bluuebunny/crossref_metadata_2025_split huggingface dataset:
Underreporting of energy intake among Japanese women aged 18–20 years and its association with reported nutrient and food group intakes
Authors: Okubo Hitomi , Sasaki Satoshi 
Published: October 2004

AbstractObjectives:To evaluate the ratio of energy intake to basal metabolic rate (EI/BMR) among young female Japanese adults, and to compare the lifestyle and dietary characteristics between relatively low and high reporters.Design:Dietary intakes were assessed over a 1-month period with a validated, self-administered, diet history questionnaire, and lifestyle variables were assessed by a second questionnaire designed for this survey. The ratio of EI/BMR was calculated from reported energy intake and estimated basal metabolic rate.Subjects:In total, 1889 female Japanese university students aged 18–20 years who were enrolled in dietetics courses.Results:Ninety-five per cent of the subjects were classified into a non-obese group (body mass index (BMI) <25 kg m−2; mean±standard deviation (SD): 20.8±2.6 kg m−2). EI/BMR was 1.43±0.40 (mean±SD). Sixty-eight per cent of the subjects showed an EI/BMR level below the possibly balanced value of 1.56, 37% showed EI/BMR below the minimum survival value of 1.27 and 2% of the subjects showed EI/BMR exceeding the maximum value for a sustainable lifestyle of 2.4. BMI, body weight and BMR decreased significantly with the increase in EI/BMR (P<0.001). The percentage of energy from carbohydrate was significantly higher, whereas those from fat and protein were significantly lower, among the lower EI/BMR groups. As for food groups, a significantly declining trend from the lowest to the highest EI/BMR groups was observed for cereals.Conclusion:Underreporting, rather than overreporting, of energy intake was predominant in this relatively lean Japanese female population. BMI was the most important factor affecting the reporting accuracy of energy intake.
Award Article: Microcirculatory Society Award for Excellence in Lymphatic Research
Authors: COX CHARLES S. , FISCHER UWE M. , ALLEN STEVEN J. , LAINE GLEN A. 
Published: October 2004

ABSTRACTObjective: Mesenteric ischemia/reperfusion (I/R) is associated with cardiac dysfunction. Mesenteric lymph primes polymorphonuclear leukocytes (PMNs) for increased superoxide release following I/R. We hypothesized that mesenteric I/R causes myocardial edema resulting in myocardial dysfunction, and that diverting mesenteric lymph would preserve myocardial function.Methods: Two canine groups were studied: lymphatic diversion (LD) and no lymphatic diversion (No LD). Preload recruitable stroke work, ±dp/dtmax, isovolumic relaxation (tau), cardiac output, and myocardial water content (MWC) were determined. I/R consisted of 60 min of ischemia followed by 180 min of reperfusion. Myocardial myeloperoxidase (MPO) was measured as an index of PMN leukosequestration. In addition, mesenteric lymph harvested after I/R was infused into normal canines and all variables measured.Results: MWC increased from baseline in No LD. Tau and −dp/dtmax were significantly affected in No LD, but not in LD. After mesenteric I/R, mesenteric lymph primed PMNs for increased superoxide production. Lymph diversion resulted in significantly lower myocardial MPO. With reinfusion of I/R lymph, MWC and tau increased. MPO was also increased post I/R mesenteric lymph reinfusion.Conclusions: Our data indicate that myocardial dysfunction after mesenteric I/R is due to lymph‐induced, PMN‐mediated microvascular alterations and myocardial edema.
Gender‐Specific Regulation of Cardiovascular Function: Estrogen as Key Player
Authors: HUANG AN , KALEY GABOR 
Published: October 2004

ABSTRACTThis review provides an overview of gender‐specific differences in the incidence and development of cardiovascular diseases, including hypertension, atherosclerosis, heart failure and the corresponding myocardial remodeling. The review discusses the possible mechanisms by which estrogen affords a beneficial effect on cardiovascular function via genomic vs non genomic regulation; estrogen receptor‐dependent vs estrogen receptor‐independent pathways, specific signal transduction cascades, especially those involving protein kinase B (Akt) and mitogen activated protein kinase (MAPK), as well as their downstream targets, such as nitric oxide synthase, cyclooxygenase, cytochrome P450 (CYP), NADPH oxidase and superoxide dismutase. Having considered the essential role of the microcirculation in the control of vascular resistance in vivo, estrogen‐related regulation of microvascular function and blood pressure is highlighted. Attention is focused on the effects of estrogen on pressure (myogenic)‐dependent and flow/shear stress‐dependent mechanisms of arterioles, which contribute significantly to the control of local blood flow and peripheral resistance via alterations in the release of endothelial mediators, such as nitric oxide, prostaglandins and endothelium‐derived hyperpolarizing factor.
Regulation of Leukocyte Recruitment by Local Wall Shear Rate and Leukocyte Delivery
Authors: KIM MICHAEL B. , SARELIUS INGRID H. 
Published: October 2004

ABSTRACTObjective: To determine the influence of wall shear rate and leukocyte delivery on leukocyte margination, rolling, and adhesion in post‐capillary venules.Methods: Leukocyte–endothelial cell interactions were characterized in cremaster muscle venules of anesthetized mice with video microscopy under control conditions and after 3 h exposure to TNF‐α. Hemodynamic parameters were measured with fluorescent particle tracking using confocal microscopy.Results: Leukocyte recruitment to the vessel wall and leukocyte rolling increased as a function of wall shear rate (P < 0.05) over the range observed (0–200 s−1) in intact post capillary venules. Leukocyte delivery affected recruitment and rolling flux only in activated vessels (P < 0.05). In addition, leukocyte firm adhesion was independent of both wall shear rate and leukocyte delivery, but showed an overall increase in TNF‐α stimulated tissues (0.9 ± 0.2 vs. 2.7 ± 0.6 cells/50 μm).Conclusions: Leukocytes are delivered to venules in excess of the capacity of the local endothelium to support interactions. Elevated shear forces increase leukocyte recruitment to the vessel wall, which correlates to elevated rolling flux. In contrast, leukocyte firm adhesion is primarily affected by the activation state of the tissue and not by hemodynamic factors. Overall, the capacity of endothelial cells to support leukocyte interactions primarily regulates leukocyte recruitment and is not limited by leukocyte supply.
Glycoprotein IIB/IIIA‐Inhibition and Microcirculatory Alterations During Experimental Endotoxemia—An Intravital Microscopic Study in the Rat
Authors: WALTHER ANDREAS , CZABANKA MARCUS , GEBHARD MARTHA MARIA , MARTIN EIKE 
Published: October 2004

ABSTRACTObjective: Endothelial damage during early endotoxemia has been shown to be leukocyte‐independent. Platelet‐activating factor (PAF) and serotonin‐receptor antagonism are known to reduce leukocyte‐independent macromolecular leakage significantly, thereby focusing the field of interest to the platelets. We hypothesized that inhibition of the GP IIb/IIIa receptor, using the unspecific GP IIb/IIIa inhibitor abciximab, would reduce leukocyte‐independent endothelial damage during early endotoxemia, and furthermore, that inhibition of the GP IIb/IIIa receptor with abciximab might improve microcirculatory disturbances, seen in a leukocyte‐dependent animal model during endotoxemia.Methods: In male Wistar rats, venular wall shear rate, macromolecular efflux, and leukocyte‐endothelial interaction were determined in mesenteric postcapillary venules using intravital microscopy at baseline, 60, and 120 min after the start of the experiment. The experiment was divided into two parts. In the first part, we investigated the effects of the GP IIb/IIIa inhibitor abciximab on leukocyte‐independent endothelial permeability during endotoxemia. In the second part of the experiment, we focused on the effects of the GP IIb/IIIa inhibitor abciximab on microcirculatory disturbances during endotoxemic states, without a modification of the leukocyte‐endothelial interaction, putting the main emphasis again on endothelial permeability.Results: GP IIb/IIIa inhibition with abciximab resulted in a significant reduction of macromolecular efflux during leukocyte‐independent endotoxemia. Both pretreatment with abciximab and post‐treatment with abciximab reduced macromolecular leakage during leukocyte‐dependent endotoxemia to values comparable to control values, and prevented an increase in leukocyte adherence, that has been reduced to values comparable to control values, too.Conclusion: GP IIb/IIIa inhibition, using abciximab, protects against endothelial dysfunction and an increase in leukocyte adherence to the vascular wall during experimental endotoxemia. The protective properties of abciximab on microcirculation seemed to be leukocyte‐independent
Expression of Cytochrome P450‐4A Isoforms in the Rat Cremaster Muscle Microcirculation
Authors: WANG JINGLI , MAIER KRISTOPHER G. , ROMAN RICHARD J. , DE LA CRUZ LOURDES , ZHU JIAXUAN , HENDERSON LISA , LOMBARD JULIAN H. 
Published: October 2004

ABSTRACTObjective: This study sought to identify any specific cytochrome P450 (CYP450) ‐4A enzyme isoforms expressed in arterioles and/or the surrounding parenchymal tissue of the rat cremaster muscle.Methods: RT‐PCR was used to detect the presence of specific CYP450‐4A isoforms in isolated muscle fibers and arterioles from the cremaster muscle of Sprague‐Dawley rats; CYP450‐4A protein expression was determined by Western blotting.Results: CYP450‐4A3 mRNA was expressed in isolated muscle fibers and in cremasteric arterioles, while CYP450‐4A8 mRNA was expressed only in cremasteric arterioles. CYP450‐4A1 and CYP450‐4A2 mRNA were not expressed in arterioles and skeletal muscle cells, although all four isoforms were strongly expressed in the liver. CYP450‐4A protein was detected in both the isolated muscle fibers and in the isolated arterioles.Conclusions: The present study identifies the specific pattern of cytochrome P450‐4A isoform expression in arterioles and parenchymal cells of the skeletal muscle microcirculation, and supports the hypothesis that the cytochrome P‐450 enzymes may play a role in the regulation of microvascular function in the skeletal muscle microcirculation.
Circular genome visualization and exploration using CGView
Authors: Stothard Paul , Wishart David S. 
Published: October 2004

Abstract
Summary: CGView (Circular Genome Viewer) is a Java application and library for generating high-quality, zoomable maps of circular genomes. It converts XML or tab-delimited input into a graphical map (PNG, JPG or Scalable Vector Graphics format), complete with sequence features, labels, legends and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any Web browser, allowing rapid genome browsing and facilitating data sharing.
Availability: CGView (the standalone application, library or applet), sample input, sample maps and documentation can be obtained from http://wishart.biology.ualberta.ca/cgview/
Contact: david.wishart@ualberta.ca
Improving conformational searches by geometric screening
Authors: Zhang Ming , White R. Allen , Wang Liqun , Goldman Ronald , Kavraki Lydia , Hassett Brendan 
Published: October 2004

AbstractMotivation: Conformational searches in molecular docking are a time-consuming process with wide range of applications. Favorable conformations of the ligands that successfully bind with receptors are sought to form stable ligand–receptor complexes. Usually a large number of conformations are generated and their binding energies are examined. We propose adding a geometric screening phase before an energy minimization procedure so that only conformations that geometrically fit in the binding site will be prompted for energy calculation.Results: Geometric screening can drastically reduce the number of conformations to be examined from millions (or higher) to thousands (or lower). The method can also handle cases when there are more variables than geometric constraints. An early-stage implementation is able to finish the geometric filtering of conformations for molecules with up to nine variables in 1 min. To the best of our knowledge, this is the first time such results are reported deterministically.Contact: mzhang@mdanderson.org
Bayesian analysis of signaling networks governing embryonic stem cell fate decisions
Authors: Woolf Peter J. , Prudhomme Wendy , Daheron Laurence , Daley George Q. , Lauffenburger Douglas A. 
Published: October 2004

AbstractMotivation: Signaling events that direct mouse embryonic stem (ES) cell self-renewal and differentiation are complex and accordingly difficult to understand in an integrated manner. We address this problem by adapting a Bayesian network learning algorithm to model proteomic signaling data for ES cell fate responses to external cues. Using this model we were able to characterize the signaling pathway influences as quantitative, logic-circuit type interactions. Our experimental dataset includes measurements for 28 signaling protein phosphorylation states across 16 different factorial combinations of cytokine and matrix stimuli as reported previously.Results: The Bayesian network modeling approach allows us to uncover previously reported signaling activities related to mouse ES cell self-renewal, such as the roles of LIF and STAT3 in maintaining undifferentiated ES cell populations. Furthermore, the network predicts novel influences such as between ERK phosphorylation and differentiation, or RAF phosphorylation and differentiated cell proliferation. Visualization of the influences detected by the Bayesian network provides intuition about the underlying physiology of the signaling pathways. We demonstrate that the Bayesian networks can capture the linear, nonlinear and multistate logic interactions that connect extracellular cues, intracellular signals and consequent cell functional responses.Availability: Datasets and software are available online from http://sysbio.engin.umich.edu/~pwoolf/mouseES/Contact: pwoolf@umich.eduSupplementary information: http://sysbio.engin.umich.edu/~pwoolf/mouseES/
Understanding protein dispensability through machine-learning analysis of high-throughput data
Authors: Chen Yu , Xu Dong 
Published: October 2004

AbstractMotivation: Protein dispensability is fundamental to the understanding of gene function and evolution. Recent advances in generating high-throughput data such as genomic sequence data, protein–protein interaction data, gene-expression data and growth-rate data of mutants allow us to investigate protein dispensability systematically at the genome scale.Results: In our studies, protein dispensability is represented as a fitness score that is measured by the growth rate of gene-deletion mutants. By the analyses of high-throughput data in yeast Saccharomyces cerevisiae, we found that a protein's dispensability had significant correlations with its evolutionary rate and duplication rate, as well as its connectivity in protein–protein interaction network and gene-expression correlation network. Neural network and support vector machine were applied to predict protein dispensability through high-throughput data. Our studies shed some lights on global characteristics of protein dispensability and evolution.Availability: The original datasets for protein dispensability analysis and prediction, together with related scripts, are available at http://digbio.missouri.edu/~ychen/ProDispen/Contact: xudong@missouri.edu
TRbase: a database relating tandem repeats to disease genes for the human genome
Authors: Boby T. , Patch A.-M. , Aves S. J. 
Published: October 2004

AbstractMotivation: Tandem repeats are associated with disease genes, play an important role in evolution and are important in genomic organization and function. Although much research has been done on short perfect patterns of repeats, there has been less focus on imperfect repeats. Thus, there is an acute need for a tandem repeats database that provides reliable and up to date information on both perfect and imperfect tandem repeats in the human genome and relates these to disease genes.Results: This paper presents a web-accessible relational tandem repeats database that relates tandem repeats to gene locations and disease genes of the human genome. In contrast to other available databases, this database identifies both perfect and imperfect repeats of 1–2000 bp unit lengths. The utility of this database has been illustrated by analysing these repeats for their distribution and frequencies across chromosomes and genomic locations and between protein-coding and non-coding regions. The applicability of this database to identify diseases associated with previously uncharacterized tandem repeats is demonstrated.Availability: TRbase is available at http://trbase.ex.ac.uk/Contact: S.J.Aves@exeter.ac.uk
ParIS Genome Rearrangement server
Authors: Miklós I. , Ittzés P. , Hein J. 
Published: October 2004

Abstract
Summary: ParIS Genome Rearrangement is a web server for a Bayesian analysis of unichromosomal genome pairs. The underlying model allows inversions, transpositions and inverted transpositions. The server generates a Markov chain using a Partial Importance Sampler technique, and samples trajectories of mutations from this chain. The user can specify several marginalizations to the posterior: the posterior distribution of number of mutations needed to transform one genome into another, length distribution of mutations, number of mutations that have occurred at a given site. Both text and graphical outputs are available. We provide a limited server, a downloadable unlimited server that can be installed locally on any linux/Unix operating system, and a database of mitochondrial gene orders.
Availability: http://www.colbud.hu:8765/paris.html and http://doob.stats.ox.ac.uk/~miklos/paris.html
Contact: miklosi@ramet.elte.hu
An empirical Bayes approach to inferring large-scale gene association networks
Authors: Schäfer Juliane , Strimmer Korbinian 
Published: October 2004

Abstract
Motivation: Genetic networks are often described statistically using graphical models (e.g. Bayesian networks). However, inferring the network structure offers a serious challenge in microarray analysis where the sample size is small compared to the number of considered genes. This renders many standard algorithms for graphical models inapplicable, and inferring genetic networks an ‘ill-posed’ inverse problem.
Methods: We introduce a novel framework for small-sample inference of graphical models from gene expression data. Specifically, we focus on the so-called graphical Gaussian models (GGMs) that are now frequently used to describe gene association networks and to detect conditionally dependent genes. Our new approach is based on (1) improved (regularized) small-sample point estimates of partial correlation, (2) an exact test of edge inclusion with adaptive estimation of the degree of freedom and (3) a heuristic network search based on false discovery rate multiple testing. Steps (2) and (3) correspond to an empirical Bayes estimate of the network topology.
Results: Using computer simulations, we investigate the sensitivity (power) and specificity (true negative rate) of the proposed framework to estimate GGMs from microarray data. This shows that it is possible to recover the true network topology with high accuracy even for small-sample datasets. Subsequently, we analyze gene expression data from a breast cancer tumor study and illustrate our approach by inferring a corresponding large-scale gene association network for 3883 genes.
Availability: The authors have implemented the approach in the R package ‘GeneTS’ that is freely available from http://www.stat.uni-muenchen.de/~strimmer/genets/, from the R archive (CRAN) and from the Bioconductor website.
Contact: korbinian.strimmer@lmu.de
Clinical Pathways in Acoustic Tumor Management
Authors: Arriaga Moisés A. , Gorum Michael , Kennedy Arthur 
Published: October 2004

AbstractClinical pathways are tools for cost containment and quality improvement in the managed care environment. This report describes our experience with developing and implementing a clinical pathway for acoustic neuroma surgery. Intensive care unit bed days and inpatient hospitalization days for cerebellopontine angle surgery significantly decreased during the months that the pathway was developed, and the incidence of complications was unchanged after adoption of the algorithm. We conclude that with joint neurootology and neurosurgery leadership clinical pathways can be a safe, cost‐effective, and clinically useful technique in acoustic neuroma surgery in a managed care setting. As this management scheme evolves, surgeons must take the leadership to ensure that decisions are based on clinically relevant parameters.
Benign Paroxysmal Positional Vertigo
Authors: Hughes C. Anthony , Proctor Leonard 
Published: October 2004

AbstractBenign paroxysmal positional vertigo (BPPV) has received renewed clinical interest. At the Johns Hopkins Otological Vestibular Laboratory, 781 patients were tested on more than one occasion between September 1976 and November 1992. Of these patients, 187 (24%) were found to have positional nystagmus consistent with a diagnosis of BPPV. A retrospective analysis of these patients' records, including vestibular test and eye movement reports, audiograms, questionnaires, and hospital charts was performed. After this review, the nystagmus, initially diagnosed as due to BPPV, was believed to be a manifestation of another disease process in 36 cases. Of the remaining 151 diseases, 52 (34%) presented with no significant preceding disorder and have been termed primary BPPV. In the remaining 99 patients we found coexisting or associated disorders which included Meniere's disease, head trauma, prior ear surgery, vestibular neuronitis, migraine, and others. Forty‐five of these 151 patients (31%) had an associated diagnosis of Meniere's disease. To our knowledge a significant association between Meniere's disease and BPPV has not been reported. A review of the literature with discussion of BPPV and the associated disorders is offered.
Midline Glossectomy and Epiglottidectomy for Obstructive Sleep Apnea Syndrome
Authors: Mickelson Samuel A. , Rosenthal Leon 
Published: October 2004

AbstractObstructive sleep apnea syndrome is caused by narrowing of the pharyngeal airway and loss of dilator tone during sleep. In patients with severe apnea surgical correction often requires attention to both the oropharynx and hypopharynx. Tongue reduction surgery has been described for persistent apnea after failure of palatal surgery. We describe our experience with midline glossectomy with epiglottidectomy in 12 patients with a mean age of 48.8 ± 14.2 years and body mass index of 36.0 ± 8.8 kg/ m2. Response to treatment was defined as a postoperative respiratory disturbance index (RDI) below 20. Three patients (25%) responded to treatment. The mean apnea index decreased from 48.9 to 35.7, RDI decreased from 73.3 to 46.6, and lowest oxygen saturation increased from 65.9 to 77.9%. RDI in responders decreased from 69.7 to 10. Midline glossectomy with epiglottidectomy has variable results, yet is effective in selected patients with hypopharyngeal narrowing related to macroglossia.