bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliability-Oriented bioinformatic networks visualization
Authors: Aladağ Ahmet Emre , Erten Cesim , Sözdinler Melih 
Published: April 2011

Abstract
Summary: We present our protein-protein interaction (PPI) network visualization system RobinViz (reliability-oriented bioinformatic networks visualization). Clustering the PPI network based on gene ontology (GO) annotations or biclustered gene expression data, providing a clustered visualization model based on a central/peripheral duality, computing layouts with algorithms specialized for interaction reliabilities represented as weights, completely automated data acquisition, processing are notable features of the system.
Availability: RobinViz is a free, open-source software protected under GPL. It is written in C++ and Python, and consists of almost 30 000 lines of code, excluding the employed libraries. Source code, user manual and other Supplementary Material are available for download at http://code.google.com/p/robinviz/.
Contacts: cesim@khas.edu.tr
Supplementary information: Supplementary data are available at Bioinformatics online.
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data
Authors: McPherson Andrew , Wu Chunxiao , Hajirasouliha Iman , Hormozdiari Fereydoun , Hach Faraz , Lapuk Anna , Volik Stanislav , Shah Sohrab , Collins Colin , Sahinalp S. Cenk 
Published: April 2011

Abstract
Motivation: Comrad is a novel algorithmic framework for the integrated analysis of RNA-Seq and whole genome shotgun sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as expressed or not expressed and accurate classification of the genomic or non-genomic origin of aberrant transcripts. A major benefit of Comrad is its ability to accurately identify aberrant transcripts and associated rearrangements using low coverage genome data. As a result, a Comrad analysis can be performed at a cost comparable to that of two RNA-Seq experiments, significantly lower than an analysis requiring high coverage genome data.
Results: We have applied Comrad to the discovery of gene fusions and read-throughs in prostate cancer cell line C4-2, a derivative of the LNCaP cell line with androgen-independent characteristics. As a proof of concept, we have rediscovered in the C4-2 data 4 of the 6 fusions previously identified in LNCaP. We also identified six novel fusion transcripts and associated genomic breakpoints, and verified their existence in LNCaP, suggesting that Comrad may be more sensitive than previous methods that have been applied to fusion discovery in LNCaP. We show that many of the gene fusions discovered using Comrad would be difficult to identify using currently available techniques.
Availability: A C++ and Perl implementation of the method demonstrated in this article is available at http://compbio.cs.sfu.ca/.
Contact: andrew.mcpherson@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Idiopathic Pancreatitis Preceding the Diagnosis of Inflammatory Bowel Disease Is More Frequent in Pediatric Patients
Authors: Broide Efrat , Dotan Iris , Weiss Batia , Wilschanski Michael , Yerushalmi Baruch , Klar Aharon , Levine Arie 
Published: April 2011

ABSTRACTBackground and Objectives:Acute pancreatitis (AP) can be a rare extraintestinal manifestation of inflammatory bowel disease (IBD). There are only a few reports of AP presenting before the diagnosis of IBD. We aimed to characterize the demographic, clinical, and laboratory data of patients with IBD in whom AP preceded disease onset and compare the presentation of AP between children and adults.Patients and Methods:Pediatric and adult patients presenting with AP as the first symptom of IBD were retrospectively identified (10 years, 7 university hospitals). Demographic and clinical data, IBD type, disease extension, and laboratory data were extracted from the charts. Imaging methods, number of AP episodes, and lag time between onset of first pancreatitis episode and onset of IBD were recorded.Results:AP preceding the diagnosis of IBD was found in 10 in 460 pediatric patients with IBD (2.17%), compared with only 2 in 3500 adults (0.06%). Eight children had colonic disease (4 Crohn disease, 4 ulcerative colitis [3 pancolitis]). Mean amylase level was 1419 and range 100 to 1370. Three children (30%) had mildly elevated transaminases. Median time between onset of first episode of AP in relation to onset of IBD was 24 (range 1–156) weeks. AP most commonly presented with abdominal pain.Conclusions:IBD presenting as AP was more frequent among the pediatric population with IBD in comparison to adults. It was more common in patients with colitis than in those with ileal disease, suggesting that patients with idiopathic AP should be observed carefully for a possible diagnosis of IBD.
Oligosaccharides in 4 Different Milk Groups, Bifidobacteria, and Ruminococcus obeum
Authors: Coppa Giovanni V , Gabrielli Orazio , Zampini Lucia , Galeazzi Tiziana , Ficcadenti Anna , Padella Lucia , Santoro Lucia , Soldi Sara , Carlucci Antonio , Bertino Enrico , Morelli Lorenzo 
Published: April 2011

AbstractObjectives:The aim of this study was to identify a link between the total amount of breast milk oligosaccharides and faecal microbiota composition of newborns at the end of the first month of life, with special attention paid to bifidobacteria, and establish the role, if any, of the different oligosaccharides in determining the gut microbiota composition.Subjects and Methods:Milk oligosaccharide groups were identified by high‐performance anion exchange chromatography analysis. DPCRNA from newborns' faecal samples at 30 days of life was isolated and processed by polymerase chain reaction analyses that allow the identification of 6 species of bifidobacteria (adolescentis, bifidum, breve, catenulatum, longum, infantis) and Ruminococcus spp; denaturing gradient gel electrophoresis analysis was also performed.Results:No substantial differences in bifidobacteria species composition within milk groups 1, 2, and 3 were observed; however, infants fed with group 4 milk show a microbiota characterised by a greater frequency of Bifidobacteria adolescentis and the absence of Bifidobacteria catenulatum. For the first time, a high percentage of the Ruminococcus genus in infants fed with all milk groups was found.Conclusions:Our data show that milk groups 1, 2, and 3, containing an amount of oligosaccharides ranging within 10 to 15 g/L, share a substantially identical composition of the intestinal microbiota in breast‐fed infants, despite quali‐quantitative difference in oligosaccharides content. Newborns taking milk with only 5 g/L of oligosaccharides (group 4) harbour a different intestinal microbiota.
Intractable Diarrhea With Tufting Enteropathy: A Favorable Outcome Is Possible
Authors: Lemale Julie , Coulomb Aurore , Dubern Béatrice , Boudjemaa Sabah , Viola Sheila , Josset Patrice , Tounian Patrick , Girardet Jean‐Philippe 
Published: April 2011

ABSTRACTBackground and Objective:Tufting enteropathy (TE) is a congenital abnormality of intestinal mucosa development characterized by severe intestinal failure requiring parenteral nutrition (PN) and, in some cases, small bowel transplantation. A few patients have had a more favorable outcome. The objective of this study was to evaluate possible correlations between histological lesion severity in duodenal biopsies and clinical outcomes in children with TE.Patients and Methods:We retrospectively reviewed the records of patients diagnosed with TE between 1993 and 2003 at our institution based on intractable neonatal‐onset diarrhea with prolonged dependence on PN and duodenal biopsy findings of villous atrophy, epithelial dysplasia with enterocyte dedifferentiation and disorganization (tufting) of the surface epithelium, and crypt abnormalities. The histological lesions were assessed semiquantitatively and compared with the clinical outcomes including dependence on PN.Results:Seven children, all from consanguineous parents, were studied for a median of 6.5 years. Three were permanently weaned off PN and experienced normal growth without nutritional assistance. Initial biopsies in all 3 children showed severe diffuse histological lesions. At weaning off PN, 2 of these 3 patients had persistent, although less diffuse, histological lesions.Conclusions:Progressive weaning off PN is possible in some children with TE. In our experience, this favorable outcome was not predicted by histological lesion severity, although the lesions improved in some patients. New biomarkers for identifying the histological lesions and predicting the outcome would be useful.
Pharmacokinetics and Tolerability of Rabeprazole in Children 1 to 11 Years Old With Gastroesophageal Reflux Disease
Authors: Zannikos Peter N , Doose Dennis R , Leitz Gerhard J , Rusch Sarah , Gonzalez Martha D , Solanki Bhavna , Haddad Ibrahim , Mulberg Andrew E 
Published: April 2011

ABSTRACTBackground:The pharmacokinetics of rabeprazole after a single oral dose and once‐daily administration for 5 consecutive days was characterized in children 1 to 11 years old with gastroesophageal reflux disease (GERD).Patients and Methods:The initial 8 patients received rabeprazole sodium (hereafter referred to as rabeprazole) 0.14 mg/kg (part 1); the next 20 patients were randomized to receive 0.5 or 1 mg/kg (part 2) to target concentrations in plasma expected to be safe and effective. Pharmacokinetic parameters of rabeprazole and the thioether metabolite were calculated using noncompartmental methods. Subjective evaluations of GERD severity, rabeprazole short‐term effectiveness, palatability, and safety were also characterized.Results:Rabeprazole concentrations increased in a dose‐dependent manner. Little or no accumulation was observed after repeated administration. The results suggest that formation of the thioether is an important metabolic pathway in young patients, which is consistent with adults. Plasma area under the concentration‐time curve values of rabeprazole and the metabolite were poorly correlated with individual age and body weight. Furthermore, oral rabeprazole clearance values (not adjusted for weight) were similar to historical adult data. However, weight‐adjusted values were higher for the pediatric patients, and approximately 2 to 3 times the milligram per kilogram dose of rabeprazole in these children was necessary to achieve comparable concentrations in adults. Subjective evaluations demonstrated an improvement of GERD symptoms in most patients after rabeprazole treatment.Conclusions:Palatability of the formulation was reported to be good or excellent. Rabeprazole was well tolerated, with no notable differences in safety among the dose groups.
Gene‐expression Profile Analysis in the Mid‐gestation Human Intestine Discloses Greater Functional Immaturity of the Colon as Compared With the Ileum
Authors: Tremblay Eric , Ferretti Emanuela , Babakissa Corentin , Seidman Ernest G , Levy Emile , Ménard Daniel , Beaulieu Jean‐François ,   Canadian Institutes of Health Research Team on Digestive Epithelium
Published: April 2011

ABSTRACTBackground and Objectives:The occurrence of many neonatal inflammatory intestinal diseases in preterm infants highlights the susceptibility of the immature intestine to responding inadequately to nutrients and microbes. A better understanding of functional intestinal development is essential for the design of optimal treatments ensuring survival and growth of premature infants. The purpose of this study was to evaluate the gene expression profiles of the human ileum and colon at mid‐gestation because these 2 segments are considered to be similar at this stage and are the sites of the most frequent pathologies in preterm infants.Subjects and Methods:We compared the gene‐expression profiles of human fetal small and large intestines using a cDNA microarray and analyzed the data with Ingenuity Pathway Analysis software.Results:We found that a significant proportion of the genes was differentially expressed in the 2 segments. Gene cluster analysis revealed an even higher level of transcriptional dissimilarity at the functional level. For instance, segment‐specific/overexpressed gene clusters in the ileum included genes involved with amino acid, vitamin, and mineral metabolism, reflecting the higher level of maturity of the small intestine as compared with the colon in which genes involved with cell cycle, cell death, and cell signaling were the predominant clusters of genes expressed.Conclusions:Functional clustering analysis of the differentially expressed genes revealed important functional differences between the 2 segments and a relative immaturity of the colon, suggesting that already at mid‐gestation, the 2 intestinal segments should be considered as 2 distinct organs.
GlobalizaÃ§Ã£o e direito internacional: da boa vizinhanÃ§a ao patrimÃ´nio comum da humanidade
Authors: Pureza JosÃ© Manuel 
Published: April 2011

Perante os desafios globais com que se defronta a Humanidade no seu conjunto, o Direito Internacional Ã© atravessado por um processo de transfiguraÃ§Ã£o de alguns de seus postulados clÃ¡ssicos. Depois de sintetizar as grandes linhas dessa mudanÃ§a, cujo sÃmbolo maior Ã© o regime internacional de patrimÃ´nio comum da humanidade, este artigo pÃµe em questÃ£o a adequaÃ§Ã£o de acentuaÃ§Ãµes correntes da dimensÃ£o institucional daquele processo Ã estrutura da sociedade internacional contemporÃ¢nea.
O direito à vida e a ética da saúde
Authors: Berlinguer Giovanni 
Published: April 2011

Defendendo ser a saÃºde uma dimensÃ£o relevante para a reflexÃ£o Ã©tica, pois que afeta a prÃ³pria vida, o autor advoga o direito Ã saÃºde opondo-se a concepÃ§Ãµes para as quais a demanda por saÃºde deve ser resolvida pelo mercado. Conjuga sua defesa a uma anÃ¡lise dos Ã³bices existentes Ã realizaÃ§Ã£o de tal direito (dentre eles a mercantilizaÃ§Ã£o da medicina) e Ã indicaÃ§Ã£o de alternativas Ã©ticas e prÃ¡ticas.
Transfer on hydrophobic substrates and AFM imaging of membrane proteins reconstituted in planar lipid bilayers
Authors: Seantier Bastien , Dezi Manuela , Gubellini Francesca , Berquand Alexandre , Godefroy Cédric , Dosset Patrice , Lévy Daniel , Milhiet Pierre‐Emmanuel 
Published: April 2011

AbstractThe lipid‐layer technique allows reconstituting transmembrane proteins at a high density in microns size planar membranes and suspended to a lipid monolayer at the air/water interface. In this paper, we transferred these membranes onto two hydrophobic substrates for further structural analysis of reconstituted proteins by Atomic Force Microscopy (AFM). We used a mica sheet covered by a lipid monolayer or a sheet of highly oriented pyrolytic graphite (HOPG) to trap the lipid monolayer at the interface and the suspended membranes. In both cases, we succeeded in the transfer of large membrane patches containing densely packed or 2D‐crystallized proteins. As a proof of concept, we transferred and imaged the soluble Shiga toxin bound to its lipid ligand and the ATP‐binding cassette (ABC) transporter BmrA reconstituted into a planar bilayer. AFM imaging with a lateral resolution in the nanometer range was achieved. Potential applications of this technique in structural biology and nanobiotechnology are discussed. Copyright © 2011 John Wiley & Sons, Ltd.
Rhodopsin is spatially heterogeneously distributed in rod outer segment disk membranes
Authors: Buzhynskyy Nikolay , Salesse Christian , Scheuring Simon 
Published: April 2011

AbstractThe visual photoreception takes place in the retina, where specialized rod and cone photoreceptor cells are located. The rod outer segments contain a stack of 500–2,000 sealed membrane disks. Rhodopsin is the visual pigment located in rod outer segment disks, it is a member of the G‐protein‐coupled receptor (GPCR) superfamily, an important group of membrane proteins responsible for the majority of physiological responses to stimuli such as light, hormones, peptides, etc. Alongside rhodopsin, peripherin/Rom proteins located in the disk rims are thought to be responsible for disk morphology. Here we describe the supramolecular structure of rod outer segment disk membranes and the spatial organization of rhodopsin and peripherin/Rom molecules. Using atomic force microscopy operated in physiological buffer solution, we found that rhodopsin is loosely packed in the central region of the disks, in average about 26 000 molecules covering approximately one third of the disk surface. Peripherin/Rom proteins form dense assemblies in the rim region. A protein‐free lipid bilayer girdle separates the rhodopsin and peripherin/Rom domains. The described supramolecular assembly of rhodospin, peripherin/Rom and lipids in native rod outer segment disks is consistent with the functional requirements of photoreception. Copyright © 2011 John Wiley & Sons, Ltd.
AFM imaging of extracellular polymer release by marine diatom Cylindrotheca closterium (Ehrenberg) Reiman & J.C. Lewin
Authors: Pletikapić Galja , Radić Tea Mišić , Zimmermann Amela Hozić , Svetličić Vesna , Pfannkuchen Martin , Marić Daniela , Godrijan Jelena , Žutić Vera 
Published: April 2011

AbstractExtracellular polysaccharide production by marine diatoms is a significant route by which photosynthetically produced organic carbon enters the trophic web and may influence the physical environment in the sea. This study highlights the capacity of atomic force microscopy (AFM) for investigating diatom extracellular polysaccharides with a subnanometer resolution. Here we address a ubiquitous marine diatom Cylindrotheca closterium, isolated from the northern Adriatic Sea, and its extracellular polymeric substance (EPS) at a single cell level. We applied a simple procedure for AFM imaging of diatom cells on mica under ambient conditions (in air) to achieve visualization of their EPS with molecular resolution. The EPS represents a web of polysaccharide fibrils with two types of cross‐linking: fibrils association forming junction zones and fibril–globule interconnections with globules connecting two or more fibrils. The fibril heights were 0.4–2.6 nm while globules height was in the range of 3–12 nm. Polymer networks of native gel samples from the Northern Adriatic and the network formed by polysaccharides extracted from the C. closterium culture share the same features regarding the fibril heights, pore openings and the mode of fibril association, proving that the macroscopic gel phase in the Northern Adriatic can be formed directly by the self‐assembly of diatom released polysaccharide fibrils. Copyright © 2011 John Wiley & Sons, Ltd.
Assembly of collagen fibril meshes using gold nanoparticles functionalized with tris(hydroxymethyl)phosphine‐alanine as multivalent cross‐linking agents
Authors: Graham John S. , Miron Yannick , Grandbois Michel 
Published: April 2011

AbstractWe report on the use of tris(hydroxymethyl)phosphine‐alanine (THPAL) functionalized gold nanoparticles as a multivalent cross‐linking agent to assemble collagen fibrils into a mesh‐like structure. Atomic force microscopy (AFM) was used for characterization of the structure after adsorption onto an atomically flat mica substrate, revealing a mesh‐like construct in which the collagen fibrils and the gold nanoparticles interact to form interconnected nodes measuring from 100 to 500 nm. As expected, the density of the collagen mesh can be increased with a higher initial concentration of gold nanoparticles. The maximum thickness of the meshes (∼20 nm) obtained through cross‐sectional height measurements confirms that the adsorbed structure consists of a single layer of collagen fibrils/gold nanoparticles assembled in two‐dimensions. We propose that the capability of gold nanoparticles functionalized with the THPAL to bind to several collagen fibrils combined with the large persistence length of the fibrils, which was reported to be in the hundreds of nanometer range, are determinant factors for the preferential 2D growth of the mesh in solution. Copyright © 2011 John Wiley & Sons, Ltd.
Analysis of risk factors for hyperbilirubinemia occurring after hepatectomy
Authors: Fukumori Daisuke , Kamiyama Toshiya , Nakanishi Kazuaki , Yokoo Hideki , Tahara Munenori , Kamachi Hirofumi , Matsushita Michiaki , Todo Satoru 
Published: April 2011

AbstractBackgroundTo further improve the outcomes of liver resection, it is important to identify and prevent the causes of the hyperbilirubinemia occurring after hepatectomy and postoperative liver failure.MethodsBetween 2004 and 2009, 591 consecutive patients underwent a hepatectomy at our center. Twenty‐two patients who developed hyperbilirubinemia (postoperative total bilirubin over 5 mg/dL) after hepatectomy were classified as Hi‐Bi group and another 569 whose total bilirubin did not increase beyond 5 mg/dL were classified as non‐Hi‐Bi group.ResultsA preoperative prothrombin test of less than 80% and a blood loss of more than 1000 mL were identified as independent risk factors for the Hi‐Bi group by multivariate analysis. The hyperbilirubinemia of 16 cases improved, while that of 6 cases was prolonged. One of these patients died of liver failure without responding to treatment. The mortality rate for postoperative liver failure in this study was 0.16% (1/591).ConclusionIt is important to reduce the length of surgery and intraoperative blood loss to prevent hyperbilirubinemia after hepatectomy. Additionally, decision‐making using our algorithm and full examination of the accurate evaluation results, including those for prothrombin time, residual liver function and liver damage, can help reduce the development of hyperbilirubinemia.
Development of Mamestra brassicae and its solitary endoparasitoid Microplitis mediator on two populations of the invasive weed Bunias orientalis
Authors: Harvey Jeffrey A. , Gols Rieta 
Published: April 2011

AbstractThe warty cabbage Bunias orientalis is an invasive pest in much of central Europe, including much of Germany since the 1980s, whereas in other countries, such as The Netherlands, it is a less common exotic species. Here, healthy larvae of Mamestra brassicae, which has been found feeding on B. orientalis plants in Germany, and larvae parasitized by one of its major larval endoparasitoids Microplitis mediator, were reared on both herbivore‐induced and noninduced leaves of B. orientalis originating from single large populations growing in The Netherlands and central Germany. Herbivore performance was less negatively affected than parasitoid performance by differences in plant quality. Development times in both M. brassicae and Mi. mediator were shorter on Dutch than German plants and also shorter on noninduced than induced plants. Moreover, survival and body size of the parasitoid was more strongly affected by plant population and induction than survival of healthy M. brassicae. Chemical analyses of defensive secondary metabolites [glucosinolates (GS)] revealed that concentrations of the major GS sinalbin were constitutively expressed in German plants whereas they were induced in Dutch plants. However, in separate feeding bioassays in which preference for induced and noninduced leaves was compared separately, L3 instars of M. brassicae preferred noninduced German plants over Dutch plants but induced Dutch plants over German plants, revealing that changes in primary metabolites or an unidentified non‐GS compound mediates population‐related differences in plant quality. The results reveal asymmetric effects of plant quality in exotic plants on organisms in the second and third trophic level.