bluuebunny/crossref_metadata_2025_split huggingface dataset:
Granulomatosis-associated common variable immunodeficiency disorder: a case–control studyversussarcoidosis
Authors: Bouvry Diane , Mouthon Luc , Brillet Pierre-Yves , Kambouchner Marianne , Ducroix Jean-Pierre , Cottin Vincent , Haroche Julien , Viallard Jean-Francois , Lazor Romain , Lebargy François , Tazi Abdellatif , Wallaert Benoît , Smail Amar , Pellegrin Jean-Luc , Nunes Hilario , Amoura Zahir , Cordier Jean-François , Valeyre Dominique , Naccache Jean-Marc ,   the Groupe Sarcoïdose Francophone
Published: August 2012

The aim of the present study was to investigate to what extent interstitial lung disease (ILD) in common variable immunodeficiency disorder (CVID)-associated granulomatous disease (GD) is similar to pulmonary sarcoidosis20 patients with CVID/GD were included in a retrospective study conducted by the Groupe Sarcoïdose Francophone. Medical records were centralised. Patients were compared with 60 controls with sarcoidosis.Clinical examination showed more frequent crackles in patients than controls (45%versus1.7%, respectively; p<0.001). On thoracic computed tomography scans, nodules (often multiple and with smooth margins), air bronchograms and halo signs were more frequent in patients than controls (80%versus42%, respectively; p=0.004) as well as bronchiectasis (65%versus23%, respectively; p<0.001). The micronodule distribution was perilymphatic in 100% of controls and in 42% of patients (p<0.001). Bronchoalveolar lavage analysis showed lower T-cell CD4/CD8 ratios in patients than in controls (mean±sd1.6±1.1versus5.3±4, respectively; p<0.01). On pathological analysis, nodules and consolidations corresponded to granulomatous lesions with or without lymphocytic disorders in most cases. Mortality was higher in patients than controls (30%versus0%, respectively) and resulted from common variable immunodeficiency complications.ILD in CVID/GD presents a specific clinical picture and evolution that are markedly different from those of sarcoidosis.
Sleep apnoea is a common occurrence in females
Authors: Franklin Karl A. , Sahlin Carin , Stenlund Hans , Lindberg Eva 
Published: August 2012

Obstructive sleep apnoea (OSA) is primarily regarded as a male disorder, presenting with snoring, daytime sleepiness and cardiovascular disease. We aimed to determine the frequency of sleep apnoea among females in the general population.We investigated 400 females from a population-based random sample of 10,000 females aged 20–70 yrs. They answered a questionnaire and performed overnight polysomnography.OSA (apnoea/hypopnoea index (AHI) ≥5) was found in 50% (95% CI 45–55%) of females aged 20–70 yrs. Sleep apnoea was related to age, obesity and hypertension, but not to daytime sleepiness. Severe sleep apnoea (AHI ≥30) was present in 14% (95% CI 8.1–21%) of females aged 55–70 yrs and in 31% (95% CI 12–50%) of obese females with a body mass index of ≥30 kg·m−2aged 55–70 yrs. Sleep apnoea with daytime sleepiness and sleep apnoea with hypertension were observed as two different phenotypes of OSA.OSA occurs in 50% of females aged 20–70 yrs. 20% of females have moderate and 6% severe sleep apnoea. Sleep apnoea in females is related to age, obesity and hypertension, but not to daytime sleepiness. When searching for sleep apnoea in females, females with hypertension or obesity should be investigated.
Reconstructing DNA copy number by joint segmentation of multiple sequences
Authors: Zhang Zhongyang , Lange Kenneth , Sabatti Chiara 
Published: August 2012

Abstract

Background
Variations in DNA copy number carry information on the modalities of genome evolution and mis-regulation of DNA replication in cancer cells. Their study can help localize tumor suppressor genes, distinguish different populations of cancerous cells, and identify genomic variations responsible for disease phenotypes. A number of different high throughput technologies can be used to identify copy number variable sites, and the literature documents multiple effective algorithms. We focus here on the specific problem of detecting regions where variation in copy number is relatively common in the sample at hand. This problem encompasses the cases of copy number polymorphisms, related samples, technical replicates, and cancerous sub-populations from the same individual.

Results
We present a segmentation method named generalized fused lasso (GFL) to reconstruct copy number variant regions. GFL is based on penalized estimation and is capable of processing multiple signals jointly. Our approach is computationally very attractive and leads to sensitivity and specificity levels comparable to those of state-of-the-art specialized methodologies. We illustrate its applicability with simulated and real data sets.

Conclusions
The flexibility of our framework makes it applicable to data obtained with a wide range of technology. Its versatility and speed make GFL particularly useful in the initial screening stages of large data sets.
Insights into the evolution of sorbitol metabolism: phylogenetic analysis of SDR196C family
Authors: Sola-Carvajal Agustín , García-García María I , García-Carmona Francisco , Sánchez-Ferrer Álvaro 
Published: August 2012

Abstract

Background
Short chain dehydrogenases/reductases (SDR) are NAD(P)(H)-dependent oxidoreductases with a highly conserved 3D structure and of an early origin, which has allowed them to diverge into several families and enzymatic activities. The SDR196C family (http://www.sdr-enzymes.org) groups bacterial sorbitol dehydrogenases (SDH), which are of great industrial interest. In this study, we examine the phylogenetic relationship between the members of this family, and based on the findings and some sequence conserved blocks, a new and a more accurate classification is proposed.

Results
The distribution of the 66 bacterial SDH species analyzed was limited to Gram-negative bacteria. Six different bacterial families were found, encompassing α-, β- and γ-proteobacteria. This broad distribution in terms of bacteria and niches agrees with that of SDR, which are found in all forms of life. A cluster analysis of sorbitol dehydrogenase revealed different types of gene organization, although with a common pattern in which the SDH gene is surrounded by sugar ABC transporter proteins, another SDR, a kinase, and several gene regulators.
According to the obtained trees, six different lineages and three sublineages can be discerned. The phylogenetic analysis also suggested two different origins for SDH in β-proteobacteria and four origins for γ-proteobacteria.
Finally, this subdivision was further confirmed by the differences observed in the sequence of the conserved blocks described for SDR and some specific blocks of SDH, and by a functional divergence analysis, which made it possible to establish new consensus sequences and specific fingerprints for the lineages and sub lineages.

Conclusion
SDH distribution agrees with that observed for SDR, indicating the importance of the polyol metabolism, as an alternative source of carbon and energy. The phylogenetic analysis pointed to six clearly defined lineages and three sub lineages, and great variability in the origin of this gene, despite its well conserved 3D structure. This suggests that SDH are very old and emerged early during the evolution. This study also opens up a new and more accurate classification of SDR196C family, introducing two numbers at the end of the family name, which indicate the lineage and the sublineage of each member, i.e, SDR196C6.3.
Characterization of biofilm-like structures formed by Pseudomonas aeruginosa in a synthetic mucus medium
Authors: Haley Cecily L , Colmer-Hamood Jane A , Hamood Abdul N 
Published: August 2012

Abstract

Background
The accumulation of thick stagnant mucus provides a suitable environment for the growth of Pseudomonas aeruginosa and Staphylococcus aureus within the lung alveoli of cystic fibrosis (CF) patients. These infections cause significant lung damage, leading to respiratory failure and death. In an artificial mucin containing medium ASM+, P. aeruginosa forms structures that resemble typical biofilms but are not attached to any surface. We refer to these structures as biofilm like structures (BLS). Using ASM+ in a static microtiter plate culture system, we examined the roles of mucin, extracellular DNA, environmental oxygen (EO2), and quorum sensing (QS) in the development of biofilm-like structures (BLS) by P. aeruginosa; and the effect of EO2 and P. aeruginosa on S. aureus BLS.

Results
Under 20% EO2, P. aeruginosa strain PAO1 produced BLS that resemble typical biofilms but are confined to the ASM+ and not attached to the surface. Levels of mucin and extracellular DNA within the ASM+ were optimized to produce robust well developed BLS. At 10% EO2, PAO1 produced thicker, more developed BLS, while under 0% EO2, BLS production was diminished. In contrast, the S. aureus strain AH133 produced well-developed BLS only under 20% EO2. In PAO1, loss of the QS system genes rhlI and rhlR affected the formation of BLS in ASM+ in terms of both structure and architecture. Whether co-inoculated into ASM+ with AH133, or added to established AH133 BLS, PAO1 eliminated AH133 within 48–56 h.

Conclusions
The thick, viscous ASM+, which contains mucin and extracellular DNA levels similar to those found in the CF lung, supports the formation of biofilm-like structures similar to the aggregates described within CF airways. Alterations in environmental conditions or in the QS genes of P. aeruginosa, as occurs naturally during the progression of CF lung infection, affect the architecture and quantitative structural features of these BLS. Thus, ASM+ provides an in vitro medium in which the effect of changing levels of substances produced by the host and the bacteria can be analyzed to determine the effect on such structures and on the susceptibility of the bacteria within the BLS to various treatments.
Differentiation in MALDI-TOF MS and FTIR spectra between two closely related species Acidovorax oryzae and Acidovorax citrulli
Authors: Wang Yanli , Zhou Qing , Li Bin , Liu Baoping , Wu Guoxing , Ibrahim Muhammad , Xie Guanlin , Li Hongye , Sun Guochang 
Published: August 2012

Abstract

Background
Two important plant pathogenic bacteria Acidovorax oryzae and Acidovorax citrulli are closely related and often not easy to be differentiated from each other, which often resulted in a false identification between them based on traditional methods such as carbon source utilization profile, fatty acid methyl esters, and ELISA detection tests. MALDI-TOF MS and Fourier transform infrared (FTIR) spectra have recently been successfully applied in bacterial identification and classification, which provide an alternate method for differentiating the two species.

Results
Characterization and comparison of the 10 A. oryzae strains and 10 A. citrulli strains were performed based on traditional bacteriological methods, MALDI-TOF MS, and FTIR spectroscopy. Our results showed that the identity of the two closely related plant pathogenic bacteria A. oryzae and A. citrulli was able to be confirmed by both pathogenicity tests and species-specific PCR, but the two species were difficult to be differentiated based on Biolog and FAME profile as well as 16 S rRNA sequence analysis. However, there were significant differences in MALDI-TOF MS and FTIR spectra between the two species of Acidovorax. MALDI-TOF MS revealed that 22 and 18 peaks were specific to A. oryzae and A. citrulli, respectively, while FTIR spectra of the two species of Acidovorax have the specific peaks at 1738, 1311, 1128, 1078, 989 cm-1 and at 1337, 968, 933, 916, 786 cm-1, respectively.

Conclusions
This study indicated that MALDI-TOF MS and FTIR spectra may give a new strategy for rapid bacterial identification and differentiation of the two closely related species of Acidovorax.
Over-expressions of AMPK subunits in ovarian carcinomas with significant clinical implications
Authors: Li Cuilan , Liu Vincent WS , Chiu Pui M , Chan David W , Ngan Hextan YS 
Published: August 2012

Abstract

Background

AMP-activated protein kinase (AMPK) has recently been considered as a potential target for cancer therapy. However, the expression status of various subunits of the heterotrimeric AMPK in human cancers is rarely reported. We decided to determine their expressions in ovarian carcinomas and their relationships with the disease.

Methods
Expressions and locations of the AMPK-α1, -α2, -β1, -β2, -γ1 and -γ2 were detected by quantitative PCR (Q-PCR) and immunohistochemical staining (IHC). Their expression levels in ovarian tumors were compared with normal controls and also correlated with clinicopathological parameters.

Results
Except AMPK-α1, expressions of the other five AMPK subunits are significantly higher in ovarian carcinomas as determined by Q-PCR. Although IHC detection of AMPK-γ1 and -γ2 were not successful, over-expressions of AMPK-α2, -β1, and -β2 were further confirmed by IHC. Over-expressions of various AMPK subunits occurred independently and were mainly detected in the cytoplasm. Interestingly, AMPK-α2 and -β1 were also detected in the nucleus and cell membrane, respectively. Clinical correlation analyses indicate that expressions of different AMPK subunits are associated with different subtypes of carcinoma. High expression of AMPK-α2 is significantly associated with endometrioid carcinomas. On the other hand, high expressions of AMPK-β and -γ subunits are associated with mucinous and serous carcinomas, respectively. Furthermore, high expressions of AMPK-β1 and -γ2 are also associated with early and late stages of disease, respectively. Finally, patients with high expression of AMPK-α2 had better prognosis.

Conclusions
Aberrant expressions of AMPK subunits may play important roles in ovarian carcinogenesis. Each AMPK subunit may have its own function other than just a component of the AMPK molecule. Correlations with clinical parameters suggest that expressions of AMPK subunits have different clinical implications in ovarian cancer development.
Protein markers of cancer-associated fibroblasts and tumor-initiating cells reveal subpopulations in freshly isolated ovarian cancer ascites
Authors: Wintzell My , Hjerpe Elisabet , Åvall Lundqvist Elisabeth , Shoshan Maria 
Published: August 2012

AbstractBackgroundIn ovarian cancer, massive intraperitoneal dissemination is due to exfoliated tumor cells in ascites. Tumor-initiating cells (TICs or cancer stem cells) and cells showing epithelial-mesenchymal-transition (EMT) are particularly implicated. Spontaneous spherical cell aggregates are sometimes observed, but although similar to those formed by TICsin vitro, their significance is unclear.MethodsCells freshly isolated from malignant ascites were separated into sphere samples (S-type samples, n=9) and monolayer-forming single-cell suspensions (M-type, n=18). Using western blot, these were then compared for expression of protein markers of EMT, TIC, and of cancer-associated fibroblasts (CAFs).ResultsS-type cells differed significantly from M-type by expressing high levels of E-cadherin and no or little vimentin, integrin-β3 or stem cell transcription factor Oct-4A. By contrast, M-type samples were enriched for CD44, Oct-4A and for CAF markers. Independently of M- and S-type, there was a strong correlation between TIC markers Nanog and EpCAM. The CAF marker α-SMA correlated with clinical stage IV. This is the first report on CAF markers in malignant ascites and on SUMOylation of Oct-4A in ovarian cancer.ConclusionsIn addition to demonstrating potentially high levels of TICs in ascites, the results suggest that the S-type population is the less tumorigenic one. Nanoghigh/EpCAMhighsamples represent a TIC subset which may be either M- or S-type, and which is separate from the CD44high/Oct-4Ahighsubset observed only in M-type samples. This demonstrates a heterogeneity in TIC populationsin vivowhich has practical implications for TIC isolation based on cell sorting. The biological heterogeneity will need to be addressed in future therapeutical strategies.
Prevalence of birth defects and risk-factor analysis from a population-based survey in Inner Mongolia, China
Authors: Zhang Xingguang , Li Su , Wu Siqintuya , Hao Xiaojin , Guo Shuyi , Suzuki Kota , Yokomichi Hiroshi , Yamagata Zentaro 
Published: August 2012

Abstract

Background
Birth Defects are a series of diseases that seriously affect children's health. Birth defects are generally caused by several interrelated factors. The aims of the article is to estimate the prevalence rate and types of birth defects in Inner Mongolia, China, to compare socio-demographic characteristics among the children with birth defects and to analyze the association between risk factors and birth defects.

Methods
Data used in this study were obtained through baseline survey of Inner Mongolia Birth Defects Program, a population-based survey conducted from 2005 to 2008. The survey used cluster sampling method in all 12 administrative districts of Inner Mongolia. Sampling size is calculated according to local population size at a certain percentage. All live births, stillbirths and abortions born from October 2005 to September 2008, whose families lived in Inner Mongolia at least one year, were included. The cases of birth defects were diagnosed by the clinical doctors according to their experiences with further laboratory tests if needed. The inclusion criteria of the cases that had already dead were decided according to death records available at local cites. We calculated prevalence rate and 95% confidence intervals of different groups. Outcome variable was the occurrence of birth defects and associations between risk factors and birth defects were analyzed by using Poisson regression analysis.

Results
976 children with birth defects were diagnosed. The prevalence rate of birth defects was 156.1 per 10000 births (95%CI: 146.3-165.8). The prevalence rate of neural tube defect (20.1 per 10000 births) including anencephaly(6.9 per 10000), spina bifida (10.6 per 10000), and encephalocele (2.7 per 10000) was the highest, followed by congenital heart disease (17.1 per 10000). The relative risk (RR) for maternal age less than 25 was 2.22 (95%CI: 2.05, 2.41). The RR of the ethnic Mongols was lower than Han Chinese (RR: 0.84; 95%CI: 0.80-0.89). The RR of the third and second pregnancy was significantly higher than the first pregnancy while a slight difference between the second and the first pregnancy was also found. Alcohol drinking of mothers, familial inheritance and living area were also found to be related to the occurrence of the birth defects.

Conclusions
Relatively higher birth defect rates were found in Inner Mongolia. This study found that maternal age less than 25, alcohol drinking, familiar inheritance, lower education level of mothers, times of pregnancies and living in rural areas may increase the risk of birth defects. Ethnic Mongols were less likely to have birth defects than Han Chinese.
Screening for type 2 diabetes in a high-risk population: study design and feasibility of a population-based randomized controlled trial
Authors: Klijs Bart , Otto Suzie J , Heine Robert J , van der Graaf Yolanda , Lous Jan J , de Koning Harry J 
Published: August 2012

Abstract

Background
We describe the design and present the results of the first year of a population-based study of screening for type 2 diabetes in individuals at high risk of developing the disease. High risk is defined as having abdominal obesity.

Methods
Between 2006 and 2007, 79,142 inhabitants of two Dutch municipalities aged 40–74 years were approached to participate in screening. Eligible participants had a self-reported waist circumference of ≥80 cm for women and ≥94 cm for men, and no known pre-existing diabetes. Of the respondents (n = 20,578; response rate 26%), 16,135 were abdominally obese. In total, 10,609 individuals gave written informed consent for participation and were randomized into either the screening (n = 5305) or the control arm (n = 5304). Participants in the screening arm were invited to have their fasting plasma glucose (FPG) measured and were referred to their general practitioner (GP) if it was ≥6.1 mmol/L. In addition, blood lipids were determined in the screening arm, because abdominal obesity is often associated with cardiovascular risk factors. Participants in both arms received written healthy lifestyle information. Between-group differences were analyzed with Chi-square tests and logistic regression (categorical variables) and unpaired t-tests (continuous variables).

Results
The screening attendance rate was 84.1%. Attending screening was associated with age at randomization (OR = 1.03, 95% CI 1.02-1.04), being married (OR = 1.57, 95% CI 1.33-1.83) and not-smoking currently (OR = 0.52, 95% CI 0.44-0.62). Of the individuals screened, 5.6% had hyperglycemia, and a further 11.6% had an estimated absolute cardiovascular disease risk of 5% or higher, according to the Systematic Coronary Risk Evaluation risk model. These participants were referred to their GP.

Conclusions
Self-reported home-assessed waist circumference could feasibly detect persons at high risk of hyperglycemia or cardiovascular disease. Continuation of the large-scale RCT is warranted to test the hypothesis that targeted population-based screening for type 2 diabetes leads to a significant reduction in cardiovascular morbidity and mortality.

Trial registration
ISRCTN75983009
Effects of brood size manipulation and common origin on phenotype and telomere length in nestling collared flycatchers
Authors: Voillemot Marie , Hine Kathryn , Zahn Sandrine , Criscuolo François , Gustafsson Lars , Doligez Blandine , Bize Pierre 
Published: August 2012

Abstract

Background
Evidence is accumulating that telomere length is a good predictor of life expectancy, especially early in life, thus calling for determining the factors that affect telomere length at this stage. Here, we investigated the relative influence of early growth conditions and origin (genetics and early maternal effects) on telomere length of collared flycatchers (Ficedula albicollis) at fledging. We experimentally transferred hatchlings among brood triplets to create reduced, control (i.e. unchanged final nestling number) and enlarged broods.

Results
Although our treatment significantly affected body mass at fledging, we found no evidence that increased sibling competition affected nestling tarsus length and telomere length. However, mixed models showed that brood triplets explained a significant part of the variance in body mass (18%) and telomere length (19%), but not tarsus length (13%), emphasizing that unmanipulated early environmental factors influenced telomere length. These models also revealed low, but significant, heritability of telomere length (h
2 = 0.09). For comparison, the heritability of nestling body mass and tarsus length was 0.36 and 0.39, respectively, which was in the range of previously published estimates for those two traits in this species.

Conclusion
Those findings in a wild bird population demonstrate that telomere length at the end of the growth period is weakly, but significantly, determined by genetic and/or maternal factors taking place before hatching. However, we found no evidence that the brood size manipulation experiment, and by extension the early growth conditions, influenced nestling telomere length. The weak heritability of telomere length suggests a close association with fitness in natural populations.