bluuebunny/crossref_metadata_2025_split huggingface dataset:
Campylobacter diarrhoea and an association of recent disease with asymptomatic shedding in Egyptian children
Authors: Pazzaglia G. , Bourgeois A. L. , Diwany K. El , Nour N. , Badran N. , Hablas R. 
Published: May 2009

SUMMARYA hospital-based case-control diarrhoea survey was conducted in Cairo. Egypt to determine the age-specific frequency of campylobacter infection among diarrhoeic and non-diarrhoeic children aged new born to 5 years. Campylobacter was the most common bacterial enteropathogen isolated from diarrhoeic stools. The overall prevalence of campylobacter isolations was 25·9% from stools of 143 diarrhoeic children compared to 15·2% of 132 non-diarrhoeic control children (P= 0·028) during the 4-month period of study. Children less than 1 year of age were at greatest risk of campylobacter infection with 32·6% of diarrhoeic patients culture positive, compared to 14·3% of controls. Asymptomatic shedding in controls was positively associated with a recent diarrhoeal episode (P= 0·019) and may be an important source of new infections.
Activated caspases are present in frozen–thawed canine sperm and may be related to post thaw sperm quality
Authors: Sokolowska A. , García B. Macías , Fernández L. González , Ortega-Ferrusola C. , Tapia J. A. , Peña F. J. 
Published: May 2009

SummaryThe identification of early changes in the sperm plasmalemma is currently a factor in the improvement of freezing protocols. We analysed the presence of active caspases in freeze–thawed (FT) dog spermatozoa, and evaluated straws from eight dogs using flow cytometry and fluorescence microscopy with fluorescein isothyocyanate–Val–Ala–Asp–fluoromethylketone (FITC–VAD–fmk) combined with ethidum homodimers. Apoptotic-like changes were evaluated using the YO–PRO-1/ethidium homodimer combination, and changes in mitochondrial membrane potential were monitored with JC-1. Sperm motility post-thaw was evaluated using a CASA system. FITC–VAD–fmk stained sperm cells in situ and the subcellular labelling pattern was consistent with known localization of caspases. On average, a high proportion of FT canine sperm showed caspase activity, ranging from 30.2 to 70.7% of the live sperm compared with 7.3 to 24.0% in dead spermatozoa. This observed differentiation between caspase activity in dead and live spermatozoa may be a simple method to disclose subtle differences in sperm quality, since this staining allowed us to find statistically significant differences among dogs. Notably, the sperm sample with overall better results in all sperm parameters studied after thawing had a lower percentage of active caspases in both dead and live spermatozoa.
DASMI: exchanging, annotating and assessing molecular interaction data
Authors: Blankenburg Hagen , Finn Robert D. , Prlić Andreas , Jenkinson Andrew M. , Ramírez Fidel , Emig Dorothea , Schelhorn Sven-Eric , Büch Joachim , Lengauer Thomas , Albrecht Mario 
Published: May 2009

AbstractMotivation: Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are required for retrieving, sharing and presenting data spread over the Internet.Results: We introduce the DASMI system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization. The decentralized architecture of DASMI affords the online retrieval of the most recent data from distributed sources and databases. DASMI can also be extended easily by adding new data sources and clients. We describe all DASMI components and demonstrate their use for protein and domain interactions.Availability: The DASMI tools are available at http://www.dasmi.de/ and http://ipfam.sanger.ac.uk/graph. The DAS registry and the DAS 1.53E specification is found at http://www.dasregistry.org/.Contact: mario.albrecht@mpi-inf.mpg.deSupplementary information: Supplementary data and all figures in color are available at Bioinformatics online.
Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes
Authors: Zhang Min , Zhang Lin , Zou Jinfeng , Yao Chen , Xiao Hui , Liu Qing , Wang Jing , Wang Dong , Wang Chenguang , Guo Zheng 
Published: May 2009

AbstractMotivation: According to current consistency metrics such as percentage of overlapping genes (POG), lists of differentially expressed genes (DEGs) detected from different microarray studies for a complex disease are often highly inconsistent. This irreproducibility problem also exists in other high-throughput post-genomic areas such as proteomics and metabolism. A complex disease is often characterized with many coordinated molecular changes, which should be considered when evaluating the reproducibility of discovery lists from different studies.Results: We proposed metrics percentage of overlapping genes-related (POGR) and normalized POGR (nPOGR) to evaluate the consistency between two DEG lists for a complex disease, considering correlated molecular changes rather than only counting gene overlaps between the lists. Based on microarray datasets of three diseases, we showed that though the POG scores for DEG lists from different studies for each disease are extremely low, the POGR and nPOGR scores can be rather high, suggesting that the apparently inconsistent DEG lists may be highly reproducible in the sense that they are actually significantly correlated. Observing different discovery results for a disease by the POGR and nPOGR scores will obviously reduce the uncertainty of the microarray studies. The proposed metrics could also be applicable in many other high-throughput post-genomic areas.Contact: guoz@ems.hrbmu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.
Ulla: a program for calculating environment-specific amino acid substitution tables
Authors: Lee Semin , Blundell Tom L. 
Published: May 2009

Abstract
Summary: Amino acid residues are under various kinds of local environmental restraints, which influence substitution patterns. Ulla,1 a program for calculating environment-specific substitution tables, reads protein sequence alignments and local environment annotations. The program produces a substitution table for every possible combination of environment features. Sparse data is handled using an entropy-based smoothing procedure to estimate robust substitution probabilities.
Availability: The Ruby source code is available under a Creative Commons Attribution-Noncommercial License along with additional documentation from http://www-cryst.bioc.cam.ac.uk/ulla.
Contact: semin@cryst.bioc.cam.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Review article: diet and inflammatory bowel disease – epidemiology and treatment
Authors: YAMAMOTO T. , NAKAHIGASHI M. , SANIABADI A. R. 
Published: May 2009

SummaryBackground  Diet is thought to have an important role in the immunopathogenesis and treatment of inflammatory bowel disease (IBD).Aim  To identify dietary constituents as risk factors for development of IBD and the therapeutic efficacy of dietary modifications or enteral nutrition in IBD.Methods  The Medline and the Cochrane Library were searched for clinical trials and meta‐analyses in the scope of diet and nutrition in IBD.Results  There are many studies in small cohorts of patients that claim that intake of certain diet constituents like fat, refined sugar, fruits, vegetables and fibre affect the expression of IBD. These are often compromised by insufficient data or methodological limitations and do not provide unequivocal evidence to incriminate any particular dietary factor. Among various dietary interventions, none has shown striking efficacy with the possible exception of complete enteral nutrition. Enteral nutrition appears effective in both active and quiescent Crohn’s disease (CD), but independent meta‐analyses have shown enteral nutrition to be inferior to corticosteroids in the management of active CD, when assessed on an intention‐to‐treat basis.Conclusions  The current levels of knowledge concerning dietary risk factors for IBD, and the therapeutic efficacy of dietary and nutritional interventions need to be supported by well‐designed trials in large cohorts of patients.
Lipid‐mediated inflammation and degeneration of bioprosthetic heart valves
Authors: Shetty R. , Pibarot P. , Audet A. , Janvier R. , Dagenais F. , Perron J. , Couture C. , Voisine P. , Després J. P. , Mathieu P. 
Published: May 2009

AbstractBackground  The durability of bioprosthetic valves is limited by structural valve degeneration (SVD) leading to bioprostheses (BPs) stenosis or regurgitation. We hypothesized that a lipid‐mediated inflammatory mechanism is involved in the SVD of BPs.Material and methods  Eighteen Freestyle stentless BP valves were explanted for SVD at a mean time of 5·9 ± 3 years after implantation and were analysed by immunohistochemistry and transmission electron microscopy (TEM).Results  The mean age of the patients was 65 ± 8 years and there were 11 male and seven female patients. Two of the 18 BPs had macroscopic calcification, whereas the other valves had minimal or no macroscopic calcification. Tears at the commissures leading to regurgitation was present in 16 BPs. Immunohistochemistry showed the presence of oxidized low‐density lipoprotein (ox‐LDL) and glycosaminoglycans in the fibrosa layer of 13 BPs. Areas with ox‐LDL were infiltrated by macrophages (CD68+) co‐expressing the scavenger receptor CD36 and metalloproteinase‐9 (MMP‐9). Zymogram showed the active form of MMP‐9 within explanted BPs. EM studies revealed the presence of lipid‐laden cells featuring foam cells and fragmented collagen. Nonimplanted control BPs obtained from the manufacturer (n = 4) had no evidence of lipid accumulation, inflammatory cell infiltration or expression of MMP9 within the leaflets.Conclusions  These results support the concept that lipid‐mediated inflammatory mechanisms may contribute to the SVD of BPs. These findings suggest that modification of atherosclerotic risk factors with the use of behavioural or pharmacological interventions could help to reduce the incidence of SVD.
SARS‐coronavirus modulation of myocardial ACE2 expression and inflammation in patients with SARS
Authors: Oudit G. Y. , Kassiri Z. , Jiang C. , Liu P. P. , Poutanen S. M. , Penninger J. M. , Butany J. 
Published: May 2009

AbstractBackground  Angiotensin converting enzyme 2 (ACE2), a monocarboxylase that degrades angiotensin II to angiotensin 1–7, is also the functional receptor for severe acute respiratory syndrome (SARS) coronavirus (SARS‐CoV) and is highly expressed in the lungs and heart. Patients with SARS also suffered from cardiac disease including arrhythmias, sudden cardiac death, and systolic and diastolic dysfunction.Materials and methods  We studied mice infected with the human strain of the SARS‐CoV and encephalomyocarditis virus and examined ACE2 mRNA and protein expression. Autopsy heart samples from patients who succumbed to the SARS crisis in Toronto (Canada) were used to investigate the impact of SARS on myocardial structure, inflammation and ACE2 protein expression.Results  Pulmonary infection with the human SARS‐CoV in mice led to an ACE2‐dependent myocardial infection with a marked decrease in ACE2 expression confirming a critical role of ACE2 in mediating SARS‐CoV infection in the heart. The SARS‐CoV viral RNA was detected in 35% (7/20) of autopsied human heart samples obtained from patients who succumbed to the SARS crisis during the Toronto SARS outbreak. Macrophage‐specific staining showed a marked increase in macrophage infiltration with evidence of myocardial damage in patients who had SARS‐CoV in their hearts. The presence of SARS‐CoV in the heart was also associated with marked reductions in ACE2 protein expression.Conclusions  Our data show that SARS‐CoV can mediate myocardial inflammation and damage associated with down‐regulation of myocardial ACE2 system, which may be responsible for the myocardial dysfunction and adverse cardiac outcomes in patients with SARS.
Systematic assessment of terrestrial biogeochemistry in coupled climate–carbon models
Authors: RANDERSON JAMES T. , HOFFMAN FORREST M. , THORNTON PETER E. , MAHOWALD NATALIE M. , LINDSAY KEITH , LEE YEN‐HUEI , NEVISON CYNTHIA D. , DONEY SCOTT C. , BONAN GORDON , STÖCKLI RETO , COVEY CURTIS , RUNNING STEVEN W. , FUNG INEZ Y. 
Published: May 2009

AbstractWith representation of the global carbon cycle becoming increasingly complex in climate models, it is important to develop ways to quantitatively evaluate model performance against in situ and remote sensing observations. Here we present a systematic framework, the Carbon‐LAnd Model Intercomparison Project (C‐LAMP), for assessing terrestrial biogeochemistry models coupled to climate models using observations that span a wide range of temporal and spatial scales. As an example of the value of such comparisons, we used this framework to evaluate two biogeochemistry models that are integrated within the Community Climate System Model (CCSM) – Carnegie‐Ames‐Stanford Approach′ (CASA′) and carbon–nitrogen (CN). Both models underestimated the magnitude of net carbon uptake during the growing season in temperate and boreal forest ecosystems, based on comparison with atmospheric CO2 measurements and eddy covariance measurements of net ecosystem exchange. Comparison with MODerate Resolution Imaging Spectroradiometer (MODIS) measurements show that this low bias in model fluxes was caused, at least in part, by 1–3 month delays in the timing of maximum leaf area. In the tropics, the models overestimated carbon storage in woody biomass based on comparison with datasets from the Amazon. Reducing this model bias will probably weaken the sensitivity of terrestrial carbon fluxes to both atmospheric CO2 and climate. Global carbon sinks during the 1990s differed by a factor of two (2.4 Pg C yr−1 for CASA′ vs. 1.2 Pg C yr−1 for CN), with fluxes from both models compatible with the atmospheric budget given uncertainties in other terms. The models captured some of the timing of interannual global terrestrial carbon exchange during 1988–2004 based on comparison with atmospheric inversion results from TRANSCOM (r=0.66 for CASA′ and r=0.73 for CN). Adding (CASA′) or improving (CN) the representation of deforestation fires may further increase agreement with the atmospheric record. Information from C‐LAMP has enhanced model performance within CCSM and serves as a benchmark for future development. We propose that an open source, community‐wide platform for model‐data intercomparison is needed to speed model development and to strengthen ties between modeling and measurement communities. Important next steps include the design and analysis of land use change simulations (in both uncoupled and coupled modes), and the entrainment of additional ecological and earth system observations. Model results from C‐LAMP are publicly available on the Earth System Grid.
Effect of marinating and vacuum storage at 6 °C on the fate of chemical, microbial and sensory quality indices of echinoid gonads Paracentrotus lividus Lamark, 1816
Authors: Stamatis Nikolaos , Vafidis Dimitris 
Published: May 2009

SummaryChemical, microbial and sensory quality indices of raw and marinated sea urchin Paracentrotus lividus Lamark, 1816, were determined. Marinades were prepared using three different formulations and stored over a 75‐day period at 6 °C, under vacuum and air (control) packaging conditions. Significant differences were found between chemical (pH, moisture, ash, NaCI, ammonia and lactic acid), microbial [pseudomonads (Ps), lactic acid bacteria (LAB) and yeast–moulds] and sensory analysis of three different marinated groups (P < 0.05) during the storage period. The marinating process did not lead to significant differences in fatty acid, protein, fat and carbohydrate contents relative to raw sample. A notable decrease of the ω‐3 per ω‐6 ratio after marinating and during storage in both packages was observed. Ammonia concentration changes were found to be useful as index of freshness and decomposition of roe in storage. Shelf life of roe marinades at 6 °C was found to be 75 and 60 days under vacuum and air storage conditions respectively.
Anti‐ischemic effects of inotropic agents in experimental right ventricular infarction
Authors: HEIN M. , ROEHL A. B. , BAUMERT J. H. , SCHERER K. , STEENDIJK P. , ROSSAINT R. 
Published: May 2009

Background: Right ventricular (RV) function is an important determinant of survival after myocardial infarction. The efficacy of reperfusion therapy might be increased by the cardioprotective action of inotropic agents, which are used for symptomatic therapy in situations with compromised hemodynamics. Therefore, we used a porcine model of RV ischemia and reperfusion (IR) injury to study the influence of milrinone, levosimendan and dobutamine on the extent and degree of myocardial injury.Methods: IR injury was induced by temporary ligation of the distal right coronary artery for 90 min, followed by 120 min of reperfusion. Treatment was initiated 30 min after coronary artery occlusion. A bolus of milrinone (n=12; 50 μg/kg) and levosimendan (n=10; 24 μg/kg) was applied in different groups, followed by continuous infusion of the drugs at 0.5 and 0.2 μg/kg/min, respectively. The effects on myocardial injury and inflammation were compared with a control (n=12) and a dobutamine group (n=10), where treatment was started with an infusion of 5 μg/kg/min.Results: Milrinone and levosimendan reduced the resulting infarct size with respect to the area at risk (41.7±10.2%, 45.7±8.1%) when compared with the control group (58.3±6.1%). In contrast, dobutamine had no effect (55.8±7.7%). All drugs reduced the number of neutrophils infiltrating into the different myocardial regions and the circulating levels of interleukin‐6. Increased levels of tumor necrosis factor α during reperfusion were only abated by milrinone and levosimendan.Conclusions: Cardioprotective properties of milrinone and levosimendan were demonstrated for the first time in a clinically relevant model of RV infarction.
Urinary proteins from patients with nephrotic syndrome alters the signalling proteins regulating epithelial–mesenchymal transition
Authors: WEN QIONG , HUANG ZHAO , ZHOU SHU‐FENG , LI XIAO‐YAN , LUO NING , YU XUE‐QING 
Published: May 2009

ABSTRACT:Aim:  Proteinuria plays an important role in the progression of tubulointerstitial fibrosis, but the mechanism for the differential renal damage induced by proteinuria is unknown. This study examined the effects of urinary proteins from patients with idiopathic minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) on several epithelial–mesenchymal transition (EMT)‐related marker proteins in cultured proximal tubular HK‐2 cells.Methods:  Urinary proteins from MCD and FSGS patients were extracted by ultrafiltration and incubated with HK‐2 cells; the expression of the cytokeratin‐18, α‐smooth muscle actin (α‐SMA) and vimentin were assessed. p38 and extracellular regulated kinase (ERK) activation were measured by western blotting, and SB203580 (a p38 inhibitor) and PD98059 (an ERK1/2 inhibitor) were used to inhibit their activation.Results:  It was observed that urinary proteins from FSGS patients more significantly induced the expression of α‐SMA and vimentin and reduced cytokeratin‐18 expression than those from MCD patients in HK‐2 cells. Both ERK1/2 and p38 were activated by urinary proteins from MCD or FSGS patients. Pretreatment of the cells with SB203580 or PD98059 abolished the effect of urinary proteins from FSGS patients on the expression of α‐SMA, vimentin and cytokeratin‐18, while only SB203580 elicited this effect when cells were treated with urinary proteins from MCD patients.Conclusion:  The urinary proteins from MCD and FSGS patients induced significant changes of EMT‐related proteins through activation of distinct mitogen‐activated protein kinase‐related signalling pathways. Quality of proteinuria may play an important role in determining the severity and progression of tubular injury associated with different kidney diseases.
Long‐term graft function with tacrolimus and cyclosporine in renal transplantation: Paired kidney analysis
Authors: CHEUNG CHI YUEN , CHAN HOI WONG , LIU YAN LUN , CHAU KA FOON , LI CHUN SANG 
Published: May 2009

SUMMARY:Aim:  The first prospective, randomized trial with paired kidney analysis was conducted to compare the efficacy and safety of tacrolimus with cyclosporine‐based immunosuppressive therapy in renal transplant recipients. This paper reports the long‐term follow‐up results of the authors' previously published study, with the main focus on graft survival and renal function.Methods:  Chinese patients transplanted in our centre between June 1998 and June 2005 with their first deceased renal transplant were included. Patients were included if both kidneys were received by the authors' centre, thus allowing a paired analysis. Patients were randomized to receive triple immunosuppressive therapy with either tacrolimus or Neoral cyclosporine, concomitantly with prednisolone and azathioprine therapy.Results:  Seventy‐six patients received cadaveric kidneys from 38 donors. Each pair of kidneys was randomly assigned to a separate group (38 subjects/group). The mean follow‐up duration was 6.1 ± 1.8 years. The mean calculated creatinine clearance was significantly higher in patients receiving tacrolimus‐based therapy. The rate of biopsy‐proven acute rejection was lower in the tacrolimus group (18.4% vs 42.1%, P = 0.03). The patient and graft survival were comparable in both treatment arms. Significantly fewer patients on tacrolimus‐based therapy developed hypercholesterolaemia (P = 0.05). However, there was no significant difference in the development of post‐transplant diabetes mellitus, hypertension, opportunistic infection and malignancy between both groups.Conclusion:  Using the immunosuppressive regimen, tacrolimus‐based therapy provided adequate immunosuppression with better renal function and less acute rejection, as compared with cyclosporine‐based therapy.
Improving clinicians' attitudes toward providing feedback on routine outcome assessments
Authors: Willis Aimee , Deane Frank P. , Coombs Tim 
Published: May 2009

ABSTRACTClinicians have been found to hold predominantly negative attitudes toward routine outcome assessments (ROA). This study aims to assess changes in clinicians' attitudes to ROA, and in particular, the provision of feedback from such assessments following a training workshop. Ninety‐six mental health workers attended a training workshop on ROA, which was supported by the use of a CD‐ROM video resource. Participants completed a questionnaire before and after training that assessed their attitudes toward ROA and the provision of feedback from these assessments. Attitudes toward feedback were predominantly positive at baseline. Significantly more positive attitudes on general attitudes and specific attitudes related to the provision of feedback were found following training. Generating positive clinician attitudes is the first step toward improving the processes and effectiveness of ROA. Controlled trials with a follow up of clinicians' behaviour are needed to determine whether the changes found are maintained and reflected in practice.