition/transversion rate, nucleotide frequency, and unequal transitional substitution but leaves out another important feature: unequal substitution rates among different sites or nucleotide positions.

Results

We incorporated a new feature for analyzing evolving DNA sequences–unequal substitution rates among different sites–into MYN method, and proposed a modified version, namely γ (gamma)-MYN, based on an assumption that the evolutionary rate at each site follows a mode of γ-distribution. We applied γ-MYN to analyze the key estimator of selective pressure ω (Ka/Ks) and other relevant parameters in comparison to two other related methods, YN and MYN, and found that neglecting the variation of substitution rates among different sites may lead to biased estimations of ω. Our new method appears to have minimal deviations when relevant parameters vary within normal ranges defined by empirical data.

Conclusion

Our results indicate that unequal substitution rates among different sites have variable influences on ω under different evolutionary rates while both transition/transversion rate ratio and unequal nucleotide frequencies affect Ka and Ks thus selective pressure ω.

Reviewers

This paper was reviewed by Kateryna Makova, David A. Liberles (nominated by David H Ardell), Zhaolei Zhang (nominated by Mark Gerstein), and Shamil Sunyaev.
Abnormal autophagy, ubiquitination, inflammation and apoptosis are dependent upon lysosomal storage and are useful biomarkers of mucopolysaccharidosis VI
Authors: Tessitore Alessandra , Pirozzi Marinella , Auricchio Alberto
Published: June 2009

Background

Lysosomal storage diseases are characterized by intracellular accumulation of metabolites within lysosomes. Recent evidence suggests that lysosomal storage impairs autophagy resulting in accumulation of polyubiquitinated proteins and dysfunctional mitochondria, ultimately leading to apoptosis. We studied the relationship between lysosome storage and impairment of different intracellular pathways and organelle function in mucopolysaccharidosis VI, which is characterized by accumulation of dermatan sulfate and signs of visceral and skeletal but not cerebral involvement.

Results

We show lysosomal storage, impaired autophagy, accumulation of polyubiquitinated proteins, and mitochondrial dysfunction in fibroblasts from mucopolysaccharidosis VI patients. We observe similar anomalies, along with inflammation and cell death, in association with dermatan sulfate storage in the visceral organs of mucopolysaccharidosis VI rats, but not in their central nervous system where dermatan sulfate storage is absent. Importantly, we show that prevention of dermatan sulfate storage in the mucopolysaccharidosis VI rat visceral organs by gene transfer results in correction of abnormal autophagy, inflammation, and apoptosis, suggesting that dermatan sulfate accumulation impairs lysosomal ability to receive and degrade molecules and organelles from the autophagic pathway, thus leading to cell toxicity.

Conclusion

These results indicate that the non-lysosomal degradation pathways we found activated in mucopolysaccharidosis VI can be both targets of new experimental therapies and biomarkers for follow-up of existing treatments.
International Foot and Ankle Biomechanics Community (i‐FAB): past, present and beyond
Authors: Nester Christopher J , Leardini Alberto , Cavanagh Peter R , Rosenbaum Dieter , Burns Joshua
Published: June 2009

The International Foot and Ankle Biomechanics Community (i‐FAB) is an international collaborative activity which will have an important impact on the foot and ankle biomechanics community. It was launched on July 2nd 2007 at the foot and ankle session of the International Society of Biomechanics (ISB) meeting in Taipei, Taiwan. i‐FAB is driven by the desire to improve our understanding of foot and ankle biomechanics as it applies to health, disease, and the design, development and evaluation of foot and ankle surgery, and interventions such as footwear, insoles and surfaces.
Unusual presentation of Lynch Syndrome
Authors: Yu Veronica PCC , Novelli Marco , Payne Stewart J , Fisher Sam , Barnetson Rebecca A , Frayling Ian M , Barrett Ann , Goudie David , Ardern-Jones Audrey , Eeles Ros , Shanley Susan
Published: June 2009

Lynch Syndrome/HNPCC is a syndrome of cancer predisposition linked to inherited mutations of genes participating in post-replicative DNA mismatch repair (MMR). The spectrum of cancer associated with Lynch Syndrome includes tumours of the colorectum, endometrium, ovary, upper gastrointestinal tract and the urothelium although other cancers are rarely described. We describe a family of Lynch Syndrome with an hMLH1 mutation, that harbours an unusual tumour spectrum and its diagnostic and management challenges.
Extended adjuvant hormonal therapy with exemestane has no detrimental effect on the lipid profile of postmenopausal breast cancer patients: final results of the ATENA lipid substudy
Authors: Markopoulos Christos , Dafni Urania , Misitzis John , Zobolas Vasilios , Tzoracoleftherakis Evagelos , Koukouras Dimitrios , Xepapadakis Grigorios , Papadiamantis John , Venizelos Basileios , Antonopoulou Zoh , Gogas Helen
Published: June 2009

Introduction

Extended adjuvant endocrine therapy for breast cancer with aromatase inhibitors may potentially alter the lipid profile of postmenopausal patients and thus increase the risk of developing cardiovascular disease. In this study, a subprotocol of the ATENA (Adjuvant post-Tamoxifen Exemestane versus Nothing Applied) trial, we compared the effect of the steroidal aromatase inactivator exemestane on the lipid profile of postmenopausal patients with operable breast cancer, in the adjuvant setting, with that of observation alone after completion of 5 to 7 years of primary treatment with tamoxifen.

Methods

In this open-label, randomized, parallel-group study, 411 postmenopausal patients with operable breast cancer, who had been treated with tamoxifen for 5 to 7 years, were randomized to either 5 additional years of exemestane (25 mg/day; n = 211) or observation only (n = 200). Assessments of total cholesterol (TC), high-density lipoprotein (HDL), low-density lipoprotein (LDL), and total serum triglycerides (TRG) were performed at baseline and then during each follow-up visit, performed at either 6 or 12 months, according to the center's clinical practice, until completing 24 months in the study.

Results

TC and LDL levels increased significantly across time for both arms; TC increase was more pronounced for the observation arm, and that was sustained up to 24 months. HDL levels decreased significantly across time for the exemestane arm, whereas no significant change was detected across time for the observation arm. Triglyceride levels decreased significantly across time on both arms, with no difference detected in changes from baseline between the exemestane and the observation arms.

Conclusions

Exemestane lacks the beneficial effect of tamoxifen on lipids; however, sequential adjuvant treatment with exemestane in postmenopausal breast cancer patients after cessation of 5 to 7 years of tamoxifen does not appear to alter the lipid profile significantly compared with that of an observational arm.

Trial Registration

ClinicalTrials.gov ID: NCT00810706.
Leptin-signaling inhibition results in efficient anti-tumor activity in estrogen receptor positive or negative breast cancer
Authors: Rene Gonzalez Ruben , Watters Amber , Xu Yanbo , Singh Udai P , Mann David R , Rueda Bo R , Penichet Manuel L
Published: June 2009

Introduction

We have shown previously that treatment with pegylated leptin peptide receptor antagonist 2 (PEG-LPrA2) reduced the expression of vascular endothelial growth factor (VEGF), vascular endothelial growth factor receptor type 2 (VEGFR2) and growth of 4T1-breast cancer (BC) in syngeneic mice. In this investigation, PEG-LPrA2 was used to evaluate whether the inhibition of leptin signaling has differential impact on the expression of pro-angiogenic and pro-proliferative molecules and growth of human estrogen receptor-positive (ER+) and estrogen receptor-negative (ER-) BC xenografts hosted by immunodeficient mice.

Methods

To test the contribution of leptin signaling to BC growth and expression of leptin-targeted molecules, PEG-LPrA2 treatment was applied to severe immunodeficient mice hosting established ER+ (MCF-7 cells; ovariectomized/supplemented with estradiol) and ER- (MDA-MB231 cells) BC xenografts. To further assess leptin and PEG-LPrA2 effects on ER+ and ER- BC, the expression of VEGF and VEGFR2 (protein and mRNA) was investigated in cell cultures.

Results

PEG-LPrA2 more effectively reduced the growth of ER+ (>40-fold) than ER- BC (twofold) and expression of pro-angiogenic (VEGF/VEGFR2, leptin/leptin receptor OB-R, and IL-1 receptor type I) and pro-proliferative molecules (proliferating cell nuclear antigen and cyclin D1) in ER+ than in ER- BC. Mouse tumor stroma in ER+ BC expressed high levels of VEGF and leptin that was induced by leptin signaling. Leptin upregulated the transcriptional expression of VEGF/VEGFR2 in MCF-7 and MDA-MB231 cells.

Conclusions

These results suggest that leptin signaling plays an important role in the growth of both ER+ and ER- BC that is associated with the leptin regulation of pro-angiogenic and pro-proliferative molecules. These data provide support for the potential use of leptin-signaling inhibition as a novel treatment for ER+ and ER- BC.
Single-Agent Bortezomib in Previously Untreated Multiple Myeloma: Efficacy, Characterization of Peripheral Neuropathy, and Molecular Correlations With Response and Neuropathy
Authors: Richardson Paul G. , Xie Wanling , Mitsiades Constantine , Chanan-Khan Asher A. , Lonial Sagar , Hassoun Hani , Avigan David E. , Oaklander Anne Louise , Kuter David J. , Wen Patrick Y. , Kesari Santosh , Briemberg Hannah R. , Schlossman Robert L. , Munshi Nikhil C. , Heffner L. Thompson , Doss Deborah , Esseltine Dixie-Lee , Weller Edie , Anderson Kenneth C. , Amato Anthony A.
Published: June 2009

Purpose

To assess efficacy and safety of single-agent bortezomib in previously untreated patients with multiple myeloma, investigate prevalence of baseline and treatment-emergent polyneuropathy, and identify molecular markers associated with response and neuropathy.

Patients and Methods

Patients received bortezomib 1.3 mg/m2 on days 1, 4, 8, and 11, for up to eight 21-day cycles. A subset of patients underwent neurophysiologic evaluation pre- and post-treatment. Bone marrow aspirates were performed at baseline for exploratory whole-genome analyses.

Results

Among 64 patients, 41% had partial response or better, including 9% complete/near-complete responses; median duration of response was 8.4 months. Response rates did not differ in the presence or absence of adverse cytogenetics. After median follow-up of 29 months, median time to progression was 17.3 months. Median overall survival had not been reached; estimated 1-year survival was 92%. Thirty-two patients successfully underwent optional stem-cell transplantation. Bortezomib treatment was generally well tolerated. At baseline, 20% of patients had sensory polyneuropathy. Sensory polyneuropathy developed during treatment in 64% of patients (grade 3 in 3%), but proved manageable and resolved in 85% within a median of 98 days. Neurologic examination, neurophysiologic testing, and measurements of epidermal nerve fiber densities in 35 patients confirmed pretreatment sensory neuropathy in 20% and new or worsening neuropathy in 63%. Pharmacogenomic analyses identified molecular markers of response and treatment-emergent neuropathy, which will require future study.

Conclusion

Single-agent bortezomib is effective in previously untreated myeloma. Baseline myeloma-associated neuropathy seems more common than previously reported, and bortezomib-associated neuropathy, although a common toxicity, is reversible in most patients.
Novel TET2 Mutations Associated With UPD4q24 in Myelodysplastic Syndrome
Authors: Mohamedali Azim M. , Smith Alexander E. , Gaken Joop , Lea Nicholas C. , Mian Syed A. , Westwood Nigel B. , Strupp Corinna , Gattermann Norbert , Germing Ulrich , Mufti Ghulam J.
Published: June 2009

Purpose

Cryptic chromosomal aberrations, such as regions of uniparental disomy (UPD), have been shown to harbor homozygous mutations and are a common feature in myelodysplastic syndrome (MDS). We investigated the sequence integrity of 4q24 candidate tumor suppressor gene TET2 in MDS patients with UPD on chromosome 4.

Patients and Methods

The coding exons of TET2 were analyzed by 454 deep sequencing and Sanger sequencing in nine patients with UPD on 4q. Four patients had refractory cytopenia with multilineage dysplasia and ringed sideroblasts (RCMD-RS) and UPD4q24, and five patients (refractory anemia with excess blasts-II, n = 1; 5q– syndrome, n = 1; RCMD-RS, n = 1; refractory anemia, n = 1; refractory cytopenia with multilineage dysplasia, n = 1) had no UPD4q24.

Results

Mutations on TET2 were identified in all four patients with UPD4q24. These were localized to exons 3, 6, and 9 and resulted in two premature stop codons, one frameshift mutation, and one cysteine to glycine amino acid change. Mutant clone size varied between 30% and 85%. One patient with UPD outside of q24 (UPD4q28.3) displayed additional TET2 mutations, but these were at low clonal levels (13%, 4%, and 4% for a silent mutation, a 180-base pair deletion in exon 3, and a lysine to phenylalanine substitution in exon 11, respectively). The other patients who did not have UPD4q24 did not have verifiable TET2 mutations.

Conclusion

Our data identify novel TET2 mutations in a dominant clone in patients with UPD4q24. The presence of UPD4q24 and mutations in RCMD-RS patients may suggest specificity to this subtype. Our preliminary results need to be confirmed in a large cohort of all MDS subtypes.