bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self‐selection Accounts for Inverse Association Between Weight and Cardiorespiratory Fitness
Authors: Williams Paul T. 
Published: January 2008

Background: Men and women who exercise regularly and who are physically fit tend to be leaner than those who are sedentary and not fit. Although exercise is known to attenuate weight gain and promote weight loss, there may also be a propensity for leaner men and women to choose to exercise vigorously (self‐selection). Pre‐exercise body weights have been shown to account for all the weight differences between fast and slow walkers, but seem to account for only a portion of the weight differences associated with walking distances. Whether these results apply to maximum exercise performance (i.e., cardiorespiratory fitness) as well as to doses of vigorous exercise (metabolic equivalents >6) remains to be determined.Objective: Assess whether the cross‐sectional relationships of BMI to cardiorespiratory fitness and vigorous activity are explained by BMI prior to exercising.Methods and Procedures: Cross‐sectional study of the relationships between cardiorespiratory fitness (running speed during 10 km foot race) and vigorous physical activity (weekly running distance) to current BMI (BMIcurrent) and BMI at the start of running (BMIstarting) in 44,370 male and 25,252 female participants of the National Runners' Health Study.Results: BMIstarting accounted entirely for the association between fitness and BMIcurrent in both sexes, but only a quarter of the association between vigorous physical activity levels and BMIcurrent in men. In women, BMIstarting accounted for 58% of the association between BMIcurrent and vigorous activity levels.Discussion: Self‐selection based on pre‐exercise BMI accounts entirely for the association found between fitness and BMI (and possibly a portion of other health outcomes).
Relation of Epicardial Fat and Alanine Aminotransferase in Subjects With Increased Visceral Fat
Authors: Iacobellis Gianluca , Pellicelli Adriano M. , Grisorio Benvenuto , Barbarini Giorgio , Leonetti Frida , Sharma Arya M. , Barbaro Giuseppe 
Published: January 2008

Background: Increased visceral adipose tissue (VAT) is a risk factor for an unfavorable cardio‐metabolic profile and fatty liver. Individuals with human immunodeficiency virus (HIV) on highly active antiretroviral therapy (HAART) can be associated with metabolic syndrome (MS) and higher visceral fat. However, the potential link between cardiac adiposity, emerging index of visceral adiposity, and fatty liver is still unexplored.Objective: To evaluate whether echocardiographic epicardial adipose tissue, index of cardiac adiposity, could be related to serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activity, surrogate markers of fatty liver, in HIV‐infected patients with (HIV+MS+) and without HAART‐associated MS (HIV+MS‐).Methods and Procedures: This was a cross‐sectional observational study on 57 HIV+MS+ patients, 52 HIV+MS− and 57 HIV‐negative subjects with MS (HIV−MS+), as control group. Epicardial fat thickness and intra‐abdominal VAT were obtained by echocardiography and magnetic resonance imaging (MRI), respectively. Serum ALT and AST activity, plasma adiponectin levels, and MS biochemical parameters were measured.Results: Echocardiographic epicardial fat thickness was correlated with MRI‐VAT (r = 0.83, P < 0.01), AST/ALT ratio (r = 0.77, P < 0.01), ALT (r = 0.58, P < 0.01), AST (r = 0.56, P < 0.01), and adiponectin (r = −0.45, P < 0.01) in HIV+MS+. MRI‐VAT and AST/ALT ratio were the best correlates of epicardial fat thickness (r 2 = 0.45, P < 0.01).Discussion: This study shows for the first time a clear relationship of epicardial fat, index of cardiac and visceral adiposity, and serum ALT and AST activity, markers of fatty liver, in subjects with increased visceral adiposity and cardio‐metabolic risk. This correlation seems to be independent of overall adiposity and rather function of excess visceral adiposity.
BMI and Health Status Among Adults With Asthma
Authors: Vortmann Michael , Eisner Mark D. 
Published: January 2008

Background: A convincing body of literature links obesity with a higher risk for developing adult‐onset asthma. The impact of obesity on asthma severity among adults with pre‐existing asthma, however, is less clear.Methods and Procedures: In a prospective cohort study of 843 adults with severe asthma, we studied the impact of BMI on asthma health status.Results: The prevalence of obesity and overweight were 44% (95% confidence interval (CI) 41–47%) and 28% (95% CI 25–32%). The obese BMI group was associated with a higher risk for daily or near daily asthma symptoms than was the normal BMI group (odds ratio (OR) 1.81; 95% CI 1.10–2.96). Compared to the normal BMI group, generic physical health status was worse in the overweight (mean score decrement −2.42 points; 95% CI −4.39 to −0.45) and the obese groups (−6.31 points; 95% CI −8.14 to −4.49). Asthma‐specific quality of life was worse in the underweight (mean score increment 8.66 points; 95% CI 2.53–14.8) and obese groups (4.51 points; 95% CI 2.21–6.81), compared to those with normal BMI. Obese persons also had a higher number of restricted activity days that past month (5.05 days; 95% CI 2.90–7.19 days).Discussion: It appears that obesity has a substantive negative effect on health status among adults with asthma. Further work is needed to clarify the precise mechanisms. Clinicians should counsel dietary modification and weight loss for their overweight and obese patients with asthma.
Restoration of Acute Insulin Response in T2DM Subjects 1 Month After Biliopancreatic Diversion
Authors: Briatore Lucia , Salani Barbara , Andraghetti Gabriella , Danovaro Cristina , Sferrazzo Elsa , Scopinaro Nicola , Adami Gian F. , Maggi Davide , Cordera Renzo 
Published: January 2008

Objective: Biliopancreatic diversion (BPD) restores normal glucose tolerance in a few weeks in morbid obese subjects with type 2 diabetes, improving insulin sensitivity. However, there is less known about the effects of BPD on insulin secretion. We tested the early effects of BPD on insulin secretion in obese subjects with and without type 2 diabetes.Methods and Procedures: Twenty‐one consecutive morbid obese subjects, 9 with type 2 diabetes (T2DM) and 12 with normal fasting glucose (NFG) were evaluated, just before and 1 month after BPD, by measuring body weight (BW), glucose, adipocitokines, homeostasis model assessment of insulin resistance (HOMA‐IR), acute insulin response (AIR) to e.v. glucose and the insulinogenic index adjusted for insulin resistance ([ΔI5/ΔG5]/HOMA‐IR).Results: Preoperatively, those with T2DM differed from those with NFG in showing higher levels of fasting glucose, reduced AIR (57.9 ± 29.5 vs. 644.9 ± 143.1 pmol/l, P < 0.01) and reduced adjusted insulinogenic index (1.0 ± 0.5 vs. 17.6 ± 3.9 1/mmol2, P < 0.001). One month following BPD, in both groups BW was reduced (by ∼11%), but all subjects were still severely obese; HOMA‐IR and leptin decreased significanlty, while high‐molecular weight (HMW) adiponectin and adjusted insulinogenic index increased. In the T2DM group, fasting glucose returned to non‐diabetic values. AIR did not change in the NFG group, while in the T2DM group it showed a significant increase (from 58.0 ± 29.5 to 273.8 ± 47.2 pmol/l, P < 0.01). In the T2DM group, the AIR percentage variation from baseline was significantly related to changes in fasting glucose (r = 0.70, P = 0.02), suggesting an important relationship exists between impaired AIR and hyperglycaemia.Discussion: BPD is able to restore AIR in T2DM even just 1 month after surgery. AIR restoration is associated with normalization of fasting glucose concentrations.
Cohort Study of the Pathogenesis and Molecular Epidemiology of Catheter-Related Bloodstream Infection in Neonates With Peripherally Inserted Central Venous Catheters
Authors: Garland Jeffery S. , Alex Colleen P. , Sevallius Jackie M. , Murphy Dawn M. , Good Mary J. , Volberding Annette M. , Hofer Leslie L. , Gordon Barbara J. , Maki Dennis G. 
Published: January 2008

Objective.To better define the pathogenesis of catheter-related bloodstream infection (BSI) in neonates with peripherally inserted central venous catheters (PICCs) to guide the development of more effective strategies for prevention.Design.Prospective nested cohort study.Setting.Level III neonatal intensive care unit in a community hospital.Methods.During a randomized trial to assess the safety and efficacy of a prophylactic vancomycin-heparin catheter-lock solution for the prevention of catheter-related BSI in neonates with PICCs, we performed cultures of peripheral and catheter-drawn blood samples, and quantitative cultures of catheter hub samples if BSI was suspected clinically. We performed semiquantitative cultures of the catheter tip and the catheter hub and the skin at the insertion site when the catheter was removed. Molecular subtyping by pulsed-field electrophoresis was used to determine the probable pathogenesis of all BSIs due to coagulase-negative staphylococci (CoNS); for BSIs caused by other microorganisms, epidemiologic concordance was based on speciation and antibiograms. Catheter-related BSI was considered extraluminally acquired if concordance was demonstrable solely between isolates recovered from the catheter tip and the blood, independent of concordance with isolates recovered from the insertion site. Catheter-related BSI was considered intraluminally acquired if concordance was demonstrated only between isolates recovered from the catheter hub and the blood. The source of the infection was considered indeterminate if both concordance patterns were present.Results.Nosocomial BSI was identified in 23 of the 82 neonates in the cohort. Fifteen of these infections, 14 of which were caused by CoNS, were considered definite or probable catheter-related BSIs. Catheter-related BSI was intraluminally acquired in 10 (67%) of 15 patients, extraluminally acquired in 3 (20%), and indeterminate in 2 (13%).Conclusions.Most catheter-related BSIs in neonates with PICCs are caused by CoNS and derive from intraluminal contamination. Strategies for prevention of catheter-related BSI directed at this predominant mechanism of infection are most likely to be effective.
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Authors: Stanke Mario , Diekhans Mark , Baertsch Robert , Haussler David 
Published: January 2008

Abstract
Motivation: Computational annotation of protein coding genes in genomic DNA is a widely used and essential tool for analyzing newly sequenced genomes. However, current methods suffer from inaccuracy and do poorly with certain types of genes. Including additional sources of evidence of the existence and structure of genes can improve the quality of gene predictions. For many eukaryotic genomes, expressed sequence tags (ESTs) are available as evidence for genes. Related genomes that have been sequenced, annotated, and aligned to the target genome provide evidence of existence and structure of genes.
Results: We incorporate several different evidence sources into the gene finder AUGUSTUS. The sources of evidence are gene and transcript annotations from related species syntenically mapped to the target genome using TransMap, evolutionary conservation of DNA, mRNA and ESTs of the target species, and retroposed genes. The predictions include alternative splice variants where evidence supports it. Using only ESTs we were able to correctly predict at least one splice form exactly correct in 57% of human genes. Also using evidence from other species and human mRNAs, this number rises to 77%. Syntenic mapping is well-suited to annotate genomes closely related to genomes that are already annotated or for which extensive transcript evidence is available. Native cDNA evidence is most helpful when the alignments are used as compound information rather than independent positionwise information.
Availability: AUGUSTUS is open source and available at http://augustus.gobics.de. The gene predictions for human can be browsed and downloaded at the UCSC Genome Browser (http://genome.ucsc.edu)
Contact: mstanke@gwdg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Comparative Genomic Sequence and Expression Analyses ofMedicago truncatulaand Alfalfa Subspeciesfalcata COLD-ACCLIMATION-SPECIFICGenes
Authors: Pennycooke Joyce C. , Cheng Hongmei , Stockinger Eric J. 
Published: January 2008

AbstractIn Arabidopsis (Arabidopsis thaliana) the low-temperature induction of genes encoding the C-REPEAT BINDING FACTOR (CBF) transcriptional activators is a key step in cold acclimation. CBFs in turn activate a battery of downstream genes known as the CBF regulon, which collectively act to increase tolerance to low temperatures. Fundamental questions are: What determines the size and scope of the CBF regulon, and is this is a major determinant of the low-temperature tolerance capacity of individual plant species? Here we have begun to address these questions through comparative analyses of Medicago truncatula and Medicago sativa subsp. falcata. M. truncatula survived to −4°C but did not cold acclimate, whereas Medicago falcata cold acclimated and survived −14°C. Both species possessed low-temperature-induced CBFs but differed in the expression of the COLD-ACCLIMATION-SPECIFIC (CAS) genes, which are candidate CBF targets. M. falcata CAS30 was robustly cold-responsive whereas the MtCAS31 homolog was not. M. falcata also possessed additional CAS30 homologs in comparison to the single CAS31 gene in M. truncatula. MfCAS30 possessed multiple pairs of closely spaced C-REPEAT/DEHYDRATION RESPONSIVE ELEMENT (CRT/DRE) motifs, the cognate CBF binding site in its upstream region whereas MtCAS31 lacked one CRT/DRE partner of the two proximal partner pairs. CAS genes also shared a promoter structure comprising modules proximal and distal to the coding sequence. CAS15, highly cold-responsive in both species, harbored numerous CRT/DRE motifs, but only in the distal module. However, fusion of the MtCAS15 promoter, including the distal module, to a reporter gene did not result in low-temperature responsiveness in stably transformed Arabidopsis. In contrast, both MtCAS31 and MfCAS30 promoter fusions were low-temperature responsive, although the MfCAS31 fusion was less robust than the MfCAS30 fusion. From these studies we conclude that CAS genes harbor CRT/DRE motifs, their proximity to one another is likely key to regulatory output in Medicago, and they may be located kilobases distal to the transcriptional start site. We hypothesize that these differences in CRT/DRE copy numbers in CAS30/CAS31 upstream regions combined with differences in gene copy numbers may be a factor in determining differences in low-temperature tolerance between M. truncatula and M. falcata.
Genome-Wide Expression Profiling Arabidopsis at the Stage ofGolovinomyces cichoracearumHaustorium Formation
Authors: Fabro Georgina , Di Rienzo Julio A. , Voigt Christian A. , Savchenko Tatyana , Dehesh Katayoon , Somerville Shauna , Alvarez María Elena 
Published: January 2008

AbstractCompatibility between plants and obligate biotrophic fungi requires fungal mechanisms for efficiently obtaining nutrients and counteracting plant defenses under conditions that are expected to induce changes in the host transcriptome. A key step in the proliferation of biotrophic fungi is haustorium differentiation. Here we analyzed global gene expression patterns in Arabidopsis thaliana leaves during the formation of haustoria by Golovinomyces cichoracearum. At this time, the endogenous levels of salicylic acid (SA) and jasmonic acid (JA) were found to be enhanced. The responses of wild-type, npr1-1, and jar1-1 plants were used to categorize the sensitivity of gene expression changes to NPR1 and JAR1, which are components of the SA and JA signaling pathways, respectively. We found that the infection process was the major source of variation, with 70 genes identified as having similarly altered expression patterns regardless of plant genotype. In addition, principal component analysis (PCA) identified genes responding both to infection and to lack of functional JAR1 (17 genes) or NPR1 (18 genes), indicating that the JA and SA signaling pathways function as secondary sources of variation. Participation of these genes in the SA or JA pathways had not been described previously. We found that some of these genes may be sensitive to the balance between the SA and JA pathways, representing novel markers for the elucidation of cross-talk points between these signaling cascades. Conserved putative regulatory motifs were found in the promoter regions of each subset of genes. Collectively, our results indicate that gene expression changes in response to infection by obligate biotrophic fungi may support fungal nutrition by promoting alterations in host metabolism. In addition, these studies provide novel markers for the characterization of defense pathways and susceptibility features under this infection condition.
Tie-dyed2Functions withTie-dyed1to Promote Carbohydrate Export from Maize Leaves
Authors: Baker R. Frank , Braun David M. 
Published: January 2008

AbstractRegulation of carbon partitioning is essential for plant growth and development. To gain insight into genes controlling carbon allocation in leaves, we identified mutants that hyperaccumulate carbohydrates. tie-dyed2 (tdy2) is a recessive mutant of maize (Zea mays) with variegated, nonclonal, chlorotic leaf sectors containing excess starch and soluble sugars. Consistent with a defect in carbon export, we found that a by-product of functional chloroplasts, likely a sugar, induces tdy2 phenotypic expression. Based on the phenotypic similarities between tdy2 and two other maize mutants with leaf carbon accumulation defects, tdy1 and sucrose export defective1 (sxd1), we investigated whether Tdy2 functioned in the same pathway as Tdy1 or Sxd1. Cytological and genetic studies demonstrate that Tdy2 and Sxd1 function independently. However, in tdy1/+; tdy2/+ F1 plants, we observed a moderate chlorotic sectored phenotype, suggesting that the two genes are dosage sensitive and have a related function. This type of genetic interaction is referred to as second site noncomplementation and has often, though not exclusively, been found in cases where the two encoded proteins physically interact. Moreover, tdy1; tdy2 double mutants display a synergistic interaction supporting this hypothesis. Additionally, we determined that cell walls of chlorotic leaf tissues in tdy mutants contain increased cellulose; thus, tdy mutants potentially represent enhanced feedstocks for biofuels production. From our phenotypic and genetic characterizations, we propose a model whereby TDY1 and TDY2 function together in a single genetic pathway, possibly in homo- and heteromeric complexes, to promote carbon export from leaves.
Ascorbate and Homoglutathione Metabolism in Common Bean Nodules under Stress Conditions and during Natural Senescence
Authors: Loscos Jorge , Matamoros Manuel A. , Becana Manuel 
Published: January 2008

Abstract
Ascorbate and glutathione are major antioxidants and redox buffers in plant cells but also play key functions in growth, development, and stress responses. We have studied the regulation of ascorbate and homoglutathione biosynthesis in common bean (Phaseolus vulgaris) nodules under stress conditions and during aging. The expression of five genes of the major ascorbate biosynthetic pathway was analyzed in nodules, and evidence was found that l-galactono-1,4-lactone dehydrogenase, the last committed step of the pathway, is posttranscriptionally regulated. Also, in nodules under stress conditions, γ-glutamylcysteine synthetase was translationally regulated, but homoglutathione synthetase (mRNA and activity) and homoglutathione (content and redox state) were not affected. Most interestingly, in nodules exposed to jasmonic acid, dehydroascorbate reductase activity was posttranslationally suppressed, ascorbate oxidase showed strong transcriptional up-regulation, and dehydroascorbate content increased moderately. These changes were not due to a direct effect of jasmonic acid on the enzyme activities but might be part of the signaling pathway in the response of nodules to stress. We determined ascorbate, homoglutathione, and ascorbate-glutathione pathway enzyme activities in two senescing stages of nodules undergoing oxidative stress. When all parameters were expressed on a nodule fresh weight basis, we found that in the first stage ascorbate decreased by 60% and homoglutathione and antioxidant activities remained fairly constant, whereas in the second stage ascorbate and homoglutathione, their redox states, and their associated enzyme activities significantly decreased. The coexistence in the same plants of nodules at different senescence stages, with different ascorbate concentrations and redox states, indicates that the life span of nodules is in part controlled by endogenous factors and points to ascorbate as one of the key players.
Characterization of the 4D5Flu single‐chain antibody with a stimulus‐responsive elastin‐like peptide linker: A potential reporter of peptide linker conformation
Authors: Blenner Mark A. , Banta Scott 
Published: January 2008

AbstractSingle‐chain antibodies (scFvs) are comprised of IgG variable light and variable heavy domains tethered together by a peptide linker whose length and sequence can affect antigen binding properties. The ability to modulate antigen binding affinity through the use of environmental triggers would be of great interest for many biotechnological applications. We have characterized the antigen binding properties of an anti‐fluorescein scFv, 4D5Flu, containing stimulus‐responsive short elastin‐like peptide linkers and nonresponsive flexible linkers. Comparison of length‐matched flexible and short elastin‐like peptide linkers indicates that a stimulus‐responsive linker can confer stimulus‐responsive control of fluorescein binding. A linker length of either six or 10 amino acids proved to have the largest thermally induced response. Similar differences in binding free energy changes indicate a common underlying mechanism of thermal responsiveness. Contrary to the thermal behavior, the effect of salt, another elastin β‐turn‐inducing stimulus, stabilized antigen binding in the six‐ and 10‐amino‐acid linkers such that elastin‐like linkers became less stimulus‐responsive as compared with flexible linkers. Again, the thermodynamic analysis indicates a common mechanism of salt responsiveness. Characterization of the room‐temperature binding affinities and evidence indicating a dimeric state of the scFvs concomitantly suggest the major contribution to the stimulus‐responsive behavior derives from the perturbation of interdomain associations, rather than the linker‐constrained disruption of the intramolecular association. The ability to use stimulus‐responsive peptide modules to exert a novel control over protein function will likely find application in the creation of allosteric antibodies and scFv‐based biosensors, and as a platform to enable the evolution of new stimulus‐responsive peptides.
Rationalizing α‐helical membrane protein crystallization
Authors: Newstead Simon , Ferrandon Sébastien , Iwata So 
Published: January 2008

AbstractX‐ray crystallography is currently the most successful method for determining the three‐dimensional structure of membrane proteins. Nevertheless, growing the crystals required for this technique presents one of the major bottlenecks in this area of structural biology. This is especially true for the α‐helical type membrane proteins that are of particular interest due to their medical relevance. To address this problem we have undertaken a detailed analysis of the crystallization conditions from 121 α‐helical membrane protein structures deposited in the Protein Data Bank. This information has been analyzed so that the success of different parameters can be easily compared for different membrane protein families. Concurrent with this analysis, we also present the new sparse matrix crystallization screen MemGold.