bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exercise reduces airway sodium ion reabsorption in cystic fibrosis but not in exercise asthma
Authors: Schmitt L. , Wiebel M. , Frese F. , Dehnert C. , Zugck C. , Bärtsch P. , Mairbäurl H. 
Published: June 2010

When ventilating large volumes of air during exercise, airway fluid secretion is essential for airway function. Since these are impaired in cystic fibrosis and exercise-induced asthma, it was the aim of this study to determine how exercise affects airway Na+and Cl-transport and whether changes depend on exercise intensity.Nasal potential was measured in Ringer’s solution, with amiloride to block Na+transport, and in low chloride-containing isoproterenol to assess Cl-channels. Nasal potential was measured at rest and during submaximal and maximal bicycle ergometer exercise in individuals with cystic fibrosis, exercise-induced asthma and controls.At rest, nasal potential was significantly higher in cystic fibroses than in the others. Maximal exercise decreased nasal potentials in cystic fibrosis and controls but not in exercise asthma. Submaximal exercise decreased nasal potentials only in cystic fibrosis. Cl-transport was not affected.Our results indicate that nasal potentials and Na+transport were decreased by maximal exercise in healthy and cystic fibrosis, whereas submaximal exercise decreased potentials in cystic fibrosis only. Exercise did not affect nasal potentials in asthmatics. Decreased reabsorption during exercise might favour airway fluid secretion during hyperpnoea. This protective effect appears blunted in patients with exercise-induced asthma.
Reconsidering the arm span–height relationship in patients referred for spirometry
Authors: Capderou A. , Berkani M. , Becquemin M-H. , Zelter M. 
Published: June 2010

The interpretation of pulmonary function tests relies on reference values corrected for age, sex and height. Height may be difficult to measure in patients with deformities of the thoracic cage or those unable to stand up properly. Current practice is to substitute arm span to height, once corrected either by a fixed factor or by an age- and sex-dependent regression equation. However arm span may be difficult to measure in some patients.This study evaluated the relationship between arm span, measured height, height as mentioned on an identity document (ID), sex and age in a population of 2,452 Caucasian subjects with no chest or spine deformities.The present study demonstrates that age and sex have to be taken into account to best predict height from arm span or ID height values. The equations predicting height from ID height give the best diagnosis concordance compared to reference in males and females. Age correction does not improve concordance below 70 yrs.The estimation of height from ID height can be substituted to that from arm span when clinically relevant, providing ID height has been measured before the occurrence of stature problems.
PoGO: Prediction of Gene Ontology terms for fungal proteins
Authors: Jung Jaehee , Yi Gangman , Sukno Serenella A , Thon Michael R 
Published: June 2010

AbstractBackgroundAutomated protein function prediction methods are the only practical approach for assigning functions to genes obtained from model organisms. Many of the previously reported function annotation methods are of limited utility for fungal protein annotation. They are often trained only to one species, are not available for high-volume data processing, or require the use of data derived by experiments such as microarray analysis. To meet the increasing need for high throughput, automated annotation of fungal genomes, we have developed a tool for annotating fungal protein sequences with terms from the Gene Ontology.ResultsWe describe a classifier called PoGO (Prediction of Gene Ontology terms) that uses statistical pattern recognition methods to assign Gene Ontology (GO) terms to proteins from filamentous fungi. PoGO is organized as a meta-classifier in which each evidence source (sequence similarity, protein domains, protein structure and biochemical properties) is used to train independent base-level classifiers. The outputs of the base classifiers are used to train a meta-classifier, which provides the final assignment of GO terms. An independent classifier is trained for each GO term, making the system amenable to updating, without having to re-train the whole system. The resulting system is robust. It provides better accuracy and can assign GO terms to a higher percentage of unannotated protein sequences than other methods that we tested.ConclusionsOur annotation system overcomes many of the shortcomings that we found in other methods. We also provide a web server where users can submit protein sequences to be annotated.
Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor
Authors: Frijters Raoul , Fleuren Wilco , Toonen Erik JM , Tuckermann Jan P , Reichardt Holger M , van der Maaden Hans , van Elsas Andrea , van Lierop Marie-Jose , Dokter Wim , de Vlieg Jacob , Alkema Wynand 
Published: June 2010

Abstract

Background
Glucocorticoids (GCs) control expression of a large number of genes via binding to the GC receptor (GR). Transcription may be regulated either by binding of the GR dimer to DNA regulatory elements or by protein-protein interactions of GR monomers with other transcription factors. Although the type of regulation for a number of individual target genes is known, the relative contribution of both mechanisms to the regulation of the entire transcriptional program remains elusive. To study the importance of GR dimerization in the regulation of gene expression, we performed gene expression profiling of livers of prednisolone-treated wild type (WT) and mice that have lost the ability to form GR dimers (GRdim).

Results
The GR target genes identified in WT mice were predominantly related to glucose metabolism, the cell cycle, apoptosis and inflammation. In GRdim mice, the level of prednisolone-induced gene expression was significantly reduced compared to WT, but not completely absent. Interestingly, for a set of genes, involved in cell cycle and apoptosis processes and strongly related to Foxo3a and p53, induction by prednisolone was completely abolished in GRdim mice. In contrast, glucose metabolism-related genes were still modestly upregulated in GRdim mice upon prednisolone treatment. Finally, we identified several novel GC-inducible genes from which Fam107a, a putative histone acetyltransferase complex interacting protein, was most strongly dependent on GR dimerization.

Conclusions
This study on prednisolone-induced effects in livers of WT and GRdim mice identified a number of interesting candidate genes and pathways regulated by GR dimers and sheds new light onto the complex transcriptional regulation of liver function by GCs.
Mass spectrometry-based quantitative proteomic analysis of Salmonella enterica serovar Enteritidis protein expression upon exposure to hydrogen peroxide
Authors: Kim Kihoon , Yang Edward , Vu Gia-Phong , Gong Hao , Su Jing , Liu Fenyong , Lu Sangwei 
Published: June 2010

AbstractBackgroundSalmonellaenterica, a common food-borne bacterial pathogen, is believed to change its protein expression profile in the presence of different environmental stress such as that caused by the exposure to hydrogen peroxide (H2O2), which can be generated by phagocytes during infection and represents an important antibacterial mechanism of host cells. AmongSalmonellaproteins, the effectors ofSalmonellapathogenicity island 1 and 2 (SPI-1 and SPI-2) are of particular interest since they are expressed during host infectionin vivoand are important for invasion of epithelial cells and for replication in organs during systemic infection, respectively. However, the expression profiles of these proteins upon exposure to H2O2or to host cellsin vivoduring the established phase of systemic infection have not been extensively studied.ResultsUsing stable isotope labeling coupled with mass spectrometry, we performed quantitative proteomic analysis ofSalmonellaentericaserovar Enteritidis and identified 76 proteins whose expression is modulated upon exposure to H2O2. SPI-1 effector SipC was expressed about 3-fold higher and SopB was expressed approximately 2-fold lower in the presence of H2O2, while no significant change in the expression of another SPI-1 protein SipA was observed. The relative abundance of SipA, SipC, and SopB was confirmed by Western analyses, validating the accuracy and reproducibility of our approach for quantitative analysis of protein expression. Furthermore, immuno-detection showed substantial expression of SipA and SipC but not SopB in the late phase of infection in macrophages and in the spleen of infected mice.ConclusionsWe have identifiedSalmonellaproteins whose expression is modulated in the presence of H2O2. Our results also provide the first direct evidence that SipC is highly expressed in the spleen at late stage of salmonellosisin vivo. These results suggest a possible role of SipC and other regulated proteins in supporting survival and replication ofSalmonellaunder oxidative stress and during its systemic infectionin vivo.
The epidemiology of hematogenous vertebral osteomyelitis: a cohort study in a tertiary care hospital
Authors: Bhavan Kavita P , Marschall Jonas , Olsen Margaret A , Fraser Victoria J , Wright Neill M , Warren David K 
Published: June 2010

Abstract

Background
Vertebral osteomyelitis is a common manifestation of osteomyelitis in adults and associated with considerable morbidity. Limited data exist regarding hematogenous vertebral osteomyelitis. Our objective was to describe the epidemiology and management of hematogenous vertebral osteomyelitis.

Methods
We performed a 2-year retrospective cohort study of adult patients with hematogenous vertebral osteomyelitis at a tertiary care hospital.

Results
Seventy patients with hematogenous vertebral osteomyelitis were identified. The mean age was 59.7 years (±15.0) and 38 (54%) were male. Common comorbidities included diabetes (43%) and renal insufficiency (24%). Predisposing factors in the 30 days prior to admission included bacteremia (19%), skin/soft tissue infection (17%), and having an indwelling catheter (30%). Back pain was the most common symptom (87%). Seven (10%) patients presented with paraplegia. Among the 46 (66%) patients with a microbiological diagnosis, the most common organisms were methicillin-susceptible S. aureus [15 (33%) cases], and methicillin-resistant S. aureus [10 (22%)]. Among the 44 (63%) patients who had a diagnostic biopsy, open biopsy was more likely to result in pathogen recovery [14 (93%) of 15 with open biopsy vs. 14 (48%) of 29 with needle biopsy; p = 0.003]. Sixteen (23%) patients required surgical intervention for therapeutic purposes during admission.

Conclusions
This is one of the largest series of hematogenous vertebral osteomyelitis. A microbiological diagnosis was made in only approximately two-thirds of cases. S. aureus was the most common causative organism, of which almost half the isolates were methicillin-resistant.
The optimal number of lymph nodes examined in stage II colorectal cancer and its impact of on outcomes
Authors: Choi Hok Kwok , Law Wai Lun , Poon Jensen TC 
Published: June 2010

Abstract

Background
Lymph node status is the most important prognostic factor for colorectal cancer. The number of lymph nodes that should be histologically examined has been controversial. The aims of this study were to assess the impact of the number of lymph nodes examined on survival of patients with stage II colorectal cancer and to determine the optimal number of lymph nodes that should be examined.

Methods
The study included 664 patients who underwent resection for stage II colorectal cancer. The clinical and histopathologic data of the patients were prospectively collected and analyzed.

Results
The median number of lymph nodes examined was 12 (range: 1 to 58). The 5-year disease free survival rate was significantly higher for patients with 12 or more lymph nodes examined compared to those with less than 12 lymph nodes examined. The significant difference in 5-year disease free survival persisted if the dividing number increased progressively from 12 to 23. However, the difference in survival was most significant (lowest p value and highest hazard ratio) for the number 21. The 5-year disease free survival of patients with 21 or more lymph nodes examined was 80% whereas that of patients with less than 21 lymph nodes examined was 60% (p = 0.001, hazard ratio 2.08). Multivariate analysis showed that 21 or more lymph nodes examined was a factor that independently influenced survival. The 5-year disease free survival also increased progressively with the number of lymph node examined up to the number 21. After the number 21, the survival rate did not increase further. It was likely that 21 was the optimal number, at and above which the chance of lymph node metastasis was minimal.

Conclusions
The number of lymph nodes examined in colorectal cancer specimen significantly influences survival. It is recommended that at least 21 lymph nodes should be examined for accurate diagnosis of stage II colorectal cancer.
Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor
Authors: Garau Gianpiero , Muzzolini Laura , Tornaghi Paola , Degano Massimo 
Published: June 2010

Abstract

Background
Pyrimidine-preferring N-ribohydrolases (CU-NHs) are a class of Ca2+-dependent enzymes that catalyze the hydrolytic cleavage of the N-glycosidic bond in pyrimidine nucleosides. With the exception of few selected organisms, their physiological relevance in prokaryotes and eukaryotes is yet under investigation.

Results
Here, we report the first crystal structure of a CU-NH bound to a competitive inhibitor, the complex between the Escherichia coli enzyme RihA bound to 3, 4-diaminophenyl-iminoribitol (DAPIR) to a resolution of 2.1 Å. The ligand can bind at the active site in two distinct orientations, and the stabilization of two flexible active site regions is pivotal to establish the interactions required for substrate discrimination and catalysis.

Conclusions
A comparison with the product-bound RihA structure allows a rationalization of the structural rearrangements required for an enzymatic catalytic cycle, highlighting a substrate-assisted cooperative motion, and suggesting a yet overlooked role of the conserved His82 residue in modulating product release. Differences in the structural features of the active sites in the two homologous CU-NHs RihA and RihB from E. coli provide a rationale for their fine differences in substrate specificity. These new findings hint at a possible role of CU-NHs in the breakdown of modified nucleosides derived from RNA molecules.
Analysis of factors influencing the outpatient workload at Chinese health centres
Authors: Xu Jing , Wang Wenxin , Li Yongbin , Zhang Juan , Pavlova Milena , Liu Hua , Yin Ping , Lu Zuxun 
Published: June 2010

Abstract

Background
Although the community health service system is now established in China, the utilisation of the community health service institutions is low due to the lack of a gate-keeping role of the primary health service providers and referrals among the three-tiered health service institutions. In addition to this, patients who can afford to pay, often seek best services in big hospitals to guarantee the quality of care. Thus, the need of guiding the patients to the community health services and increasing the utilisation of the community health service institutions is becoming an urgent problem, which hinders the future development of community health services. This study focuses on the question of how to increase the utilisation of Chinese community health centres (HCs).

Methods
A cross-sectional Base-line Survey of Chinese City Community Health Service System Building using the multi-staged cluster sampling was conducted to collect data from all HCs in 28 key contact cities. Relevant indicators of totally 1790 HCs were analysed. The statistical methods included ANONVA and logistic regression.

Results and Conclusions
The analysis suggested several key factors for increasing the outpatient workload (OW) at the HCs: establishing an adequate referral system among the different levels of the health system; enhancing the qualification of health personnel and increasing the compensation by the health insurance for services provided at HCs. Other key factors with a positive effect on the OW included: the government ownership of the HCs, the scale of the institutions, the medical equipment used, the mix of health services provided, and the women in childbearing age in the residence.
Household headship and child death: Evidence from Nepal
Authors: Adhikari Ramesh , Podhisita Chai 
Published: June 2010

Abstract

Background
Nepal has seen substantial improvements in its reproductive health outcomes, but infant and child mortality are still high. This study attempts to examine the prevalence and factors influencing the experience of child death of mothers who have given birth during a five-year period. More specifically, this paper aims to investigate whether household headship has an impact on child death in Nepal.

Methods
This paper reports on data drawn from the Nepal Demographic and Health Survey (NDHS 2006), a nationally representative sample survey. The analysis is confined to women who had given birth during the five years preceding the survey (n = 4066). The association between experience of child death of mother and the explanatory variables was assessed via bivariate analysis using a chi-square test. The variables were also examined using multivariate analysis (binary logistic regression) to assess the net effect of household headship on child death after controlling for the other variables.

Results
Out of all the mothers who had given birth during a five-years period, 3,229 (79.4%) were from male-headed households; the remaining 837 (20.6%) were from female-headed households. A significantly higher proportion of mothers from male-headed households (6.5%) than female-headed households (4.5%) had experienced the death of a child over the five years preceding the survey. Several socio-demographic, economic, and cultural variables were significant predicators for death of a child. For instance, women who had given birth to three or more children and who were Hindu were more likely to experience a child's death than were their counterparts. On the other hand, women who were literate, who had ever used family planning methods, who had visited a health facility, who utilized antenatal care for the last pregnancy, and who were from female-headed households were less likely to see a child die than were women in their comparison group. Notably, keeping all other control variables constant in the logistic model, women from female-headed households were 31 percent less likely to experience the death of a child (odds ratio = 0.69) than were women from male-headed households.

Conclusion
The death of children is not uncommon in Nepal. No single factor can account for the high child mortality in the country; many factors contribute to the problem. After controlling for other variables, this study found that, among many other factors, household headship was a strong predictor. Programs seeking to help remedy this problem should focus on the issues identified here regarding women's autonomy, such as reducing the number of children born, increasing women's literacy status, increasing the use of family planning, increasing the use of antenatal care, and increasing female household headship so that child mortality will decrease and the overall well-being of the family can be maintained and enhance.
Proteomic analysis of the fish pathogen Flavobacterium columnare
Authors: Dumpala Pradeep R , Gülsoy Nagihan , Lawrence Mark L , Karsi Attila 
Published: June 2010

Abstract

Background

Flavobacterium columnare causes columnaris disease in cultured and wild fish populations worldwide. Columnaris is the second most prevalent bacterial disease of commercial channel catfish industry in the United States. Despite its economic importance, little is known about the expressed proteins and virulence mechanisms of F. columnare. Here, we report the first high throughput proteomic analysis of F. columnare using 2-D LC ESI MS/MS and 2-DE MALDI TOF/TOF MS.

Results
Proteins identified in this study and predicted from the draft F. columnare genome were clustered into functional groups using clusters of orthologous groups (COGs), and their subcellular locations were predicted. Possible functional relations among the identified proteins were determined using pathway analysis. The total number of unique F. columnare proteins identified using both 2-D LC and 2-DE approaches was 621, of which 10.95% (68) were identified by both methods, while 77.29% (480) and 11.76% (73) were unique in 2-D LC and 2-DE, respectively. COG groupings and subcellular localizations were similar between our data set and proteins predicted from the whole genome. Twenty eight pathways were significantly represented in our dataset (P < 0.05).

Conclusion
Results from this study provide experimental evidence for many proteins that were predicted from the F. columnare genome annotation, and they should accelerate functional and comparative studies aimed at understanding virulence mechanisms of this important pathogen.
Disability status and quality of life in multiple sclerosis: non-linearity of the Expanded Disability Status Scale (EDSS)
Authors: Twork Sabine , Wiesmeth Susanne , Spindler Milena , Wirtz Markus , Schipper Sabine , Pöhlau Dieter , Klewer Jörg , Kugler Joachim 
Published: June 2010

Abstract

Background
Progression in disability as measured by increase in the Expanded Disability Status Scale (EDSS) is commonly used as outcome variable in clinical trials concerning multiple sclerosis (MS). In this study, we addressed the question, whether there is a linear relationship between disability status and health related quality of life (HRQOL) in MS.

Methods
7305 MS patients were sent a questionnaire containing a German version of the "Multiple Sclerosis Quality of Life (MSQOL)-54" and an assessment of self-reported disability status analogous to the EDSS. 3157 patients participated in the study. Patients were allocated to three groups according to disability status.

Results
Regarding the physical health composite and the mental health composite as well as most MSQOL-54 subscales, the differences between EDSS 4.5-6.5 and EDSS >= 7 were clearly smaller than the differences between EDSS <= 4 and EDSS 4.5-6.5.

Conclusion
These results indicate a non-linear relationship between disability status and HRQOL in MS. The EDSS does not seem to be interval scaled as is commonly assumed. Consequently, absolute increase in EDSS does not seem to be a suitable outcome variable in MS studies.