bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age‐ and Gender‐specific BMI in Terms of the Lowest Mortality in Japanese General Population
Authors: Matsuo Tomoaki , Sairenchi Toshimi , Iso Hiroyasu , Irie Fujiko , Tanaka Kiyoji , Fukasawa Nobuko , Ota Hitoshi , Muto Takashi 
Published: August 2008

Objective: The primary purposes of our study were to establish age‐ and gender‐specific BMIs in terms of lowest mortality (risk nadir BMIs) for the Japanese population, and to then compare those to (i) BMIs for whites as determined by similar studies and to (ii) the official BMI guidelines.Methods and Procedures: A total of 32,060 men and 61,916 women aged 40–79 years underwent health check‐ups in Ibaraki prefecture, Japan, in 1993 and were followed through 2003. To determine the age‐ and gender‐specific risk nadir BMIs, coefficients and the lowest point from a quadratic model with transformed BMI were calculated by a Cox proportional hazard model. This included the quadratic term of 1/BMI and adjusted values (age, alcohol intake, and smoking status).Results: For both age and both gender categories, the relationship between all‐cause mortality risk and BMI categories are illustrated as U‐shaped curves. The risk nadir BMIs for men in the age groups of 40–59 and 60–79 years were 23.4 and 25.3 kg/m2, respectively. Similarly, in women, the risk nadir BMIs were 21.6 and 23.4 kg/m2, respectively.Discussion: Among the general Japanese population, the risk nadir BMI for the age group of 60–79 years was higher compared to the age group of 40–59 years, which was similar to the study for whites, and the age‐dependent risk nadir BMI differed from the official guidelines criteria. Our findings underscore the importance of weight control following appropriate indicators of body weight according to age.
Low Resting Energy Expenditure in Asians Can Be Attributed to Body Composition
Authors: Wouters‐Adriaens Mirjam P.E. , Westerterp Klaas R. 
Published: August 2008

Objective: To compare resting energy expenditure (REE) between Asians and whites after adjusting for fat‐free mass measured with a two‐ or more‐compartment model.Methods and Procedures: Participants were 10 white men (28 ± 3 years), 10 Asian men (30 ± 4 years), 10 white women (22 ± 4 years), and 11 Asian women (31 ± 7 years). REE was measured with a ventilated hood system under strictly controlled conditions. Body composition was measured with a two‐compartment model based on body mass (BM) and body volume (hydrodensitometry), a three‐compartment model adding total body water (TBW) (deuterium dilution), and a four‐compartment model incorporating bone mass (dual‐energy X‐ray absorptiometry (DXA)) as well. Lean BM in the trunk and in the extremities was assessed with DXA. All measurements were performed at Maastricht University. Measurements on Asian subjects were performed within 3 months after their arrival in the Netherlands.Results: Absolute REE was lower in Asians (5.87 ± 0.91 MJ/day) than in whites (7.00 ± 1.11 MJ/day). There was no significant difference in REE between the two races after adjustment for fat‐free mass.Discussion: There were no significant differences in REE between Asians and whites after adjustment for differences in body composition based on a two‐ or more‐compartment model.
Theoretical Modeling in Hemodynamics of Microcirculation
Authors: LEE JACK , SMITH NICOLAS P. 
Published: August 2008

ABSTRACTOver the past decades, theoretical modeling has become an indispensable component of research into the hemodynamics of microcirculation. Numerous studies rely on modeling to provide quantitative insights into the interacting biophysical mechanisms that govern microcirculatory flow. The mechanical deformation of hematocytes has been addressed by continuum and molecular‐informed computational models based on a growing body of experimental information. Theoretical analyses of single‐vessel flow and blood rheology have led to a range of modeling approaches. Until recently, computational constraints limited direct simulations of multi‐particle flows involving deformation and/or aggregation, but recent studies have begun to address this challenge. Network‐level analyses have provided insights into the biophysical principles underlying the design of the microcirculation. This approach has been used to complement available experimental data and to derive empirical models of microvascular blood rheology. Continued increases in computational performance applied to current modeling techniques will enable larger scale simulations. In order to exploit this opportunity, integration of diverse theoretical approaches within a multi‐scale framework is needed.
Neutrophil Recruitment under Shear Flow: It's All about Endothelial Cell Rings and Gaps
Authors: ALCAIDE PILAR , AUERBACH SCOTT , LUSCINSKAS FRANCIS W. 
Published: August 2008

ABSTRACTLeukocyte recruitment to tissues and organs is an essential component of host defense. The molecular mechanisms controlling this process are complex and remain under active investigation. The combination of biochemical techniques and live cell imaging using in vivo and in vitro flow‐model approaches have shed light on several aspects of neutrophil transmigration through the vascular endothelial lining of blood vessels. Here, we focus on the role of adhesion molecule signaling in endothelial cells and their downstream targets during the process of transendothelial migration at cell‐cell borders (paracellular transmigration). An emerging model involves the leukocyte β2 integrin engagement of endothelial cell ICAM‐1, which triggers integrin‐ICAM‐1 clustering (rings) and stabilizes leukocyte adhesion at cell‐cell junctions. This step recruits nonreceptor tyrosine kinases that phosphorylate key tyrosine residues in the cytoplasmic tail of VE‐cadherin, which destabilizes its linkage to catenins and the actin cytoskeleton, triggering the transient opening of VE‐cadherin homodimers to form a gap in the cell junction, through which the neutrophil transmigrates. Interestingly, the signaling events that lead to neutrophil transmigration occur independently of shear flow in vitro.
A study of the relationship between personality traits and theoretical orientation preferences
Authors: Ogunfowora Babatunde , Drapeau Martin 
Published: August 2008

AbstractThis study explored the relationship between personality and theoretical orientation preferences in two separate samples of psychotherapy practitioners and students. A total of 493 participants (274 practitioners and 219 students) completed a web‐based survey. Preference for theoretical orientation was assessed using a measure adapted from the Theoretical Orientation Profile Scale‐Revised, while personality was assessed with the HEXACO Personality Inventory. After controlling for the effects of gender, profession, and degree type, personality was found to predict preference for the humanistic/existential, cognitive‐behavioural, psychodynamic, and feminist theoretical orientations across both samples. Personality also predicted preference for the multicultural, family systems, and neuropsychological orientations, although these findings were applicable to only one sample. Implications for future research, psychotherapy training, and practice are discussed.
Learning from experience: Examining the impact of client work upon two trainee therapists
Authors: Turner Sarah , Gibson Neil , Bennetts Christine , Hunt Cheryl 
Published: August 2008

AbstractThis qualitative research study, focusing on the learning and change of two trainee therapists over a nine‐month period, was conducted by the trainees themselves. In collecting and analysing their data, the researchers made use of the heuristic methodology, to which some of the principles of the co‐operative inquiry methodology were added. The findings shed light on some of the ways in which trainee counsellors and psychotherapists might learn through their work with clients, the forms and contexts in which this learning may arise, and how the learning might affect the trainees. The findings additionally highlight some of the possible benefits of engaging in research for trainee counsellors and psychotherapists, in terms of their roles as practitioners. These include positive changes in the ways in which they work with clients, and changes in the ways they think about their practice.
Automated Surveillance for Central Line–Associated Bloodstream Infection in Intensive Care Units
Authors: Woeltje Keith F. , Butler Anne M. , Goris Ashleigh J. , Tutlam Nhial T. , Doherty Joshua A. , Westover M. Brandon , Ferris Vicky , Bailey Thomas C. 
Published: August 2008

Objective.To develop and evaluate computer algorithms with high negative predictive values that augment traditional surveillance for central line–associated bloodstream infection (CLABSI).Setting.Barnes-Jewish Hospital, a 1,250-bed tertiary care academic hospital in Saint Louis, Missouri.Methods.We evaluated all adult patients in intensive care units who had blood samples collected during the period from July 1, 2005, to June 30,2006, that were positive for a recognized pathogen on culture. Each isolate recovered from culture was evaluated using the definitions for nosocomial CLABSI provided by the National Healthcare Safety Network of the Centers for Disease Control and Prevention. Using manual surveillance by infection prevention specialists as the gold standard, we assessed the ability of various combinations of dichotomous rules to determine whether an isolate was associated with a CLABSI. Sensitivity, specificity, and predictive values were calculated.Results.Infection prevention specialists identified 67 cases of CLABSI associated with 771 isolates recovered from blood samples. The algorithms excluded approximately 40%-62% of the isolates from consideration as possible causes of CLABSI. The simplest algorithm, with 2 dichotomous rules (ie, the collection of blood samples more than 48 hours after admission and the presence of a central venous catheter within 48 hours before collection of blood samples), had the highest negative predictive value (99.4%) and the lowest specificity (44.2%) for CLABSI. Augmentation of this algorithm with rules for common skin contaminants confirmed by another positive blood culture result yielded in a negative predictive value of 99.2% and a specificity of 68.0%.Conclusions.An automated approach to surveillance for CLABSI that is characterized by a high negative predictive value can accurately identify and exclude positive culture results not representing CLABSI from further manual surveillance.
Discordant QuantiFERON-TB Gold Test Results Among US Healthcare Workers With Increased Risk of Latent Tuberculosis Infection: A Problem or Solution?
Authors: Pollock Nira R. , Campos-Neto Antonio , Kashino Suely , Napolitano Danielle , Behar Samuel M. , Shin Daniel , Sloutsky Alex , Joshi Swati , Guillet Jasmine , Wong Michael , Nardell Edward 
Published: August 2008

Objective.In late 2006, our hospital implemented use of the QuantiFERON-TB Gold (QFT-G) assay, a whole-blood interferon-γ release assay, for detection of tuberculosis infection. All newly hired healthcare workers (HCWs) with positive Mantoux tuberculin skin test (TST) results were routinely tested with the QFT-G assay, to take advantage of its higher specificity. We then undertook a quality assurance review to evaluate the QFT-G test results in HCWs with multiple risk factors for latent tuberculosis infection (LTBI).Methods.The clinical records for TST-positive HCWs tested with the QFT-G assay were reviewed. HCWs with 2 or more risk factors commonly associated with LTBI were classified as “increased risk” (IR). IR HCWs who had negative QFT-G test results underwent repeat QFT-G testing and were offered testing with a different interferon-γ release assay (T-SPOT.TB) and with extended T cell stimulation assays.Results.Ofl43 TST-positive HCWs tested with the QFT-G assay, 26 (18%) had positive results, 115 (81%) had negative results, and 2 (1 %) had indeterminate results. Of 82 IR HCWs, 23 (28%) had positive QFT-G test results, and 57 (70%) had negative results. Of the 57 IR HCWs with negative results, 43 underwent repeat QFT-G testing: 41 had negative results again, and 2 had positive results. These 43 HCWs were also offered additional testing with the T-SPOT.TB diagnostic, and 36 consented: 31/36 tested negative, and 5/36 tested positive. Extended assays using the antigens ESAT-6 and CFP-10 confirmed the positive results detected by the overnight assays and yielded positive results for an additional 7/36 (19%) of individuals; strikingly, all 36 HCWs had strongly positive test results with assays using purified protein derivative.Conclusions.The extreme discordance between the results of our clinical diagnostic algorithm and the results of QFT-G testing raises concern about the sensitivity of the QFT-G assay for detection of LTBI in our HCWs. Results of extended stimulation assays suggest that many of our IR HCWs have indeed been sensitized to Mycobacterium tuberculosis. It is possible that the QFT-G assay identifies those at higher reactivation risk rather than all previously infected, but, in the absence of long-term follow-up data, we should interpret negative QFT-G results with some caution.
Optimal contact map alignment of protein–protein interfaces
Authors: Pulim Vinay , Berger Bonnie , Bienkowska Jadwiga 
Published: August 2008

Abstract
The long-standing problem of constructing protein structure alignments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order to identify homologous residues across chains. A critical next step of this is the alignment of protein complexes and their interfaces. Here, we introduce the program CMAPi, a two-dimensional dynamic programming algorithm that, given a pair of protein complexes, optimally aligns the contact maps of their interfaces: it produces polynomial-time near-optimal alignments in the case of multiple complexes. We demonstrate the efficacy of our algorithm on complexes from PPI families listed in the SCOPPI database and from highly divergent cytokine families. In comparison to existing techniques, CMAPi generates more accurate alignments of interacting residues within families of interacting proteins, especially for sequences with low similarity. While previous methods that use an all-atom based representation of the interface have been successful, CMAPi's use of a contact map representation allows it to be more tolerant to conformational changes and thus to align more of the interaction surface. These improved interface alignments should enhance homology modeling and threading methods for predicting PPIs by providing a basis for generating template profiles for sequence–structure alignment.
Contact: bab@mit.edu; jbienkowska@gmail.com
Supplementary information: Supplementary data are available at http://theory.csail.mit.edu/cmapi
Accurate sequence-based prediction of catalytic residues
Authors: Zhang Tuo , Zhang Hua , Chen Ke , Shen Shiyi , Ruan Jishou , Kurgan Lukasz 
Published: August 2008

Abstract
Motivation: Prediction of catalytic residues provides useful information for the research on function of enzymes. Most of the existing prediction methods are based on structural information, which limits their use. We propose a sequence-based catalytic residue predictor that provides predictions with quality comparable to modern structure-based methods and that exceeds quality of state-of-the-art sequence-based methods.
Results: Our method (CRpred) uses sequence-based features and the sequence-derived PSI-BLAST profile. We used feature selection to reduce the dimensionality of the input (and explain the input) to support vector machine (SVM) classifier that provides predictions. Tests on eight datasets and side-by-side comparison with six modern structure- and sequence-based predictors show that CRpred provides predictions with quality comparable to current structure-based methods and better than sequence-based methods. The proposed method obtains 15–19% precision and 48–58% TP (true positive) rate, depending on the dataset used. CRpred also provides confidence values that allow selecting a subset of predictions with higher precision. The improved quality is due to newly designed features and careful parameterization of the SVM. The features incorporate amino acids characterized by the highest and the lowest propensities to constitute catalytic residues, Gly that provides flexibility for catalytic sites and sequence motifs characteristic to certain catalytic reactions. Our features indicate that catalytic residues are on average more conserved when compared with the general population of residues and that highly conserved amino acids characterized by high catalytic propensity are likely to form catalytic sites. We also show that local (with respect to the sequence) hydrophobicity contributes towards the prediction.
Availability: http://biomine.ece.ualberta.ca/CRpred/CRpred.htm
Contact: lkurgan@ece.ualberta.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex
Authors: Tang Chaka , Reyes Josephine F. , Luciani Fabio , Francis Andrew R. , Tanaka Mark M. 
Published: August 2008

Abstract
spolTools is a collection of online programs designed to manipulate and analyze spoligotype datasets of the Mycobacterium tuberculosis complex. These tools are integrated into a repository currently containing 1179 spoligotypes and 6278 isolates across 30 datasets. Users can search this database to export for external use or to pass on to the integrated tools. These tools include the computation of basic population genetic quantities, the visualization of clusters of spoligotype patterns based on an estimated evolutionary history and a procedure to predict emerging strains – genotypes associated with elevated transmission.
Availability: Database, programs and documentation may be accessed online at http://www.emi.unsw.edu.au/spolTools.
Contact: j.reyes@student.unsw.edu.au; m.tanaka@unsw.edu.au
Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison
Authors: Dai Qi , Yang Yanchun , Wang Tianming 
Published: August 2008

Abstract
Motivation: Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information. They are related in spirit because all the ideas for sequence comparison try to use the information on the k-word distributions, Markov model or both. Motivated by adding k-word distributions to Markov model directly, we investigated two novel statistical measures for sequence comparison, called wre.k.r and S2.k.r.
Results: The proposed measures were tested by similarity search, evaluation on functionally related regulatory sequences and phylogenetic analysis. This offers the systematic and quantitative experimental assessment of our measures. Moreover, we compared our achievements with these based on alignment or alignment-free. We grouped our experiments into two sets. The first one, performed via ROC (receiver operating curve) analysis, aims at assessing the intrinsic ability of our statistical measures to search for similar sequences from a database and discriminate functionally related regulatory sequences from unrelated sequences. The second one aims at assessing how well our statistical measure is used for phylogenetic analysis. The experimental assessment demonstrates that our similarity measures intending to incorporate k-word distributions into Markov model are more efficient.
Availability: The software, data and supplement material are freely available at http://math.dlut.edu.cn/daiqi/mplusd.html.
Contact: daiailiu2004@yahoo.com.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Influence of Protein and Energy Intakes on Body Composition of Formula‐fed Preterm Infants After Term
Authors: Roggero P , Giannì ML , Amato O , Orsi A , Piemontese P , Puricelli V , Mosca F 
Published: August 2008

ABSTRACTThe aim of the present study was to evaluate changes in body composition in 48 preterm infants in relation to protein and energy intakes from term up to 3 months of corrected age, using air displacement plethysmography. Protein intake (grams per kilogram per day) was negatively associated with percentage of fat mass at 1 month of corrected age. The high‐protein‐intake group showed greater gain in lean body mass gain than did the low‐protein‐intake group. This finding suggests that during the first month of corrected age, high protein intake results in a significantly different weight gain composition.
Fructose Intolerance in Children Presenting With Abdominal Pain
Authors: Gomara Robert E , Halata Michael S , Newman Leonard J , Bostwick Howard E , Berezin Stuart H , Cukaj Lynnette , See Mary C , Medow Marvin S 
Published: August 2008

ABSTRACTObjectives:We determined the occurrence of fructose malabsorption in pediatric patients with previous diagnoses of abdominal pain caused by a functional bowel disorder, whether the restriction of fructose intake changes the reporting of symptoms, the role of fructose dosage, and the severity of resultant symptoms.Patients and Methods:We administered a fructose breath test to children presenting with persistent unexplained abdominal pain. Patients randomly received 1, 15, or 45 g fructose, and breath hydrogen was measured for 3 hours after ingestion. Test results were positive when breath hydrogen was 20 ppm greater than baseline and was accompanied by gastrointestinal symptoms.Results:A total of 32 patients was enrolled, and none of the 9 who received 1 g had positive results. Three of 10 who received 15 g and 8 of 13 who received 45 g had positive results. All patients with positive test results restricted their fructose intake. Among the group with positive results, 9 of 11 had rapid improvement of their gastrointestinal symptoms. After 2 months, all 9 patients continued to report improvement.Conclusions:We concluded that fructose malabsorption may be a significant problem in children and that management of dietary intake can be effective in reducing gastrointestinal symptoms.
Pediatric Gastroenterology Fellows, Class of 2007: How Well Are They Prepared for the Future?
Authors: Qualia Cary M , Baldwin Constance D , Rossi Thomas M , Wang Hongyue , Brown Marilyn R 
Published: August 2008

ABSTRACTObjectives:Pediatric gastroenterology fellows are expected to acquire skills as clinicians, researchers, and educators. An e‐mail survey was conducted to examine training experiences of individual fellows; to understand how graduating fellows rate their abilities as clinicians, researchers, and teachers; and to answer whether the size of a pediatric gastroenterology training program affects a fellow's training and future position choice.Materials and Methods:A survey was e‐mailed to 76 third‐year pediatric gastroenterology fellows. Respondents were ranked according to the size of their training program.Results:Completed surveys were returned by 50 respondents. Of these, 75% planned to pursue careers in academic medicine and 16% in private practice. In all, 68% of trainees participated in some type of basic research and 64% in clinical research. As attending physicians, 22% of fellows hoped to conduct basic science research and 74% clinical research. The majority thought they were competent or proficient teachers, and rated themselves as advanced beginners or competent when asked to evaluate their research skills. The North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition recommends that fellows perform 100 colonoscopies, 20 liver biopsies, and 5 paracenteses to be considered competent. We found that regardless of program size, 48% of fellows performed fewer than 100 colonoscopies, 62% performed fewer than 20 liver biopsies, and 80% performed fewer than 5 paracenteses.Conclusions:The majority of fellows will pursue academic careers. Trainees may not be performing sufficient numbers of procedures. The number of procedures performed during fellowship was independent of program size.