bluuebunny/crossref_metadata_2025_split huggingface dataset:
FCRL2 expression predicts IGHV mutation status and clinical progression in chronic lymphocytic leukemia
Authors: Li Fu Jun , Ding Shouluan , Pan Jicun , Shakhmatov Mikhail A. , Kashentseva Elena , Wu Jiongru , Li Yufeng , Soong Seng-jaw , Chiorazzi Nicholas , Davis Randall S. 
Published: February 2008

AbstractCD38 and ZAP-70 are both useful prognostic markers for B-cell chronic lymphocytic leukemia (CLL), but are variably discordant with IGHV mutation status. A total of 5 human Fc receptor–like molecules (FCRL1-5) have tyrosine-based immunoregulatory potential and are expressed by B-lineage subpopulations. To determine their prognostic potential in CLL, FCRL expression was compared with IGHV mutation status, CD38 and ZAP-70 expression, and clinical features from 107 patients. FCRL1, FCRL2, FCRL3, and FCRL5 were found at markedly higher levels on CLL cells bearing mutated IGHV genes than on unmutated CLL cells or CD19+ polyclonal B lymphocytes. Univariate comparisons found that similar to CD38 and ZAP-70, FCRL expression was strongly associated with IGHV mutation status; however, only FCRL2 maintained independent predictive value by multivariate logistic analysis. Strikingly, FCRL2 demonstrated 94.4% concordance with IGHV mutation compared with 76.6% for CD38 and 80.4% for ZAP-70. Compared with other indicators, FCRL2 was also superior at predicting the time to first therapy; the median treatment-free interval was 15.5 years for patients with high FCRL2 expression compared with 3.75 years for FCRL2-low patients. Our studies indicate that FCRL2 has robust predictive value for determining IGHV gene mutation status and clinical progression and thus may further improve prognostic definition in CLL.
Using quality scores and longer reads improves accuracy of Solexa read mapping
Authors: Smith Andrew D , Xuan Zhenyu , Zhang Michael Q 
Published: February 2008

Abstract

Background
Second-generation sequencing has the potential to revolutionize genomics and impact all areas of biomedical science. New technologies will make re-sequencing widely available for such applications as identifying genome variations or interrogating the oligonucleotide content of a large sample (e.g. ChIP-sequencing). The increase in speed, sensitivity and availability of sequencing technology brings demand for advances in computational technology to perform associated analysis tasks. The Solexa/Illumina 1G sequencer can produce tens of millions of reads, ranging in length from ~25–50 nt, in a single experiment. Accurately mapping the reads back to a reference genome is a critical task in almost all applications. Two sources of information that are often ignored when mapping reads from the Solexa technology are the 3' ends of longer reads, which contain a much higher frequency of sequencing errors, and the base-call quality scores.

Results
To investigate whether these sources of information can be used to improve accuracy when mapping reads, we developed the RMAP tool, which can map reads having a wide range of lengths and allows base-call quality scores to determine which positions in each read are more important when mapping. We applied RMAP to analyze data re-sequenced from two human BAC regions for varying read lengths, and varying criteria for use of quality scores. RMAP is freely available for downloading at http://rulai.cshl.edu/rmap/.

Conclusion
Our results indicate that significant gains in Solexa read mapping performance can be achieved by considering the information in 3' ends of longer reads, and appropriately using the base-call quality scores. The RMAP tool we have developed will enable researchers to effectively exploit this information in targeted re-sequencing projects.
The evolution of body size under environmental gradients in ectotherms: why should Bergmann's rule apply to lizards?
Authors: Pincheira-Donoso Daniel , Hodgson David J , Tregenza Tom 
Published: February 2008

AbstractBackgroundThe impact of environmental gradients on the evolution of life history traits is a central issue in macroecology and evolutionary biology. A number of hypotheses have been formulated to explain factors shaping patterns of variation in animal mass. One such example is Bergmann's rule, which predicts that body size will be positively correlated with latitude and elevation, and hence, with decreasing environmental temperatures. A generally accepted explanation for this phenotypic response is that as body mass increases, body surface area gets proportionally smaller, which contributes to reduced rates of heat-loss. Phylogenetic and non-phylogenetic evidence reveals that endotherms follow Bergmann's rule. In contrast, while previous non-phylogenetic studies supported this prediction in up to 75% of ectotherms, recent phylogenetic comparative analyses suggest that its validity for these organisms is controversial and less understood. Moreover, little attention has been paid to why some ectotherms conform to this rule, while others do not. Here, we investigate Bergmann's rule in the six main clades forming theLiolaemusgenus, one of the largest and most environmentally diverse genera of terrestrial vertebrates. A recent study conducted on some species belonging to four of these six clades concluded thatLiolaemusspecies follow Bergmann's rule, representing the only known phylogenetic support for this model in lizards. However, a later reassessment of this evidence, performed on one of the four analysed clades, produced contrasting conclusions.ResultsOur results fail to support Bergmann's rule inLiolaemuslizards. Non-phylogenetic and phylogenetic analyses showed that none of the studied clades experience increasing body size with increasing latitude and elevation.ConclusionMost physiological and behavioural processes in ectotherms depend directly upon their body temperature. In cold environments, adaptations to gain heat rapidly are under strong positive selection to allow optimal feeding, mating and predator avoidance. Therefore, evolution of larger body size in colder environments appears to be a disadvantageous thermoregulatory strategy. The repeated lack of support for Bergmann's rule in ectotherms suggests that this model should be recognized as a valid rule exclusively for endotherms.
Secretion of celiac disease autoantibodies after in vitro gliadin challenge is dependent on small-bowel mucosal transglutaminase 2-specific IgA deposits
Authors: Stenman Satumarja M , Lindfors Katri , Korponay-Szabo Ilma R , Lohi Olli , Saavalainen Päivi , Partanen Jukka , Haimila Katri , Wieser Herbert , Mäki Markku , Kaukinen Katri 
Published: February 2008

Abstract

Background
In celiac disease gluten, the disease-inducing toxic component in wheat, induces the secretion of autoantibodies which are targeted against transglutaminase 2 (TG2). These autoantibodies are produced in the small-intestinal mucosa, where they can be found deposited extracellularly below the epithelial basement membrane and around mucosal blood vessels. In addition, during gluten consumption these autoantibodies can also be detected in patients' serum but disappear from the circulation on a gluten-free diet. Interestingly, after adoption of a gluten-free diet the serum autoantibodies disappear from the circulation more rapidly than the small-intestinal mucosal autoantibody deposits. The toxicity of gluten and the secretion of the disease-specific autoantibodies have been widely studied in organ culture of small-intestinal biopsy samples, but results hitherto have been contradictory. Since the mucosal autoantibodies disappear slowly after a gluten-free diet, our aim was to establish whether autoantibody secretion to organ culture supernatants in treated celiac disease patient biopsies is related to the duration of the diet and further to the pre-existence of mucosal TG2-specific IgA deposits in the cultured biopsy samples.

Results
In the organ culture system conducted with biopsies derived from treated celiac disease patients, gliadin induced secretion of autoantibodies to culture supernatants, reduced epithelial cell height and increased the density of lamina proprial CD25+ cells. However, these changes could be demonstrated only in biopsies from short-term treated celiac disease patients, where the small-intestinal mucosal TG2-specific IgA autoantibody deposits were still present. Furthermore, in these biopsies autoantibody secretion could be stimulated fully only after a 48-hour gliadin challenge.

Conclusion
Our results show that studies focusing on the toxic effects of gliadin in the organ culture system should be carried out with biopsy samples from short-term treated celiac disease patients who are likely still to have mucosal IgA deposits present. In addition to providing an explanation for the discrepancies in previous publications, the present study also enables further validation of the organ culture method.
Fieldable genotyping of Bacillus anthracis and Yersinia pestis based on 25-loci Multi Locus VNTR Analysis
Authors: Ciammaruconi Andrea , Grassi Saverio , De Santis Riccardo , Faggioni Giovanni , Pittiglio Valentina , D'Amelio Raffaele , Carattoli Alessandra , Cassone Antonio , Vergnaud Gilles , Lista Florigio 
Published: February 2008

Abstract

Background
Anthrax and plague are diseases caused by Bacillus anthracis and Yersinia pestis respectively. These bacteria are etiological agents for worldwide zoonotic diseases and are considered among the most feared potential bioterror agents. Strain differentiation is difficult for these microorganisms because of their high intraspecies genome homogeneity. Moreover, fast strain identification and comparison with known genotypes may be crucial for naturally occurring outbreaks versus bioterrorist events discrimination.

Results
Thirty-nine B. anthracis and ten Y. pestis strains, representative of the species genetic diversity, were genotyped by Agilent 2100 Bioanalyzer using previously described Multiple Locus VNTR Analysis assays (MLVA). Results were compared to previous data obtained by standard genotyping system (capillary electrophoresis on automatic sequencer) and, when necessary, direct amplicon sequencing. A reference comparison table containing actual fragment sizes, sequencer sizes and Agilent sizes was produced.

Conclusion
In this report an automated DNA electrophoresis apparatus which provides a cheaper alternative compared to capillary electrophoresis approaches was applied for genotyping of B. anthracis and Y. pesti s. This equipment, uses pre-cast gels and provides easy transportation, low maintenance and overall general logistic requirements and costs, is easy to set up and provides rapid analysis. This platform is a candidate for on-site MLVA genotyping of biothreat agents as well as other bacterial pathogens. It is an alternative to the more expensive and demanding capillary electrophoresis methods, and to the less expensive but more time-consuming classical gel electrophoresis approach.
Study of the role of Mce3R on the transcription of mce genes of Mycobacterium tuberculosis
Authors: Santangelo María P , Blanco Federico C , Bianco María V , Klepp Laura I , Zabal Osvaldo , Cataldi Angel A , Bigi Fabiana 
Published: February 2008

Abstract

Background

mce3 is one of the four virulence-related mce operons of Mycobacterium tuberculosis. In a previous work we showed that the overexpression of Mce3R in Mycobacterium smegmatis and M. tuberculosis abolishes the expression of lacZ fused to the mce3 promoter, indicating that Mce3R represses mce3 transcription.

Results
We obtained a knockout mutant strain of M. tuberculosis H37Rv by inserting a hygromycin cassette into the mce3R gene. The mutation results in a significant increase in the expression of mce3 genes either in vitro or in a murine cell macrophages line as it was determined using promoter-lacZ fusions in M. tuberculosis. The abundance of mce1, mce2 and mce4 mRNAs was not affected by this mutation as it was demonstrated by quantitative RT-PCR. The mce3R promoter activity in the presence of Mce3R was significantly reduced compared with that in the absence of the regulator, during the in vitro culture of M. tuberculosis.

Conclusion
Mce3R repress the transcription of mce3 operon and self regulates its own expression but does not affect the transcription of mce1, mce2 and mce4 operons of M. tuberculosis.
AtMRP6/AtABCC6, an ATP-Binding Cassette transporter gene expressed during early steps of seedling development and up-regulated by cadmium in Arabidopsis thaliana
Authors: Gaillard Stéphane , Jacquet Hélène , Vavasseur Alain , Leonhardt Nathalie , Forestier Cyrille 
Published: February 2008

Abstract

Background
ABC proteins constitute one of the largest families of transporters found in all living organisms. In Arabidopsis thaliana, 120 genes encoding ABC transporters have been identified. Here, the characterization of one member of the MRP subclass, AtMRP6, is described.

Results
This gene, located on chromosome 3, is bordered by AtMRP3 and AtMRP7. Using real-time quantitative PCR (RT-Q-PCR) and the GUS reporter gene, we found that this gene is essentially expressed during early seedling development, in the apical meristem and at initiation point of secondary roots, especially in xylem-opposite pericycle cells where lateral roots initiate. The level of expression of AtMRP6 in response to various stresses was explored and a significant up-regulation after cadmium (Cd) treatment was detected. Among the three T-DNA insertion lines available from the Salk Institute library, two knock-out mutants, Atmrp6.1 and Atmrp6.2 were invalidated for the AtMRP6 gene. In the presence of Cd, development of leaves was more affected in the mutants than wild-type plants, whereas root elongation and ramification was comparable.

Conclusion
The position of AtMRP6 on chromosome 3, flanked by two other MRP genes, (all of which being induced by Cd) suggests that AtMRP6 is part of a cluster involved in metal tolerance, although additional functions in planta cannot be discarded.
Ankle blood pressure as a predictor of total and cardiovascular mortality
Authors: Hietanen Heikki , Pääkkönen Rauni , Salomaa Veikko 
Published: February 2008

Abstract

Background
The ankle blood pressure is commonly used as a ratio to the brachial blood pressure, called ankle-brachial index (ABI). Very few studies have considered the independent value of the ankle blood pressure without indexing it to the brachial blood pressure. We examined the value of ankle blood pressure, together with the exercise blood pressure, as a predictor of cardiovascular (CVD) and total mortality.

Methods
A prospective follow-up study of 3,858 consecutive ambulatory patients (mean age 51 years, 65,9% male) referred to a symptom-limited exercise test between August 1989 and December 1995. The cohort was followed up for all-cause and CVD mortality until December 31, 2004, by record linkage with the National Causes-of-Death Register. The independent value of ankle blood pressure as a predictor of cardiovascular and total mortality was assessed using Cox proportional hazards modelling.

Results
The average follow-up time was 14 years, during which 346 persons died, 108 of them due to CVD. Persons with normal (<140 mmHg) resting brachial blood pressure, ankle blood pressure < 175 mmHg and exercise blood pressure at moderate exercise level ≤215 mmHg at baseline investigation, had the best prognosis and were taken as the reference category. Among persons with elevated ankle blood pressure (≥175 mmHg) but normal or borderline resting brachial pressure and normal exercise blood pressure (≤215 mmHg) at moderate exercise level the multivariate-adjusted hazard ratios (HR, 95% confidence interval) for CVD and total mortality were 2.70 (1.52 – 4.80) and 2.13 (1.58 – 2.85), respectively. Similar and equally significant HRs were observed in persons with both elevated ankle blood pressure and elevated exercise blood pressure, as well as in those persons with elevated exercise blood pressure but ankle blood pressure < 175 mmHg.

Conclusion
These results suggest that the ankle blood pressure has an independent value as a marker of arterial stiffness or subclinical atherosclerosis and a risk of future mortality in middle-aged, asymptomatic persons.
Transmitted drug resistance, selection of resistance mutations and moderate antiretroviral efficacy in HIV-2: Analysis of the HIV-2 Belgium and Luxembourg database
Authors: Ruelle Jean , Roman François , Vandenbroucke Anne-Thérèse , Lambert Christine , Fransen Katrien , Echahidi Fedoua , Piérard Denis , Verhofstede Chris , Van Laethem Kristel , Delforge Marie-Luce , Vaira Dolorès , Schmit Jean-Claude , Goubau Patrick 
Published: February 2008

AbstractBackgroundGuidelines established for the treatment of HIV-1 infection and genotype interpretation do not apply for HIV-2. Data about antiretroviral (ARV) drug efficacy and resistance mutations is scarce.MethodsClinical data about HIV-2 infected patients in Belgium and Luxembourg were collected and the effect of ARV therapy on plasma viral load and CD4 counts were analysed. Viral RNA encoding for protease (PR) and reverse transcriptase (RT) from ARV-naïve and treated patients were sequenced.ResultsSixty-five HIV-2 infected patients were included in this cohort. Twenty patients were treated with 25 different ARV combinations in a total of 34 regimens and six months after the start of ARV therapy, only one third achieved viral load suppression. All of these successful regimens bar one contained protease inhibitors (PIs). Mean CD4 gains in the group of viral load suppressors and the group of patients treated with PI-containing regimens were respectively significantly higher than in the group of non-suppressors and the group of PI-sparing regimens. The most frequent mutations selected under therapy (compared to HIV-2 ROD) were V71I, L90M and I89V within PR. Within RT, they were M184V, Q151M, V111I and K65R. All of these mutations, except K65R and M184V, were also found in variable proportions in ARV-naïve patients.ConclusionDespite a high rate of ARV treatment failure, better virological and immunological results were achieved with PI-containing regimens. The analysis of polymorphic positions and HIV-2 specific mutations selected during therapy showed for the first time that transmission of drug resistant viruses has occurred in Belgium and Luxembourg. The high heterogeneity in ARV combinations reflects a lack of guidelines for the treatment of HIV-2 infection.
A review on slurry bioreactors for bioremediation of soils and sediments
Authors: Robles-González Ireri V , Fava Fabio , Poggi-Varaldo Héctor M 
Published: February 2008

Abstract
The aim of this work is to present a critical review on slurry bioreactors (SB) and their application to bioremediation of soils and sediments polluted with recalcitrant and toxic compounds. The scope of the review encompasses the following subjects: (i) process fundamentals of SB and analysis of advantages and disadvantages; (ii) the most recent applications of SB to laboratory scale and commercial scale soil bioremediation, with a focus on pesticides, explosives, polynuclear aromatic hydrocarbons, and chlorinated organic pollutants; (iii) trends on the use of surfactants to improve availability of contaminants and supplementation with degradable carbon sources to enhance cometabolism of pollutants; (iv) recent findings on the utilization of electron acceptors other than oxygen; (v) bioaugmentation and advances made on characterization of microbial communities of SB; (vi) developments on ecotoxicity assays aimed at evaluating bioremediation efficiency of the process.
From this review it can be concluded that SB is an effective ad situ and ex situ technology that can be used for bioremediation of problematic sites, such as those characterized by soils with high contents of clay and organic matter, by pollutants that are recalcitrant, toxic, and display hysteretic behavior, or when bioremediation should be accomplished in short times under the pressure and monitoring of environmental agencies and regulators. SB technology allows for the convenient manipulation and control of several environmental parameters that could lead to enhanced and faster treatment of polluted soils: nutrient N, P and organic carbon source (biostimulation), inocula (bioaugmentation), increased availability of pollutants by use of surfactants or inducing biosurfactant production inside the SB, etc. An interesting emerging area is the use of SB with simultaneous electron acceptors, which has demonstrated its usefulness for the bioremediation of soils polluted with hydrocarbons and some organochlorinated compounds. Characterization studies of microbial communities of SB are still in the early stages, in spite of their significance for improving reactor operation and design optimization.
We have identified the following niches of research needs for SB in the near and mid term future, inter alia: (i) application of SB with sequential and simultaneous electron acceptors to soils polluted with contaminants other than hydrocarbons (i.e., pesticides, explosives, etc.), (ii) evaluation of the technical feasibility of triphasic SB that use innocuous solvents to help desorbing pollutants strongly attached to soils, and in turn, to enhance their biodegradation, (iii) gaining deeper insight of microbial communities present in SB with the intensified application of molecular biology tools such as PCR-DGGE, PCR-TGGE, ARDRA, etc., (iv) development of more representative ecotoxicological assays to better assess the effectiveness of a given bioremediation process.
The influence of obesity on falls and quality of life
Authors: Fjeldstad Cecilie , Fjeldstad Anette S , Acree Luke S , Nickel Kevin J , Gardner Andrew W 
Published: February 2008

Abstract

Objective
To determine (1) whether obese older adults had higher prevalence of falls and ambulatory stumbling, impaired balance and lower health-related quality of life (HRQL) than their normal weight counterparts, and (2) whether the falls and balance measures were associated with HRQL in obese adults.

Methods
Subjects who had a body mass index (BMI) greater than 30 kg/m2 were classified into an obese group (n = 128) while those with BMI between 18.5 and 24.9 kg/m2 were included into a normal weight group (n = 88). Functional tests were performed to assess balance, and questionnaires were administered to assess history of falls, ambulatory stumbling, and HRQL.

Results
The obese group reported a higher prevalence of falls (27% vs. 15%), and ambulatory stumbling (32% vs. 14%) than the normal weight group. Furthermore, the obese group had lower HRQL, (p ≤ 0.05) for physical function (63 ± 27 vs. 75 ± 26; mean ± SD), role-physical (59 ± 40 vs. 74 ± 37), vitality (58 ± 23 vs. 66 ± 20), bodily pain (62 ± 25 vs. 74 ± 21) and general health (64 ± 19 vs. 70 ± 18). In the obese group, a history of falls was related (p ≤ 0.05) to lower scores in 4 domains of HRQL, and ambulatory stumbling was related (p ≤ 0.01) to 7 domains.

Conclusion
In middle-aged and older adults, obesity was associated with a higher prevalence of falls and stumbling during ambulation, as well as lower values in multiple domains of HRQL. Furthermore, a history of falls and ambulatory stumbling were related to lower measures of HRQL in obese adults.