bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accelerating epistasis analysis in human genetics with consumer graphics hardware
Authors: Sinnott-Armstrong Nicholas A , Greene Casey S , Cancare Fabio , Moore Jason H 
Published: July 2009

Abstract

Background
Human geneticists are now capable of measuring more than one million DNA sequence variations from across the human genome. The new challenge is to develop computationally feasible methods capable of analyzing these data for associations with common human disease, particularly in the context of epistasis. Epistasis describes the situation where multiple genes interact in a complex non-linear manner to determine an individual's disease risk and is thought to be ubiquitous for common diseases. Multifactor Dimensionality Reduction (MDR) is an algorithm capable of detecting epistasis. An exhaustive analysis with MDR is often computationally expensive, particularly for high order interactions. This challenge has previously been met with parallel computation and expensive hardware. The option we examine here exploits commodity hardware designed for computer graphics. In modern computers Graphics Processing Units (GPUs) have more memory bandwidth and computational capability than Central Processing Units (CPUs) and are well suited to this problem. Advances in the video game industry have led to an economy of scale creating a situation where these powerful components are readily available at very low cost. Here we implement and evaluate the performance of the MDR algorithm on GPUs. Of primary interest are the time required for an epistasis analysis and the price to performance ratio of available solutions.

Findings
We found that using MDR on GPUs consistently increased performance per machine over both a feature rich Java software package and a C cluster implementation. The performance of a GPU workstation running a GPU implementation reduces computation time by a factor of 160 compared to an 8-core workstation running the Java implementation on CPUs. This GPU workstation performs similarly to 150 cores running an optimized implementation on a Beowulf cluster. Furthermore this GPU system provides extremely cost effective performance while leaving the CPU available for other tasks. The GPU workstation containing three GPUs costs $2000 while obtaining similar performance on a Beowulf cluster requires 150 CPU cores which, including the added infrastructure and support cost of the cluster system, cost approximately $82,500.

Conclusion
Graphics hardware based computing provides a cost effective means to perform genetic analysis of epistasis using MDR on large datasets without the infrastructure of a computing cluster.
Relations between chemical changes and mechanical properties of thermally treated wood 10th EWLP, Stockholm, Sweden, August 25–28, 2008
Authors: Windeisen Elisabeth , Bächle Helmut , Zimmer Bernhard , Wegener Gerd 
Published: July 2009

Abstract
Thermal treatments of wood (Fagus sylvatica and Fraxinus excelsior) were examined. The temperature load on wood causes characteristic changes in the chemical composition, which were determined by means of several defined methods. The results confirm that in addition to the degradation of polyoses lignin, known as the thermally most stable compound, also shows significant thermal alterations. In addition, mechanical properties of the specimens were examined in order to correlate these results with the effects of chemical changes of thermally treated wood. It was shown, e.g., that the decomposition of the polyoses can affect the strength properties both positively and negatively.
A novel, mild and selective methylation of carboxyl groups in cellulosic pulps 10th EWLP, Stockholm, Sweden, August 25–28, 2008
Authors: Tot Ivana , Müller Yvonne , Werner Carsten , Rosenau Thomas , Potthast Antje 
Published: July 2009

Abstract
A method for selective, fast, and near-quantitative methylation of carboxyl groups in the presence of aliphatic hydroxyl groups of cellulose was developed. The main advantage of the method is the complete maintenance of cellulose integrity; no degradation of cellulose whatsoever during the methylation procedure was observed, making the protocol extremely useful in advanced cellulose analytics. Trimethylsilyl diazomethane (TMS-DAM) was used as the methylation agent. The methylation conditions were pre-optimized by means of carbohydrate model compounds with low-molecular weight, such as derivatives of glucuronic acid and hexenuronic acid, and then re-optimized for methylation of cellulose. The influence of reaction parameters, such as time, temperature, solvents, and concentration, was also determined. The reaction kinetics was monitored by fluorescence labeling of the remaining carboxyl groups according to the common FDAM protocol. A general protocol for the fast methylation of carboxyl groups in pulp samples is presented. The methylation with TMS-DAM is a very fast process, both in comparison to general heterogeneous reactions on cellulosic pulps, and especially in comparison to other methylation approaches. In dissolving and paper grade pulps, methylation of xylan carboxyls proceeded faster than methylation of cellulosic carboxyls. The methylation rate and kinetics are dependent on the pulp type. As application examples, electrokinetic measurements were used to demonstrate the “blocked” reactivity of carboxyl groups in spin-coated films of methylated pulp samples, and ICP-MS was used to demonstrate the drastically decreased metal ion binding capacity of pulp after such methylation.
Generalized Fitting Parameters of Three Permeability Functions for Predicting Water Coefficient of Permeability of Lateritic Soil
Authors: Gui Meen-Wah , Hsu Chun-Seng 
Published: July 2009

Abstract
The understanding of water flowing through unsaturated soil, such as in the upper layer of a residual hillside or earth dam, is particularly important for numerous geotechnical and geo-environmental problems. However, the effect of the water coefficient of permeability on flow of seepage through unsaturated soil, which is a function of void ratio and volumetric water content (or matric suction), is often ignored in engineering practice due to the requirements of a more advanced testing equipment and a longer testing duration for the determination of such a coefficient. A flexible-wall permeameter has been manufactured and used to determine the water coefficient of permeability of unsaturated lateritic soil under wetting condition. Three permeability functions have been evaluated and fitted to the laboratory measured results. From this, generalized fitting parameters, in terms of effective normal stress, of the three permeability functions have been derived for the study soil. The proposed generalized fitting parameters together with the permeability functions will provide practicing engineers with the essential parameter for the analysis of seepage related problems involving lateritic soil.
Evaluating Parameters for Characterization of Cracking in Asphalt Concrete
Authors: Tarefder Rafiqul A. , Kias Evan M. , Stormont John C. 
Published: July 2009

Abstract
This study evaluates parameters derived from laboratory tests to characterize crack initiation and propagation within the semi-circular asphalt concrete samples in the laboratory. Asphalt samples are compacted using a Superpave gyratory compactor, and then sliced and notched using a laboratory saw. The notch acts to facilitate crack initiation. Notched samples are subjected to a strain controlled compressive load in three point bending. Crack opening displacements (CODs) and loads are recorded in real time using four linear variable displacement transducers. Ultimate load, COD at ultimate load, cracking potential, fracture load, crack velocity, and slope of the crack propagation curve are determined from laboratory test results and evaluated for their suitability in characterizing crack initiation and crack propagation. In essence, these parameters are evaluated through examining the effects of notch tip location, moisture condition, and void ratio on crack initiation and propagation. It is shown that crack initiation can be best characterized by the ultimate load. Crack velocity and slope of the crack propagation curve show promise in characterizing crack propagation in the notched asphalt samples.
Cultural and Family Challenges to Managing Type 2 Diabetes in Immigrant Chinese Americans
Authors: Chesla Catherine A. , Chun Kevin M. , Kwan Christine M.L. 
Published: July 2009

OBJECTIVEAlthough Asians demonstrate elevated levels of type 2 diabetes, little attention has been directed to their unique cultural beliefs and practices regarding diabetes. We describe cultural and family challenges to illness management in foreign-born Chinese American patients with type 2 diabetes and their spouses.RESEARCH DESIGN AND METHODSThis was an interpretive comparative interview study with 20 foreign-born Chinese American couples (n = 40) living with type 2 diabetes. Multiple (six to seven) semistructured interviews with each couple in individual, group, and couple settings elicited beliefs about diabetes and narratives of care within the family and community. Interpretive narrative and thematic analysis were completed. A separate respondent group of 19 patients and spouses who met the inclusion criteria reviewed and confirmed the themes developed from the initial couples.RESULTSCultural and family challenges to diabetes management within foreign-born Chinese American families included how 1) diabetes symptoms challenged family harmony, 2) dietary prescriptions challenged food beliefs and practices, and 3) disease management requirements challenged established family role responsibilities.CONCLUSIONSCulturally nuanced care with immigrant Chinese Americans requires attentiveness to the social context of disease management. Patients' and families' disease management decisions are seldom made independent of their concerns for family well-being, family face, and the reciprocal responsibilities required by varied family roles. Framing disease recommendations to include cultural concerns for balance and significant food rituals are warranted.
Clinical Interpretation of a Lower-Extremity Functional Scale–Derived Computerized Adaptive Test
Authors: Wang Ying-Chih , Hart Dennis L. , Stratford Paul W. , Mioduski Jerome E. 
Published: July 2009

BackgroundThe increasing use of computerized adaptive tests (CATs) to generate outcome measures during rehabilitation has prompted questions concerning score interpretation.ObjectiveThe purpose of this study was to describe meaningful interpretations of functional status (FS) outcome measures estimated with a body part–specific CAT developed from the Lower-Extremity Functional Scale (LEFS).DesignThis investigation was a prospective cohort study of 8,714 people who had hip impairments and were receiving physical therapy in 257 outpatient clinics in 31 states (United States) between January 2005 and June 2007.MethodsFour approaches were used to clinically interpret outcome data. First, the standard error of the estimate was used to construct the 90% confidence interval for each CAT-generated score estimate. Second, percentile ranks were applied to FS scores. Third, 2 threshold approaches were used to define individual subject–level change: statistically reliable change and clinically important change. The fourth approach was a functional staging method.ResultsThe precision of a single score was estimated from the FS score ±4. On the basis of the score distribution, 25th, 50th, and 75th percentile ranks corresponded to intake FS scores of 40, 48, and 59 and discharge FS scores of 50, 61, and 75, respectively. The reliable change index supported the conclusion that changes in FS scores of 7 or more units represented statistically reliable change, and receiver operating characteristic analyses supported the conclusion that changes in FS scores of 6 or more units represented minimal clinically important improvement. Participants were classified into 5 hierarchical levels of FS using a functional staging method.LimitationsBecause this study was a secondary analysis of prospectively collected data via a proprietary database management company, generalizability of results may be limited to participating clinics.ConclusionsThe results demonstrated how outcome measures generated from the hip LEFS CAT can be interpreted to improve clinical meaning. This finding might facilitate the use of patient-reported outcomes by clinicians during rehabilitation services.
Fine Needle Aspiration Cytology of Prostatic Lesions with Histologic Correlation
Authors: Islam Tariqul , Chowdhury Tamanna , Khan KH , Barua AR , Kamal Mohammed , Rahman AJE Nahar 
Published: July 2009

Cytologic diagnosis by fine needle aspiration of the prostate was compared to histological diagnosis by either core biopsy or transurethral prostatic resection in 58 patients suspected to have prostatic lesion by rectal examination.The diagnostic accuracy between cytological and histological diagnosis was 93% and the false negative rate was 3.03% for fine needle aspiration. Inadequate cytological samples occurred only in two cases. This study was conducted during the period of April 2003 to February 2004. Fine needle aspiration cytology of prostatic lesions is a recently introduced procedure in Bangladesh. Our results indicate that fine needle aspiration is an easily performed, diagnostically reliable outpatient procedure with minimal complication. Ibrahim Med. Coll. J. 2007; 1(1): 7-10 Key words : FNAC, Franzen, Papaniculaou doi: 10.3329/imcj.v1i1.2888
Mise en place d'un service de veille collective pour la recherche : déroulement du projet, évaluation et perspectives
Authors: Bodart Marie-Gabrielle , Falize Caroline 
Published: July 2009

Résumé À la suite de réformes menées par le ministère de la Recherche ont été créées des unités mixtes de recherche qui, sur une même thématique, associent des partenaires de divers horizons. Restructurant son département d’économie et sociologie rurales, l’INRA de Montpellier a ainsi créé deux UMR dotées d’un centre de documentation commun. Simultanément, un audit de ce centre a fait ressortir le besoin des scientifiques de disposer d’un service de veille. Cet article relate l’expérience engagée en étroite collaboration avec les chercheurs : enquête de besoins, lancement du projet, organisation de la veille, résultats obtenus, bilan de l’investissement des documentalistes, bénéfices retirés par chercheurs et documentalistes, perspectives.
Journée d'étude ADBS audiovisuel
Authors: Boulogne Arlette , Jadoul Marie-Berthe , Masse Claudine , Ménillet Dominique , Pappano Hortensia 
Published: July 2009

Résumé Au moment de la sortie du numéro spécial thématique de Documentaliste – Sciences de l’information consacré à l’image et à l’audiovisuel (vol. 42, n? 6, 2005), le secteur Audiovisuel de l’ADBS proposait, le 9 mars 2006 à l’IRD, une journée d’étude consacrée à l’indexation des images et des sons. Quelles conséquences la numérisation des images et des documents sonores et musicaux peut-elle avoir sur le travail documentaire en général et plus précisément sur la pratique de l’indexation ? Quel usage faire des métadonnées ? Comment fonctionnent les outils de recherche par le contenu ? Exposés théoriques et présentations d’expérimentations ont tenté de répondre à ces questions.
Journée d'étude ADBS-INTD
Authors: Baudry de Vaux Marie , Dalbin Sylvie 
Published: July 2009

Résumé Les différents usages des métadonnées pour la gestion du cycle de vie des documents et pour la production et la diffusion d’information par différents canaux, l’impact des métadonnées sur la valorisation de l’information grâce à sa manipulation par des programmes informatiques : tels étaient les thèmes d’une journée d’étude conjointement organisée le 4 avril 2006 au CNAM par a commission Technologies et méthodes de l’Association des professionnels de l’information et de la documentation (ADBS) et l’Institut national des techniques de la documentation (INTD-CNAM).
Journée d'étude ADBS
Authors: Ferchaud Bernadette 
Published: July 2009

Résumé Dans le cadre du dernier Forum de la GEIDE, l’Association des professionnels de l’information et de la documentation (ADBS) proposait le 3 octobre 2006 une demi-journée d’étude pour faire le point sur l’usage de la gestion électronique de documents pour la constitution de fonds documentaires : les différentes étapes à respecter, les précautions à prendre selon les documents que l’on traite et les objectifs assignés à leur numérisation, les formats de représentation auxquels on peut recourir. L’exemple du portail documentaire de Radio France a été présenté en illustration.
Conference Juriconnexion 2006
Authors: Battisti Michèle 
Published: July 2009

Résumé Sous le titre « Internet juridique 2.0 : comment la nouvelle génération des outils et moyens de l’internet juridique peut améliorer immédiatement et facilement votre service d’information juridique (veille, recherches, stockage, échanges, etc.) ? », l’association Juriconnexion proposait, le 23 novembre 2006 à Paris, sa conférence annuelle. Elle s’est attachée à identifier les techniques à maîtriser et les stratégies à développer pour utiliser au mieux les outils du web 2.0 dans le domaine juridique. Parmi les sujets abordés : l’importance des wikis dans l’évolution de la circulation du droit, l’optimisation de l’utilisation des blogs et des fils RSS, les enjeux du XML dans le monde de la documentation juridique, ainsi que les questions juridiques soulevées par l’utilisation de ces nouvelles techniques.
Quantification of gypsum crystal nucleation, growth, and breakage rates in a wet flue gas desulfurization pilot plant
Authors: Hansen Brian B. , Kiil Søren , Johnsson Jan E. 
Published: July 2009

AbstractThe aim of this work is to study the influence of nucleation, growth and breakage on the particle size distribution (PSD) of gypsum crystals produced by the wet flue gas desulfurization (FGD) process. The steady state PSD, obtained in a falling film wet FGD pilot plant during desulfurization of a 1000 ppm(v) SO2 gas stream, displayed a strong nonlinear behaviour (in a ln(n(l)) vs. l plot) at the lower end of the particle size range, compared to the well‐known linear mixed suspension mixed product removal model. A transient population balance breakage model, fitted to experimental data, was able to model an increase in the fraction of small particles, but not to the extent observed experimentally. A three‐parameter, size‐dependent growth model, previously used for sodium sulphate decahydrate and potash alum, was able to describe the experimental data, indicating either size‐dependent integration kinetics or growth rate dispersion. © 2009 American Institute of Chemical Engineers AIChE J, 2009
Development, testing, and validation of a patient satisfaction questionnaire for use in the clinical genetics setting
Authors: Zellerino Barbara , Milligan Sharon A. , Brooks Ron , Freedenberg Debra L. , Collingridge Dave S. , Williams Marc S. 
Published: July 2009

AbstractPatient satisfaction is an important component of assessing quality of care. The purpose of this study is to develop a concise patient satisfaction tool specifically for use in the clinical genetics setting. An international survey identified two domains, “Respect Given” and “Patient Questions Answered” as being important components of satisfaction in the genetic encounter. A working group of professionals assembled a 14‐question pilot questionnaire that was subsequently tested in 13 clinical sites. Nearly 400 responses were used to validate the tool and ultimately construct a 7‐item questionnaire. The 7‐item questionnaire was found to be reliable and valid and addresses two key components of patient satisfaction: technical aspects of care and interpersonal relations. The tool is compared to other patient satisfaction tools developed for use in the clinical genetics setting. A Spanish version is also provided. © 2009 Wiley‐Liss, Inc.
Development of a fluorimetric detection method for cinnabarinic acid using ortho‐tolyl hydrazine as the derivatization reagent
Authors: Iizuka Hideaki , Obata Kensaku , Yajima Takehiko , Ichiba Hideaki , Fukushima Takeshi 
Published: July 2009

AbstractA fluorimetric detection method for one of the tryptophan metabolites, cinnabarinic acid (CA), which has recently been reported to have the ability to induce apoptosis in thymocytes, was developed using o‐tolyl hydrazine (TH) as the derivatization reagent. The carbonyl group at position 3 in CA was tagged with the hydrazino moiety of TH at 100°C for 30 min, and the generated derivative, CA tagged with TH, fluoresced at 412 nm with a 316 nm excitation wavelength. The CA tagged with TH was separated on a reversed‐phase HPLC and detected fluorometrically. The relative standard deviation was in the range of 1.1–8.9% (n = 3), and the detection limit was approximately 12?fmol (signal‐to‐noise ratio, 3). The proposed HPLC method can be useful for the sensitive detection of CA. Copyright © 2009 John Wiley & Son, Ltd.
HPLC of basic drugs using non‐aqueous ionic eluents: evaluation of a 3 μm strong cation‐exchange material
Authors: Morgan Phillip E. , Manwaring Victoria , Flanagan Robert J 
Published: July 2009

AbstractHPLC columns packed with 3 μm particle size HPLC Technology Techsphere SCX (propylsulfonic acid‐modified) silica offer considerable advantages over 5 μm SCX packings in the analysis of basic drugs using 100% methanol eluents containing an ionic modifier such as ammonium perchlorate. The basic drugs studied included clozapine and norclozapine, olanzapine, quinine and quinidine, and amitriptyline, nortriptyline, imipramine and desipramine. The 3 μm column was not only more efficient for a given column length compared with 5 μm materials, but also elution times were less, a phenomenon observed in reversed‐phase systems. The high efficiencies and excellent peak shapes obtained with the 3 μm SCX‐modified packing together with the relatively low back‐pressures attained show that such materials deserve serious consideration by laboratories involved in the analysis of basic drugs. Manufacturers should offer such packings as a matter of routine. Alternative ionic modifiers such as ammonium acetate are available for use with mass spectrometric detection if required. Copyright © 2009 John Wiley & Sons, Ltd.
A sensitive liquid chromatography–electrospray ionization–mass spectrometry method for the simultaneous determination of pentoxyverine citrate and guaifenesin in human plasma—application to pharmacokinetic and bioequivalence studies
Authors: Wen Jinhua , Zhang Hong , Xia Chunhua , Hu Xiao , Xu Wenwei , Cheng Xiaohua , Gao Jun , Xiong Yuqing 
Published: July 2009

AbstractA sensitive and specific liquid chromatography–electrospray ionization–mass spectrometry method for the identification and quantification of pentoxyverine citrate and guaifenesin in human plasma has been developed. After extraction from plasma samples by ethyl acetate, the internal standard and analytes were separated by high‐performance liquid chromatographic on a Shim‐pack VP‐ODS C18 column (150 × 2.0 mm) using a mobile phase consisting of A (methanol) and B (0.4% glacial acetic acid and 4 mmol/L ammonium acetate) (A:B, 43 : 57). Analysis was performed on a Shimadzu LC/MS‐2010A in selected ion monitoring mode with a positive electrospray ionization interface. The method was linear in the concentration range of 1.0–640.0 ng/mL for pentoxyverine citrate and 0.025–6.4 μg/mL for guaifenesin. The inter‐ and intra‐ precision were all within 12% and accuracy ranged from 85 to 115%.The lower limits of quantification were 1.0 ng/mL for pentoxyverine citrate and 25.0 ng/mL for guaifenesin. The extraction recovery was on average 81.95% for pentoxyverine citrate and 89.03% for guaifenesin. This is the first assay method reported for the simultaneous determination of pentoxyverine citrate and guaifenesin in plasma using one chromatographic run. Copyright © 2009 John Wiley & Sons, Ltd.