bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic syndrome in the elderly living in marginal peri-urban communities in Quito, Ecuador
Authors: Sempértegui Fernando , Estrella Bertha , Tucker Katherine L , Hamer Davidson H , Narvaez Ximena , Sempértegui Mercy , Griffiths Jeffrey K , Noel Sabrina E , Dallal Gerard E , Selhub Jacob , Meydani Simin N 
Published: October 2010

AbstractObjectiveThe proportion of the Latin American population aged >60 years is expected to double during the next few decades. Metabolic syndrome (MetS) is associated with high morbidity and mortality worldwide. However, little is known about MetS in Latin America in general, and in Ecuador in particular. The present study aimed to examine the prevalence of MetS and its association with blood micronutrient, homocysteine (Hcy) and C-reactive protein (CRP) concentrations in the elderly living in a low-income urban area.DesignWe performed a cross-sectional study. MetS, using the International Diabetes Federation definition, dietary intake and plasma micronutrient, CRP and Hcy concentrations were assessed.SubjectsA total of 352 elderly (≥65 years) Ecuadorians.SettingQuito, Ecuador.ResultsMetS was prevalent (40 %) – considerably more so among women (81 %) than men (19 %;χ2= 32·6,P< 0·0001). Further, 53 % of those without MetS exhibited two or more of its components. Micronutrient deficiencies were prevalent, including those of vitamin C, zinc, vitamin B12and folate. Vitamin C and E concentrations were inversely (OR = 0·78, 95 % CI 0·71, 0·86; OR = 0·16, 95 % CI 0·03, 0·81, respectively) and CRP (OR = 1·79, 95 % CI 1·04, 3·06) was positively associated with MetS.ConclusionsThe coexistence of MetS with micronutrient deficiencies suggests that elderly Ecuadorians suffer from the double burden of diseases that are increasingly being observed in less developed countries. More research is needed to determine the causal factors, but results presented suggest that these older adults would benefit from interventions to reduce the risk factors for MetS, in particular higher consumption of micronutrient-rich foods.
An Eventful Life Remembered: Recent Considerations of the Contributions and Legacy of Francis O'Neill
Authors: SOMMERS SMITH SALLY K. 
Published: October 2010

AbstractFrancis O'Neill, one of the towering figures of Irish traditional music, was among the first to collect and publish Irish dance music. His compilations form the most complete glimpse into Irish musical practice at the turn of the twentieth century and are still regarded as the definitive source for traditional tunes. Three recent publications on O'Neill and his times throw light on his life, his passion for the music, and his legacy among today's traditional music community.
Wheels of the World: How Recordings of Irish Traditional Music Bridged the Gap between Homeland and Diaspora
Authors: SPENCER SCOTT 
Published: October 2010

AbstractAt the dawn of the twentieth century and the height of the Recording Age, Irish American musicians began to record Irish traditional music on both commercial and subcommercial recordings. Circulated within the diaspora during a changing sense of Irish identity and sent home to a nationalist revival, these recordings had a profound impact on both traditional performance practices and modes of transmission. Quickly accepted by many at the heart of the tradition, these recordings were used by practitioners to bridge vast geographic distances and solidify vital lines of communication, allowing the diaspora to engage actively with the larger tradition.
60 GHz current gain cut-off frequency graphene nanoribbon FET
Authors: Meng Nan , Ferrer Francsico-Javier , Vignaud Dominique , Dambrine Gilles , Happy Henri 
Published: October 2010

We report investigations on the fabrication and characterization of graphene nanoribbon (GNR) field-effect transistors. Graphene layers are obtained from the thermal decomposition of a Si-face 4H-SiC substrate. To achieve high dynamic performance, a structure with an array of GNR connected in parallel was fabricated by e-beam lithography. The best intrinsic current gain cut-off frequency of 60 GHz and maximum oscillation frequency of 28 GHz were achieved. This study demonstrates the exciting potential of GNR in high-frequency electronics.
Foregut microbiome in development of esophageal adenocarcinoma
Authors: Nossa Carlos , Francois Fritz , Torralba Manolito , Brown Stuart , Traube Morris , Yooseph Shibu , Chen Yu , Singh Navjeet , Rogers Yu-Hui , Liu Mengling , DeSantis Todd , Brodie Eoin , Andersen Gary , Nelson Karen , Yang Liying , Bihan Monika , Pei Zhiheng , Oberdorf William , Foster Les , Gerz Erika , Tenney Aaron , Parsons Tamasha , Brami Daniel , Thiagarajan Mathangi , Shah Pinak , Poles Michael , Singh Indresh , Bedi Sukhleen 
Published: October 2010

AbstractEsophageal adenocarcinoma (EA), the type of cancer linked to heartburn due to gastroesophageal reflux diseases (GERD), has increased six fold in the past 30 years. This cannot currently be explained by the usual environmental or by host genetic factors. EA is the end result of a sequence of GERD-related diseases, preceded by reflux esophagitis (RE) and Barrett’s esophagus (BE). Preliminary studies by Pei and colleagues at NYU on elderly male veterans identified two types of microbiotas in the esophagus. Patients who carry the type II microbiota are >15 fold likely to have esophagitis and BE than those harboring the type I microbiota. In a small scale study, we also found that 3 of 3 cases of EA harbored the type II biota. The findings have opened a new approach to understanding the recent surge in the incidence of EA.Our long-term goal is to identify the cause of GERD sequence. The hypothesis to be tested is that changes in the foregut microbiome are associated with EA and its precursors, RE and BE in GERD sequence. We will conduct a case control study to demonstrate the microbiome disease association in every stage of GERD sequence, as well as analyze the trend in changes in the microbiome along disease progression toward EA, by two specific aims. Aim 1 is to conduct a comprehensive population survey of the foregut microbiome and demonstrate its association with GERD sequence. Furthermore, spatial relationship between the esophageal microbiota and upstream (mouth) and downstream (stomach) foregut microbiotas as well as temporal stability of the microbiome-disease association will also be examined. Aim 2 is to define the distal esophageal metagenome and demonstrate its association with GERD sequence. Detailed analyses will include pathway-disease and gene-disease associations. Archaea, fungi and viruses, if identified, also will be correlated with the diseases. A significant association between the foregut microbiome and GERD sequence, if demonstrated, will be the first step for eventually testing whether an abnormal microbiome is required for the development of the sequence of phenotypic changes toward EA. If EA and its precursors represent a microecological disease, treating the cause of GERD might become possible, for example, by normalizing the microbiota through use of antibiotics, probiotics, or prebiotics. Causative therapy of GERD could prevent its progression and reverse the current trend of increasing incidence of EA.
Trends in High-Temperature Polymer Electrolyte Fuel Cells
Authors: Lehnert Werner , Wannek Christoph , Zeis Roswitha 
Published: October 2010

The HT-PEFC, based on polybenzimidazole type membranes doped with phosphoric acid, has a typical operating temperature of 160 °C. As a result of the high temperature level, it has a high CO tolerance, which means that it is particularly suitable for operation in combination with reformers. Compared to Nafion-based polymer electrolyte membrane fuel cells, water is not required for the ionic conductivity of the membrane; therefore the gases do not need to be humidified. Another advantage of HT-PEFC technology is that due to the high temperature difference between the stack and the ambient temperatures, cooling can be designed in a much more compact manner than is necessary in classical PEMFC systems.
However, for all these advantages, prevention measures must be in place to ensure that the acid is not discharged from the membrane. Operating conditions that could create liquid water in the cells should be avoided. Save operation below 120°C is possible only with pure hydrogen. Due to the decreasing CO tolerance with decreasing temperature operation above 120°C is necessary if the fuel contains typical CO concentrations of 1%. Operation in low temperature ranges should therefore be avoided. This has been taken into account by operating strategies and the specific areas of application. In this context the oxygen reduction reaction and operation behaviour of cells and stacks will be discussed.
PICMI: mapping point mutations on genomes
Authors: Le Pera Loredana , Marcatili Paolo , Tramontano Anna 
Published: October 2010

Abstract
Motivation: Several international collaborations and local projects are producing extensive catalogues of genomic variations that are supplementing existing collections such as the OMIM catalogue. The flood of this type of data will keep increasing and, especially, it will be relevant to a wider user base, including not only molecular biologists, geneticists and bioinformaticians, but also clinical researchers. Mapping the observed variations, sometimes only described at the amino acid level, on a genome, identifying whether they affect a gene and—if so—whether they also affect different isoforms of the same gene, is a time consuming and often frustrating task.
Results: The PICMI server is an easy to use tool for quickly mapping one or more amino acid or nucleotide variations on a genome and its products, including alternatively spliced isoforms.
Availability: The server is available at www.biocomputing.it/picmi
Contact: anna.tramontano@uniromal.it
Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules
Authors: Cheng Tiejun , Wang Yanli , Bryant Stephen H. 
Published: October 2010

Abstract
Motivation: Most of the previous data mining studies based on the NCI-60 dataset, due to its intrinsic cell-based nature, can hardly provide insights into the molecular targets for screened compounds. On the other hand, the abundant information of the compound–target associations in PubChem can offer extensive experimental evidence of molecular targets for tested compounds. Therefore, by taking advantages of the data from both public repositories, one may investigate the correlations between the bioactivity profiles of small molecules from the NCI-60 dataset (cellular level) and their patterns of interactions with relevant protein targets from PubChem (molecular level) simultaneously.
Results: We investigated a set of 37 small molecules by providing links among their bioactivity profiles, protein targets and chemical structures. Hierarchical clustering of compounds was carried out based on their bioactivity profiles. We found that compounds were clustered into groups with similar mode of actions, which strongly correlated with chemical structures. Furthermore, we observed that compounds similar in bioactivity profiles also shared similar patterns of interactions with relevant protein targets, especially when chemical structures were related. The current work presents a new strategy for combining and data mining the NCI-60 dataset and PubChem. This analysis shows that bioactivity profile comparison can provide insights into the mode of actions at the molecular level, thus will facilitate the knowledge-based discovery of novel compounds with desired pharmacological properties.
Availability: The bioactivity profiling data and the target annotation information are publicly available in the PubChem BioAssay database (ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/).
Contact: ywang@ncbi.nlm.nih.gov; bryant@ncbi.nlm.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Graph-based Word Sense Disambiguation of biomedical documents
Authors: Agirre Eneko , Soroa Aitor , Stevenson Mark 
Published: October 2010

Abstract
Motivation: Word Sense Disambiguation (WSD), automatically identifying the meaning of ambiguous words in context, is an important stage of text processing. This article presents a graph-based approach to WSD in the biomedical domain. The method is unsupervised and does not require any labeled training data. It makes use of knowledge from the Unified Medical Language System (UMLS) Metathesaurus which is represented as a graph. A state-of-the-art algorithm, Personalized PageRank, is used to perform WSD.
Results: When evaluated on the NLM-WSD dataset, the algorithm outperforms other methods that rely on the UMLS Metathesaurus alone.
Availability: The WSD system is open source licensed and available from http://ixa2.si.ehu.es/ukb/. The UMLS, MetaMap program and NLM-WSD corpus are available from the National Library of Medicine http://www.nlm.nih.gov/research/umls/, http://mmtx.nlm.nih.gov and http://wsd.nlm.nih.gov. Software to convert the NLM-WSD corpus into a format that can be used by our WSD system is available from http://www.dcs.shef.ac.uk/∼marks/biomedical_wsd under open source license.
Contact: m.stevenson@dcs.shef.ac.uk
GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation
Authors: Zhang Jian , Zhang Yang 
Published: October 2010

Abstract
Summary: G protein-coupled receptors (GPCRs) comprise the largest family of integral membrane proteins. They are the most important class of drug targets. While there exist crystal structures for only a very few GPCR sequences, numerous experiments have been performed on GPCRs to identify the critical residues and motifs. GPCRRD database is designed to systematically collect all experimental restraints (including residue orientation, contact and distance maps) available from the literature and primary GPCR resources using an automated text mining algorithm combined with manual validation, with the purpose of assisting GPCR 3D structure modeling and function annotation. The current dataset contains thousands of spatial restraints from mutagenesis, disulfide mapping distances, electron cryo-microscopy and Fourier-transform infrared spectroscopy experiments.
Availability: http://zhanglab.ccmb.med.umich.edu/GPCRRD/
Contact: zhng@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads
Authors: Reuman Elizabeth C. , Margeridon-Thermet Severine , Caudill Harrison B. , Liu Tommy , Borroto-Esoda Katyna , Svarovskaia Evguenia S. , Holmes Susan P. , Shafer Robert W. 
Published: October 2010

AbstractMotivation: G → A hypermutation is an innate antiviral defense mechanism, mediated by host enzymes, which leads to the mutational impairment of viruses. Sensitive and specific identification of host-mediated G → A hypermutation is a novel sequence analysis challenge, particularly for viral deep sequencing studies. For example, two of the most common hepatitis B virus (HBV) reverse transcriptase (RT) drug-resistance mutations, A181T and M204I, arise from G → A changes and are routinely detected as low-abundance variants in nearly all HBV deep sequencing samples.Results: We developed a classification model using measures of G → A excess and predicted indicators of lethal mutation and applied this model to 325 920 unique deep sequencing reads from plasma virus samples from 45 drug treatment-naïve HBV-infected individuals. The 2.9% of sequence reads that were classified as hypermutated by our model included most of the reads with A181T and/or M204I, indicating the usefulness of this model for distinguishing viral adaptive changes from host-mediated viral editing.Availability: Source code and sequence data are available at http://hivdb.stanford.edu/pages/resources.html.Contact: ereuman@stanfordalumni.orgSupplementary information: Supplementary data are available at Bioinformatics online.
IgA antibodies to Chlamydia trachomatis and metabolic syndrome
Authors: Sehnem Luciele , Bodanese Luiz Carlos , Repetto Giuseppe , Staub Henrique L. 
Published: October 2010

ABSTRACT Chlamydia pneumoniae may trigger atherogenesis. Chlamydia trachomatis (CT) can also induce endothelial activation. However, its role in metabolic syndrome (METS), a proatherogenic entity, has remained unexplored. In this study the frequencies of IgA and IgG anti‐CT antibodies were evaluated by immunoenzymatic assay in METS patients and healthy controls. The survey included 238 individuals (148 with METS). The mean age was 59.7 years. IgA anti‐CT antibodies were found significantly more frequently in METS patients (16.9%) than in controls (5.6%) (P= 0.015). The role of such IgA response in METS should be further investigated.
Differentiating new cannabis use from residual urinary cannabinoid excretion in chronic, daily cannabis users
Authors: Schwilke Eugene W. , Gullberg Rod G. , Darwin William D. , Chiang C. Nora , Cadet Jean Lud , Gorelick David A. , Pope Harrison G. , Huestis Marilyn A. 
Published: October 2010

ABSTRACTAims To develop and validate empirically a mathematical model for identifying new cannabis use in chronic, daily cannabis smokers.Design Models were based on urinary creatinine‐normalized (CN) cannabinoid excretion in chronic cannabis smokers.Setting For model development, participants resided on a secure research unit for 30 days. For model validation, participants were abstinent with daily observed urine specimens for 28 days.Participants A total of 48 (model development) and 67 (model validation) daily cannabis smokers were recruited.Measurements All voided urine was collected and analyzed for 11‐nor‐9‐carboxy‐Δ9‐tetrahydrocannabinol (THCCOOH) by gas chromatography‐mass spectrometry (GCMS; limit of quantification 2.5 ng/ml) and creatinine (mg/ml). Urine THCCOOH was normalized to creatinine, yielding ng/mg CN‐THCCOOH concentrations. Urine concentration ratios were determined from 123 513 specimen pairs collected 2–30 days apart.Findings A mono‐exponential model (with two parameters, initial urine specimen CN‐THCCOOH concentration and time between specimens), based on the Marquardt–Levenberg algorithm, provided a reasonable data fit. Prediction intervals with varying probability levels (80, 90, 95, 99%) provide upper ratio limits for each urine specimen pair. Ratios above these limits suggest cannabis re‐use. Disproportionate numbers of ratios were higher than expected for some participants, prompting development of two additional rules that avoid misidentification of re‐use in participants with unusual CN‐THCCOOH excretion patterns.Conclusions For the first time, a validated model is available to aid in the differentiation of new cannabis use from residual creatinine‐normalized 11‐nor‐9‐carboxy‐Δ9‐tetrahydrocannabinol (CN‐THCCOOH) excretion in chronic, daily cannabis users. These models are valuable for clinicians, toxicologists and drug treatment staff and work‐place, military and criminal justice drug‐testing programs.
The effects of itopride on oesophageal motility and lower oesophageal sphincter function in man
Authors: Scarpellini E. , Vos R. , Blondeau K. , Boecxstaens V. , Farré R. , Gasbarrini A. , Tack J. 
Published: October 2010

Aliment Pharmacol Ther 2011; 33: 99–105SummaryBackground  Itopride is a new prokinetic agent that combines antidopaminergic and cholinesterase inhibitory actions. Previous studies suggested that itopride improves heartburn in functional dyspepsia, and decreases oesophageal acid exposure in gastro‐oesophageal reflux disease. It remains unclear whether this effect is due to effects of itopride on the lower oesophageal sphincter (LES).Aims  To study the effects of itopride on fasting and postprandial LES function in healthy subjects.Methods  Twelve healthy volunteers (five men; 32.6 ± 2.0 years) underwent three oesophageal sleeve manometry studies after 3 days premedication with itopride 50 mg, itopride 100 mg or placebo t.d.s. Drug was administered after 30 min and a standardized meal was administered after 90 min, with measurements continuing to 120 min postprandially. Throughout the study, 10 wet swallows were administered at 30‐min intervals, and gastrointestinal symptoms were scored on 100 mm visual analogue scales at 15‐min intervals.Results  Lower oesophageal sphincter resting pressures, swallow‐induced relaxations and the amplitude or duration of peristaltic contractions were not altered by both doses of itopride, at all time points. Itopride pre‐treatment inhibited the meal‐induced rise of transient LES relaxations (TLESRs).Conclusions  Itopride inhibits TLESRs without significantly affecting oesophageal peristaltic function or LES pressure. These observations support further studies with itopride in gastro‐oesophageal reflux disease.
Risk stratification of normotensive patients with acute symptomatic pulmonary embolism
Authors: Jiménez David , Aujesky Drahomir , Yusen Roger D. 
Published: October 2010

SummaryTreatment guidelines recommend strong consideration of thrombolysis in patients with acute symptomatic pulmonary embolism (PE) that present with arterial hypotension or shock because of the high risk of death in this setting. For haemodynamically stable patients with PE, the categorization of risk for subgroups may assist with decision‐making regarding PE therapy. Clinical models [e.g. Pulmonary Embolism Severity Index (PESI)] may accurately identify those at low risk of overall death in the first 3 months after the diagnosis of PE, and such patients might benefit from an abbreviated hospital stay or outpatient therapy. Though some evidence suggests that a subset of high‐risk normotensive patients with PE may have a reasonable risk to benefit ratio for thrombolytic therapy, single markers of right ventricular dysfunction (e.g. echocardiography, spiral computed tomography, or brain natriuretic peptide testing) and myocardial injury (e.g. cardiac troponin T or I testing) have an insufficient positive predictive value for PE‐specific mortality to drive decision‐making toward such therapy. Recommendations for outpatient treatment or thrombolytic therapy for patients with PE necessitate further development of prognostic models and conduct of clinical trials that assess various treatment strategies.