bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cystic fibrosis neutrophils have normal intrinsic reactive oxygen species generation
Authors: McKeon D. J. , Cadwallader K. A. , Idris S. , Cowburn A. S. , Pasteur M. C. , Barker H. , Haworth C. S. , Bilton D. , Chilvers E. R. , Condliffe A. M. 
Published: October 2009

Previous studies have identified abnormalities in the oxidative responses of the neutrophil in cystic fibrosis (CF), but it is unclear whether such changes relate to loss of membrane cystic fibrosis transmembrane conductance regulator (CFTR) or to the inflammatory environment present in this disease. The aim of the present study was to determine whether neutrophils from CF patients demonstrate an intrinsic abnormality of the respiratory burst.The respiratory burst activity of neutrophils isolated from stable ΔF508 homozygote CF patients and matched healthy controls was quantified by both chemiluminscence and cytochrome C reduction. Expression of NADPH oxidase components and CFTR was determined by Western blotting and RT-PCR.The oxidative output from neutrophils from CF in response to receptor-linked and particulate stimuli did not differ from that of controls. Expression of NADPH oxidase components was identical in CF and non-CF neutrophils. While low levels of CFTR mRNA could be identified in the normal human neutrophil, we were unable to detect CFTR protein in human neutrophil lysates or immunoprecipitates.CFTR has no role in controlling neutrophil oxidative activity; previously reported differences in neutrophil function between CF and non-CF subjects most likely relate to the inflammatory milieu from which the cells were isolated.
No evidence for interstitial lung oedema by extensive pulmonary function testing at 4,559 m
Authors: Dehnert C. , Luks A. M. , Schendler G. , Menold E. , Berger M. M. , Mairbäurl H. , Faoro V. , Bailey D. M. , Castell C. , Hahn G. , Vock P. , Swenson E. R. , Bärtsch P. 
Published: October 2009

The aim of the present study was to better understand previously reported changes in lung function at high altitude.Comprehensive pulmonary function testing utilising body plethysmography and assessment of changes in closing volume were carried out at sea level and repeatedly over 2 days at high altitude (4,559 m) in 34 mountaineers.In subjects without high-altitude pulmonary oedema (HAPE), there was no significant difference in total lung capacity, forced vital capacity, closing volume and lung compliance between low and high altitude, whereas lung diffusing capacity for carbon monoxide increased at high altitude. Bronchoconstriction at high altitude could be excluded as the cause of changes in closing volume because there was no difference in airway resistance and bronchodilator responsiveness to salbutamol. There were no significant differences in these parameters between mountaineers with and without acute mountain sickness. Mild alveolar oedema on radiographs in HAPE was associated only with minor decreases in forced vital capacity, diffusing capacity and lung compliance and minor increases in closing volume.Comprehensive lung function testing provided no evidence of interstitial pulmonary oedema in mountaineers without HAPE during the first 2 days at 4,559 m. Data obtained in mountaineers with early mild HAPE suggest that these methods may not be sensitive enough for the detection of interstitial pulmonary fluid accumulation.
Transcriptomic and proteomic analyses of seasonal photoperiodism in the pea aphid
Authors: Le Trionnaire G , Francis F , Jaubert-Possamai S , Bonhomme J , De Pauw E , Gauthier J-P , Haubruge E , Legeai F , Prunier-Leterme N , Simon J-C , Tanguy S , Tagu D 
Published: October 2009

AbstractBackgroundAphid adaptation to harsh winter conditions is illustrated by an alternation of their reproductive mode. Aphids detect photoperiod shortening by sensing the length of the night and switch from viviparous parthenogenesis in spring and summer, to oviparous sexual reproduction in autumn. The photoperiodic signal is transduced from the head to the reproductive tract to change the fate of the future oocytes from mitotic diploid embryogenesis to haploid formation of gametes. This process takes place in three consecutive generations due to viviparous parthenogenesis. To understand the molecular basis of the switch in the reproductive mode, transcriptomic and proteomic approaches were used to detect significantly regulated transcripts and polypeptides in the heads of the pea aphidAcyrthosiphon pisum.ResultsThe transcriptomic profiles of the heads of the first generation were slightly affected by photoperiod shortening. This suggests that trans-generation signalling between the grand-mothers and the viviparous embryos they contain is not essential. By analogy, many of the genes and some of the proteins regulated in the heads of the second generation are implicated in visual functions, photoreception and cuticle structure. The modification of the cuticle could be accompanied by a down-regulation of theN-β-alanyldopamine pathway and desclerotization. InDrosophila, modification of the insulin pathway could cause a decrease of juvenile hormones in short-day reared aphids.ConclusionThis work led to the construction of hypotheses for photoperiodic regulation of the switch of the reproductive mode in aphids.
Glycogenome expression dynamics during mouse C2C12 myoblast differentiation suggests a sequential reorganization of membrane glycoconjugates
Authors: Janot Mathilde , Audfray Aymeric , Loriol Céline , Germot Agnès , Maftah Abderrahman , Dupuy Fabrice 
Published: October 2009

Abstract

Background
Several global transcriptomic and proteomic approaches have been applied in order to obtain new molecular insights on skeletal myogenesis, but none has generated any specific data on glycogenome expression, and thus on the role of glycan structures in this process, despite the involvement of glycoconjugates in various biological events including differentiation and development. In the present study, a quantitative real-time RT-PCR technology was used to profile the dynamic expression of 375 glycogenes during the differentiation of C2C12 myoblasts into myotubes.

Results
Of the 276 genes expressed, 95 exhibited altered mRNA expression when C2C12 cells differentiated and 37 displayed more than 4-fold up- or down-regulations. Principal Component Analysis and Hierarchical Component Analysis of the expression dynamics identified three groups of coordinately and sequentially regulated genes. The first group included 12 down-regulated genes, the second group four genes with an expression peak at 24 h of differentiation, and the last 21 up-regulated genes. These genes mainly encode cell adhesion molecules and key enzymes involved in the biosynthesis of glycosaminoglycans and glycolipids (neolactoseries, lactoseries and ganglioseries), providing a clearer indication of how the plasma membrane and extracellular matrix may be modified prior to cell fusion. In particular, an increase in the quantity of ganglioside GM3 at the cell surface of myoblasts is suggestive of its potential role during the initial steps of myogenic differentiation.

Conclusion
For the first time, these results provide a broad description of the expression dynamics of glycogenes during C2C12 differentiation. Among the 37 highly deregulated glycogenes, 29 had never been associated with myogenesis. Their biological functions suggest new roles for glycans in skeletal myogenesis.
Newly formed cystic lesions for the development of pneumomediastinum in Pneumocystis jirovecii pneumonia
Authors: Cho Ju-Yeon , Kim Dong-Min , Kwon Yong Eun , Yoon Sung Ho , Lee Seung Il 
Published: October 2009

Abstract

Background

Pneumocystis jirovecii, formerly named Pneumocystis carinii, is one of the most common opportunistic infections in human immunodeficiency virus (HIV)-infected patients.

Case presentations
We encountered two cases of spontaneous pneumomediastinum with subcutaneous emphysema in HIV-infected patients being treated for Pneumocystis jirovecii pneumonia with trimethoprim/sulfamethoxazole.

Conclusion
Clinicians should be aware that cystic lesions and bronchiectasis can develop in spite of trimethoprim/sulfamethoxazole treatment for P. jirovecii pneumonia. The newly formed bronchiectasis and cyst formation that were noted in follow up high resolution computed tomography (HRCT) but were not visible on HRCT at admission could be risk factors for the development of pneumothorax or pneumomediastinum with subcutaneous emphysema in HIV-patients.
Motorcyclists' reactions to safety helmet law: a qualitative study
Authors: Zamani-Alavijeh Fereshteh , Niknami Shamsaddin , Mohammadi Eesa , Montazeri Ali , Ghofranipour Fazlollah , Ahmadi Fazlollah , Bazargan Shahrzad Hejazi 
Published: October 2009

Abstract

Background
Extensive body of the literature reveals that proper use of helmets is an effective way to reduce the severity of injuries and fatalities among motorcyclists. However, many motorcyclists do not use safety helmet properly. This study aimed to empirically explore reactions of motorcyclists to the safety helmet laws, in Iran.

Methods
Qualitative data were collected via four focus groups and 11 in-depth interviews. Participants were 28 male motorcyclists who never used a safety helmet during rides, and 4 male police officers. All transcripts, codes and categories were read for several times to exhaust identifiable major themes. During this process data were reduced from text to codes and themes.

Results
Five major themes emerged from the data analyses, including themes related to the following: (1) circumventing or dodging police officers; (2) simulating a helmet wearing behavior; (3) accepting the probability of receiving a ticket; (4) taking advantage of the police neglect and carelessness; and (5) using a cheap or convenient helmet.

Conclusion
Our findings suggest certain levels of reckless driving among the participating motorcyclists in this study. They also point to a system of law enforcement that operates haphazardly and fails to consistently penalize those who deviate from it. Further studies are needed to investigate how "risks" are perceived and relate to "reactions", and how a 'culture of masculinity' may encourage risk tolerance and a disposition toward lawlessness and carelessness among male motorcyclists. Also, there is a need for the development and implementation of multidimensional interventions that would offer socio-culturally sensitive educational and motivational messages to the motorcyclists and the in-service traffic-enforcement officers in Iran.
Machine learning integration for predicting the effect of single amino acid substitutions on protein stability
Authors: Özen Ayşegül , Gönen Mehmet , Alpaydın Ethem , Haliloğlu Türkan 
Published: October 2009

AbstractBackgroundComputational prediction of protein stability change due to single-site amino acid substitutions is of interest in protein design and analysis. We consider the following four ways to improve the performance of the currently available predictors: (1) We include additional sequence- and structure-based features, namely, the amino acid substitution likelihoods, the equilibrium fluctuations of the alpha- and beta-carbon atoms, and the packing density. (2) By implementing different machine learning integration approaches, we combine information from different features or representations. (3) We compare classification vs. regression methods to predict the sign vs. the output of stability change. (4) We allow a reject option for doubtful cases where the risk of misclassification is high.ResultsWe investigate three different approaches: early, intermediate and late integration, which respectively combine features, kernels over feature subsets, and decisions. We perform simulations on two data sets: (1) S1615 is used in previous studies, (2) S2783 is the updated version (as of July 2, 2009) extracted also from ProTherm. For S1615 data set, our highest accuracy using both sequence and structure information is 0.842 on cross-validation and 0.904 on testing using early integration. Newly added features, namely, local compositional packing and the mobility extent of the mutated residues, improve accuracy significantly with intermediate integration. For S2783 data set, we also train regression methods to estimate not only the sign but also the amount of stability change and apply risk-based classification to reject when the learner has low confidence and the loss of misclassification is high. The highest accuracy is 0.835 on cross-validation and 0.832 on testing using only sequence information. The percentage of false positives can be decreased to less than 0.005 by rejecting 10 per cent using late integration.ConclusionWe find that in both early and late integration, combining inputs or decisions is useful in increasing accuracy. Intermediate integration allows assessing the contributions of individual features by looking at the assigned weights. Overall accuracy of regression is not better than that of classification but it has less false positives, especially when combined with the reject option. The server for stability prediction for three integration approaches and the data sets are available athttp://www.prc.boun.edu.tr/appserv/prc/mlsta.
Identification of a haplotype block in the 5q31 cytokine gene cluster associated with the susceptibility to severe malaria
Authors: Naka Izumi , Nishida Nao , Patarapotikul Jintana , Nuchnoi Pornlada , Tokunaga Katsushi , Hananantachai Hathairad , Tsuchiya Naoyuki , Ohashi Jun 
Published: October 2009

Abstract

Background
It has been previously demonstrated that a single nucleotide polymorphism (SNP) in the IL13 promoter region, IL13 -1055T>C (rs1800925), was associated with susceptibility to severe malaria in Thais. In the present study, fine association mapping for a cytokine gene cluster including IL4, IL5, and IL13 on chromosome 5q31 was conducted using the same malaria subjects to refine the region containing a primary variant or a haplotype susceptible to severe malaria.

Methods
A total of 82 SNPs spanning 522 kb of the 5q31 region were analysed in 368 patients with Plasmodium falciparum malaria (203 mild malaria and 165 severe malaria patients).

Results
Only rs1881457 located in the promoter region of IL13, which is in linkage disequilibrium with rs1800925 (r2 = 0.73), showed a significant association with severe malaria after adjusting for multiple testing (P = 0.046 by permutation test). This SNP was in a haplotype block spanning 97 kb (from rs2069812 to rs2240032). The detected haplotype block contained the RAD50 gene and the promoter of IL13, but not the other genes.

Conclusion
A haplotype block in which a primary polymorphism associated with severe malaria is likely to be encoded was identified in Thai malaria patients.
The infective cycle of Cabbage leaf curl virus (CaLCuV) is affected by CRUMPLED LEAF (CRL) gene in Arabidopsis thaliana
Authors: Trejo-Saavedra Diana L , Vielle-Calzada Jean P , Rivera-Bustamante Rafael F 
Published: October 2009

Abstract

Background
Geminiviruses are single-stranded DNA viruses that cause serious crop losses worldwide. Successful infection by these pathogens depends extensively on virus-host intermolecular interactions that allow them to express their gene products, to replicate their genomes and to move to adjacent cells and throughout the plant.

Results
To identify host genes that show an altered regulation in response to Cabbage leaf curl virus (CaLCuV) infection, a screening of transposant Arabidopsis thaliana lines was carried out. Several genes were identified to be virus responsive and one, Crumpled leaf (CRL) gene, was selected for further characterization. CRL was previously reported by Asano et al., (2004) to affect the morphogenesis of all plant organs and the division of plastids. We report here that CRL expression, during CaLCuV infection, shows a short but strong induction at an early stage (3-5 days post inoculation, dpi). To study the role of CRL in CaLCuV infection, CRL over-expressing and silenced transgenic plants were generated. We compared the replication, movement and infectivity of CaLCuV in transgenic and wild type plants.

Conclusion
Our results showed that CRL over-expressing plants showed an increased susceptibility to CaLCuV infection (as compared to wt plants) whereas CRL-silenced plants, on the contrary, presented a reduced susceptibility to viral infection. The possible role of CRL in the CaLCuV infection cycle is discussed.
Different responsiveness to a high-fat/cholesterol diet in two inbred mice and underlying genetic factors: a whole genome microarray analysis
Authors: Zhu Mingzhe , Ji Guozhen , Jin Gang , Yuan Zuobiao 
Published: October 2009

Abstract

Background
To investigate different responses to a high-fat/cholesterol diet and uncover their underlying genetic factors between C57BL/6J (B6) and DBA/2J (D2) inbred mice.

Methods
B6 and D2 mice were fed a high-fat/cholesterol diet for a series of time-points. Serum and bile lipid profiles, bile acid yields, hepatic apoptosis, gallstones and atherosclerosis formation were measured. Furthermore, a whole genome microarray was performed to screen hepatic genes expression profile. Quantitative real-time PCR, western blot and TUNEL assay were conducted to validate microarray data.

Results
After fed the high-fat/cholesterol diet, serum and bile total cholesterol, serum cholesterol esters, HDL cholesterol and Non-HDL cholesterol levels were altered in B6 but not significantly changed in D2; meanwhile, biliary bile acid was decreased in B6 but increased in D2. At the same time, hepatic apoptosis, gallstones and atherosclerotic lesions occurred in B6 but not in D2. The hepatic microarray analysis revealed distinctly different genes expression patterns between B6 and D2 mice. Their functional pathway groups included lipid metabolism, oxidative stress, immune/inflammation response and apoptosis. Quantitative real time PCR, TUNEL assay and western-blot results were consistent with microarray analysis.

Conclusion
Different genes expression patterns between B6 and D2 mice might provide a genetic basis for their distinctive responses to a high-fat/cholesterol diet, and give us an opportunity to identify novel pharmaceutical targets in related diseases in the future.
Breaking the hierarchy - a new cluster selection mechanism for hierarchical clustering methods
Authors: Zahoránszky László A , Katona Gyula Y , Hári Péter , Málnási-Csizmadia András , Zweig Katharina A , Zahoránszky-Köhalmi Gergely 
Published: October 2009

Abstract

Background
Hierarchical clustering methods like Ward's method have been used since decades to understand biological and chemical data sets. In order to get a partition of the data set, it is necessary to choose an optimal level of the hierarchy by a so-called level selection algorithm. In 2005, a new kind of hierarchical clustering method was introduced by Palla et al. that differs in two ways from Ward's method: it can be used on data on which no full similarity matrix is defined and it can produce overlapping clusters, i.e., allow for multiple membership of items in clusters. These features are optimal for biological and chemical data sets but until now no level selection algorithm has been published for this method.

Results
In this article we provide a general selection scheme, the level independent clustering selection method, called LInCS. With it, clusters can be selected from any level in quadratic time with respect to the number of clusters. Since hierarchically clustered data is not necessarily associated with a similarity measure, the selection is based on a graph theoretic notion of cohesive clusters. We present results of our method on two data sets, a set of drug like molecules and set of protein-protein interaction (PPI) data. In both cases the method provides a clustering with very good sensitivity and specificity values according to a given reference clustering. Moreover, we can show for the PPI data set that our graph theoretic cohesiveness measure indeed chooses biologically homogeneous clusters and disregards inhomogeneous ones in most cases. We finally discuss how the method can be generalized to other hierarchical clustering methods to allow for a level independent cluster selection.

Conclusion
Using our new cluster selection method together with the method by Palla et al. provides a new interesting clustering mechanism that allows to compute overlapping clusters, which is especially valuable for biological and chemical data sets.
Statin prophylaxis and inflammatory mediators following cardiopulmonary bypass: a systematic review
Authors: Morgan Catherine , Zappitelli Michael , Gill Peter 
Published: October 2009

Abstract
Introduction
Induction of an inflammatory response is thought to have a significant role in the complications that follow cardiopulmonary bypass (CPB). The statin drugs are increasingly being recognized as having potent anti-inflammatory effects and hence have potential to influence an important mechanism of injury in CPB, although there is no current confirmation that this is indeed the case. Our objective was to systematically review if pre-operative prophylactic statin therapy, compared with placebo or standard of care, can decrease the inflammatory response in people undergoing heart surgery with CPB.

Methods
We performed a systematic and comprehensive literature search for all randomized controlled trials (RCTs) of open heart surgery with CPB in adults or children who received prophylactic statin treatment prior to CPB, with reported outcomes which included markers of inflammation. Two authors independently identified eligible studies, extracted data, and assessed study quality using standardized instruments. Weighted mean difference (WMD) was the primary summary statistic with data pooled using a random effects model. Descriptive analysis was used when data could not be pooled.

Results
Eight RCTs were included in the review, with the number of trials for each inflammatory outcome being even more limited. Pooled data demonstrated benefit with the use of statin to attenuate the post-CPB increase in interleukins 6 and 8 (IL-6, IL-8), peak high sensitivity C-reactive protein (hsCRP), and tumor necrosis factor-alpha (TNF-α) post-CPB (WMD [95% confidence interval (CI)] -23.5 pg/ml [-36.6 to -10.5]; -23.4 pg/ml [-35.8 to -11.0]; -15.3 mg/L [CI -26.9 to -3.7]; -2.10 pg/ml [-3.83 to -0.37] respectively). Very limited RCT evidence suggests that prophylactic statin therapy may also decrease adhesion molecules following CPB including neutrophil CD11b and soluble P (sP)-selectin.

Conclusions
Although the RCT evidence may suggest a reduction in post-CPB inflammation by statin therapy, the evidence is not definitive due to significant limitations. Several of the trials were not methodologically rigorous and statin intervention was highly variable in this small number of studies. This systematic review demonstrates that there is a significant gap that exists in the current literature in regards to the potential anti-inflammatory effect of statin therapy prior to CPB.