bluuebunny/crossref_metadata_2025_split huggingface dataset:
No association between coffee, tea or caffeine consumption and breast cancer risk in a prospective cohort study
Authors: Fagherazzi Guy , Touillaud Marina S , Boutron-Ruault Marie-Christine , Clavel-Chapelon Françoise , Romieu Isabelle 
Published: April 2011

AbstractObjectiveNumerous mechanisms for the effects of coffee, tea and caffeine on the risk of breast cancer have been suggested. Caffeine intake has already been associated with high plasma levels of female hormones, but associations have not been clearly demonstrated in epidemiological studies.DesignWe examined prospectively the association of coffee, tea and caffeine consumption with breast cancer risk in a French cohort study.SettingDietary information was obtained from a 208-item diet history questionnaire self-administered in 1993–1995. Multivariable Cox proportional hazards regression models were used to estimate hazards ratios and 95 % confidence intervals.SubjectsThe study was conducted on 67 703 women with available dietary information. During a median follow-up of 11 years, 2868 breast cancer cases were diagnosed.ResultsMedian intake was 280 ml/d (2·2 cups/d) for coffee and 214 ml/d (1·7 cups/d) for tea. Median caffeine intake was 164 mg/d. No association was found between consumption of coffee, tea or caffeine and breast cancer risk. Sub-analyses by tumour receptor status, menopausal status, type of coffee (regular or decaffeinated) and meals at which beverages were drunk led to the same conclusion.ConclusionsResults from this prospective study showed no relationship between coffee, tea or caffeine intake and breast cancer risk overall or by hormone receptor status.
In Principle Method for Noninvasive Determination of the Fetal Genome
Authors: Fan Christina , Quake Stephen 
Published: April 2011

AbstractWe illustrate the concept of noninvasive determination of the fetal genome by shotgun sequencing maternal plasma. The approach is based on molecular counting of alleles in maternal cell-free DNA: the inheritance of paternal haplotypes can be determined by counting paternal specific alleles present on each of the paternal haplotypes; the inheritance of maternal haplotypes can be revealed by counting the alleles on each maternal haplotype and determining the relative representation of the two maternal haplotypes. The concept was experimentally proven by sequencing a synthetic mixture of genomic DNA samples from a child and her mother, whose whole-genome haplotypes (defined by ~800,000 SNPs), together with those of the father, were previously determined. Light sequencing (0.25x) of such sample containing ~16% child’s DNA enabled the inheritance of parental haplotypes to be correctly resolved over most part of the genome, and partially resolved when prior knowledge of paternal whole-genome haplotypes is absent. Translating this approach to maternal plasma DNA samples, together with increased sequencing depth and phase knowledge of additional numbers of parental SNPs, should enable clinically practical sequencing of the fetal genome.
Using a data triangle to understand molecular nutrition
Authors: Evelo Chris 
Published: April 2011

AbstractUntil recently nutrigenomics was mainly about transcriptomics related data. That already confronted us with overwhelming analytical problems. We learned to mathematically and statistically treat genome wide expression studies and studies directed to gene expression regulation. Nutrigenomics researchers had to become bilingual speaking: English and R1 and learned to think about co-expression, clusters and false discovery rates. The latter in fact proofed to be a trap. Removing all the false positives made us loose the information we were really interested in. To understand the results of our genomics experiments we often had to confront what we were measuring with what we already knew. After all false positives are not likely to all be related to the same meaningful biological process. That asked for the development of new analytical tools like Cytoscape for network analysis and PathVisio for pathway analysis. More importantly we had to structure what we know. Text mining and data mining helped us to do that, but what was really needed was mobilization of all the knowledge that is present in the heads of the scientific community. WikiPathways was our contribution to the rapidly emerging field of community curation. Thus we started to become able to integrate different types of technologies that span the full gene expression pipeline and to understand that in the biological context.Today the story repeats itself. Genome wide genetics is becoming real. We can do Genome Wide Association Studies and soon we can sequence individual genomes in relation to food intake and phenotypic responses. And then what? How can we deal with that new avalanche of data? The oversampling problems will be a few orders of magnitude larger; after all there can be hundreds of SNPs in every gene. There will just be too many to understand which SNPs are important from the data alone. We will again have to relate them to the biological processes. But is that enough? I think not. We will only understand the outcome of those large scale genetics studies if we not only attribute the SNPs to genes and thereby to pathways. We will also have to consider the actual sequences and see what the functional effect is that the SNP causes. Is it likely to influence transcription factor binding, miRNA effects, or protein-protein interactions? This calls for new types of data integration, for which we already have the tools. And it calls for new creative ways to do that. What we really need is teams of creative minds. Some new initiatives seem to show that these are already being formed.1: http://www.r-project.org
Evidence of Massive Horizontal Gene Transfer Between Humans and Plasmodium vivax
Authors: Bar Daniel 
Published: April 2011

AbstractThe horizontal transfer of DNA between different organisms is a major force shaping the genomes of prokaryotes, but is considered to have a minor role in eukaryotes, with only a handful of known examples, mostly of limited size. The nucleotide databases of Plasmodium genomes were divided into small fragments and compared to human, as well as to other Plasmodium genomes. This computational approach revealed that the Plasmodium vivax genome is interlaced with multiple DNA fragments that were likely acquired via horizontal transfer from humans. Contamination is a major concern in such studies; moreover, it must be determined if the identified homologies might be due to chance. These reservations are supported by the fact that the identified homologous sequences were found to be predominantly within short contigs. Re-sequencing of candidate sites using distinct isolations of P. vivax genomic DNA showed deletions not found in the human genome, and with much greater similarity to the P. vivax than human genome. Moreover, the identified fragments were enriched for mRNA coding sequences and genes that are known to be functionally important for P. vivax, including nitric oxide synthase 1 (neuronal) adaptor and Interleukin-1 family, suggesting a functional role. These results are important for two reasons. First, a directional massive horizontal transfer of genetic material from humans to another eukaryote is shown for the first time. This sheds light on parasite evolution, co-adaptation and immune evasion. Second, the DNA found is enriched for Interleukin-1 family, which is known to be essential for malaria protection. This indicates a functional role and might serve to better understand how Plasmodium vivax and the immune system interact.
Development of a method for phenotyping Black Rot (Guignardia bidwellii) resistance on grapevine (Vitis_ spp.)
Authors: Rex Friederike , Fechter Iris , Hausmann Ludger , Töpfer Reinhard 
Published: April 2011

AbstractBlack Rot of grapevine is caused by the Ascomycet Guignardia bidwellii. The pathogen was introduced from North America to Europe in the 19th century. Since 2002, increased effects of the disease have been noticed, causing significant yield losses in the region of Mosel and infections in all German wine-growing regions. For that reason, it is important to breed Black Rot-resistant grapevine cultivars. A method has been developed to characterize lots of vines in a fast and reliable way concerning their susceptibility. Initial data has been collected and can be used for genetic analysis (here QTL). The aim of the project is to develop a molecular marker correlating with Black Rot resistance which can be used to select juvenile plants and therefore support the breeding of resistant cultivars.
Detection of substrate binding motifs for morphine biosynthetic pathway intermediates in novel wound inducible (R,S)-reticuline 7-O-methyltransferase of Papaver somniferum
Authors: Mishra Sonal , Meena Abha , Singh Sema , Yadav Dharmendra Kumar , Khan Feroz , Shukla Rakesh 
Published: April 2011

AbstractThe benzylisoquinoline alkaloids (BIA) comprise a large and diverse group of nitrogen-containing secondary metabolites with about 2500 compounds identified in plants. BIA biosynthesis begins with the condensation of the tyrosine derived precursors dopamine and p-hydroxyphenylacetaldehyde to (S)-norcoclaurine. Subsequent regiospecific O- and N-methylations and aromatic ring hydroxylation lead to (S)-reticuline, which is the central intermediate for almost all BIAs. For morphinan alkaloid biosynthesis, (S)-reticuline undergoes an inversion of stereochemistry to (R)-reticuline, followed by C-C phenol coupling catalyzed by a unique cytochrome P450-dependent monooxygenase to yield salutaridine. The cDNA sequence of enzymes leading to (S)-reticuline, as well as those involved in the conversion of (R)-reticuline to salutaridine-7-O-acetate are already characterized. The inversion of (S)-reticuline to (R)-reticuline represent the important steps in morphine biosynthesis. Wound induced transcript accumulation in Papaver reveals a novel wound inducible EST (NCBI DbEST: GO238757) showing homology with (R,S)-reticuline 7-O-methyltransferase (ID: Q6WUC2) isolated from Papaver somniferum. We compare the substrate binding homology of this novel wound inducible (R,S)-reticuline 7-O-methyltransferase (7-OMT) using template of P. somniferum (Q6WUC2; gb∣AAQ01668) as experimental control. Homology modeling with 70% identity & 85% similarity with catalytic site of template protein i.e., (Q6WUC2) short chain dehydrogenase/reductase (SDR), showed docking energy -69.9 and -75.8 kcal/mol with (S)-Reticuline (CID:439653) and (R)-Reticuline (CID:440586) respectively, which are comparable with experimental control binding site interaction energies. Docking of S- & R-reticuline into the active site revealed eight (F(5), E(18), W(24), C(47), F(44), P(45), C(46) and I(47) amino acids presumably responsible for the high substrate specificity of (R,S)-reticuline 7-O-methyltransferase.
Developing Predictive Molecular Maps of Human Disease through Community-based Modeling
Authors: Derry Jonathan , Mangravite Lara , Suver Christine , Furia Matt , Henderson David , Schildwachter Xavier , Izant Jonathan , Sieberts Solveig , Kellen Michael , Friend Stephen 
Published: April 2011

AbstractThe failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics.
Attention induces dynamic changes in coherence between monkey area V1 and V4
Authors: Grothe Iris , Neitzel Simon , Mandon Sunita , Kreiter Andreas 
Published: April 2011

AbstractNeurons receive a vast number of synaptic inputs at the same time. To successfully process a relevant piece of information, a neuron needs to select relevant, while suppressing irrelevant signals. In order to dynamically route a meaningful set of signals through processing pathways, neurons need to have a fast and flexible mechanism to change their effective connectivity. Here, we hypothesize that attention changes effective connectivity by modulating the synchrony between neuronal populations.We investigated whether attention dynamically changes effective connectivity between area V4 neurons and their V1 input. Single unit activity, multi unit activity and local field potentials (LFP) were recorded simultaneously from macaque monkeys’ areas V1 and V4. While maintaining their gaze on a fixation spot, the monkeys had to attend to one of two continuously morphing shapes and respond to reoccurrence of the initial sample shape in the attended stream. Size and position of the shapes were adjusted such that both fitted into a single V4 receptive field (RF) while covering two separate, non-overlapping V1 RFs.We found strong phase-coherence of gamma-band LFPs between the V1 populations responding to the attended stimulus and the V4 population. At the same time, V1 populations responding to the unattended stimulus showed only weak LFP phase-coherence with the V4 population. Furthermore, spike-triggered averages (STAs) of at least 40% of the recording pairs revealed that spikes recorded from area V4 were precisely timed with respect to the phase of the gamma oscillation in the upstream area V1. More importantly, almost all these cases showed an increased effect with attention. These results support the hypothesis that attention induces dynamic changes in the effective connectivity between two anatomically hard-wired neuronal populations by selectively modulating synchrony.
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version1.0
Authors: White James , Arze Cesar , Matalka Malcolm , Team The CloVR , Angiuoli Samuel , Fricke W. Florian 
Published: April 2011

AbstractThe CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:A) Mothur [1] – a C++ - based software package used for clustering 16SrRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);B)The Ribosomal Database (RDP) naive Bayesian classifier [2] assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;C) Qiime [3] – a python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including phylogenetic distance (UniFrac [4]) for within- (alpha diversity) and between- (beta diversity) sample analysis;D) Metastats [5] and custom R scripts used to generate additional statistical and graphical evaluations.Though some of the different protocols used in CloVR-16S overlap in purpose (e.g. OTU clustering), the end-user benefits from their overall complementary nature as they focus on different aspects of the phylogenetic analysis. CloVR-16S accepts as input raw multiplex 454-pyrosequencer output, i.e. pooled pyrotagged sequences from multiple samples, or alternatively, pre-processed sequences from multiple samples in separate files. This protocol is available in CloVR beta versions 0.5 and 0.6.
Architecture and dynamics of an A-kinase anchoring protein 79 (AKAP79) signaling complex
Authors: Gold Matthew G. , Stengel Florian , Nygren Patrick J. , Weisbrod Chad R. , Bruce James E. , Robinson Carol V. , Barford David , Scott John D. 
Published: April 2011

A-kinase anchoring protein 79 (AKAP79) is a human anchoring protein that organizes cAMP-dependent protein kinase (PKA), Ca
2+
/calmodulin (CaM)-dependent protein phosphatase (PP2B), and protein kinase C (PKC) for phosphoregulation of synaptic signaling. Quantitative biochemical analyses of selected AKAP79 complexes have determined the quaternary structure of these signaling complexes. We show that AKAP79 dimerizes, and we demonstrate that, upon addition of a lysine-reactive cross-linker, parallel homomeric dimers are stabilized through K328–K328 and K333–K333 cross-links. An assembly of greater complexity comprising AKAP79, PP2B, a type II regulatory subunit fragment (RII 1–45) of PKA, and CaM was reconstituted in vitro. Using native MS, we determined the molecular mass of this complex as 466 kDa. This indicates that dimeric AKAP79 coordinates two RII 1–45 homodimers, four PP2B heterodimers, and two CaM molecules. Binding of Ca
2+
/CaM to AKAP79 stabilizes the complex by generating a second interface for PP2B. This leads to activation of the anchored phosphatases. Our architectural model reveals how dimeric AKAP79 concentrates pockets of second messenger responsive enzyme activities at the plasma membrane.
Gluten Enhances Cooking, Textural, and Sensory Properties of Oat Noodles
Authors: Zhou Bai‐Ling , Zhu Fan , Shan Fang , Cai Yi‐Zhong , Corke Harold 
Published: April 2011

ABSTRACTWhole grain oats are widely regarded as conferring significant health benefits. Composite flour of whole grain oat flour, wheat flour, and tapioca starch in the ratio 1:1:0.16 was formulated to make oat noodles with the addition of gluten at various levels. The influence of gluten on pasting and gelling properties of composite flour, and on cooking, textural, and sensory properties of salted oat noodles was evaluated. Addition of gluten decreased the paste viscosity, reduced hardness and springiness of gel, reduced cooking yield, cooking loss, and broken ratio during cooking, and increased the tensile strength and firmness of cooked noodles. Scanning electron microscopy showed that gluten tightened the network of protein in the noodles by forming oriented fibrils. Addition of gluten had little effect on the color of raw and cooked oat noodles, which were somewhat yellow. Sensory evaluation indicated that addition of gluten could enhance the overall acceptability of cooked oat noodles. This study may stimulate further interest in using functional whole grain cereal ingredients in developing healthy staple foods.
Incidence of Gastroesophageal Reflux During Transpyloric Feeds
Authors: Rosen Rachel , Hart Kristen , Warlaumont Mary 
Published: April 2011

ABSTRACTObjectives:Transpyloric feeding has been proposed as an alternative method for controlling gastroesophageal reflux, but there have been no pediatric studies to determine how transpyloric feeding affects reflux burden. The aim of the present study was to determine the reflux burden in patients receiving transpyloric feeds.Patients and Methods:We reviewed the multichannel intraluminal impedance tracings of patients who had persistent symptoms and were fed transpylorically during the multichannel intraluminal impedance recording. We compared the reflux profiles during feed and nonfeed periods. We also compared the number of reflux‐related hospitalizations at Children's Hospital Boston in the year before and the year after the initiation of transpyloric feeds.Results:The mean number of reflux events per hour was 1.4 ± 1.3 and 0.8 ± 1.1 during feed and nonfeed periods, respectively (P = 0.06). There was no significant difference in the percentage of time that boluses were present in the esophagus during feed periods (1.0% ± 1.4%) compared with the nonfeed periods (0.6% ± 1.1%, P = 0.5). There was no significant difference in the mean number of reflux‐related hospitalizations in the year before (1.2 ± 1.4) or after (1.4 ± 1.2, P = 0.7) the initiation of transpyloric feeds.Conclusions:There is more reflux during transpyloric feeding periods than nonfeeding periods, which may explain why some patients continue to have reflux‐related hospitalizations even after the initiation of transpyloric feeds.
Portal Gastropathy and Duodenopathy in Children With Extrahepatic and Intrahepatic Portal Hypertension: Endoscopic Diagnosis and Histologic Scoring
Authors: Aydoğan Ayşen , Güllüoğlu Mine , Önder Semen Yeşil , Gökçe Selim , Çeltik Coşkun , Durmaz Özlem 
Published: April 2011

ABSTRACTObjectives:The aim of the study was to determine the frequency of portal gastropathy (PG) and duodenopathy (PD) in children, to document the correlation of various clinical and laboratory parameters associated with portal hypertensive gastroduodenal lesions, to compare the endoscopic portal hypertensive lesions with different histologic findings, and to evaluate the use of a possible histologic scoring system.Methods:All children undergoing endoscopic investigation for portal hypertension (PH) between January 2006 and November 2007 were analysed retrospectively. Clinical and demographical data and endoscopic and histologic findings were recorded. Histologic findings suggestive of PG and PD (capillary dilation, increased numbers of capillaries, histologic bleeding, and edema) were scored.Results:Of 51 consecutive children (29 boys, mean age 10.1± 3.6 years [range 2.5–15.8 years]), 28 were cirrhotic. PG was diagnosed in 58.8% endoscopically. Children with cirrhotic PH had the highest rate of PG (64.3%), whereas those with extrahepatic or intrahepatic noncirrhotic PH were alike (50% and 54.5%, respectively). Baveno PG scores were higher in children with cirrhosis with higher Child‐Pugh scores. Capillary dilation was the only histologic finding showing significant association with the endoscopic diagnosis. Only 9% had PD on endoscopy. None of the histologic findings correlated with endoscopic diagnosis of PD.Conclusions:PG and PD are seen in children with extrahepatic and intrahepatic PH at rates similar to those reported in adult studies. Baveno PG scores increased in parallel with Child‐Pugh class in children with cirrhosis. Capillary dilation was the only histologic finding showing significant association with the endoscopic diagnosis of PG in this study.
Pathophysiology, Diagnosis, and Management of Pediatric Ascites
Authors: Giefer Matthew J , Murray Karen F , Colletti Richard B 
Published: April 2011

ABSTRACTThe pediatric population has a number of unique considerations related to the diagnosis and treatment of ascites. This review summarizes the physiologic mechanisms for cirrhotic and noncirrhotic ascites and provides a comprehensive list of reported etiologies stratified by the patient's age. Characteristic findings on physical examination, diagnostic imaging, and abdominal paracentesis are also reviewed, with particular attention to those aspects that are unique to children. Medical and surgical treatments of ascites are discussed. Both prompt diagnosis and appropriate management of ascites are required to avoid associated morbidity and mortality.