bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating vascular endothelial growth factor and systemic inflammatory markers in patients with stable and exacerbated chronic obstructive pulmonary disease
Authors: Valipour Arschang , Schreder Martin , Wolzt Michael , Saliba Sleman , Kapiotis Sonja , Eickhoff Philipp , Burghuber Otto Chris 
Published: May 2008

The aim of the present study was to assess circulating levels of VEGF (vascular endothelial growth factor), a biomarker with prognostic significance in cardiovascular disease, and markers of systemic inflammation in patients with stable and exacerbated COPD (chronic obstructive pulmonary disease). Lung function parameters, arterial blood gas analysis and circulating levels of VEGF, IL-6 (interleukin-6), TNF-α (tumour necrosis factor-α), CRP (C-reactive protein), fibrinogen and the peripheral blood neutrophil cell count were assessed in 30 patients on admission to the hospital for acute exacerbation of COPD, in 30 age-, gender- and BMI (body mass index)-matched patients with stable COPD, and 30 matched controls with normal lung function. Patients with acute exacerbated COPD had higher circulating concentrations of VEGF (P&lt;0.001), IL-6 (P&lt;0.05) and CRP (P&lt;0.01) and an increased blood neutrophil cell count (P&lt;0.05) compared with patients with stable COPD and healthy controls. VEGF levels in exacerbated COPD correlated with systemic inflammatory markers, such as CRP (r=0.61, P&lt;0.005), IL-6 (r=0.46; P&lt;0.01) and fibrinogen (r=0.39, P&lt;0.05). In patients with stable COPD, there was a significant relationship between circulating VEGF levels and the percentage of the predicted FEV1 (forced expiratory volume in 1 s) (r=0.47, P&lt;0.01). Recovery from the exacerbation resulted in a significant decrease in both circulating VEGF levels and markers of systemic inflammation. In conclusion, circulating levels of VEGF and markers of systemic inflammation are up-regulated in patients with acute exacerbated COPD and decrease after recovery from the exacerbation.
Importance of the high-molecular-mass isoform of adiponectin in improved insulin sensitivity with rosiglitazone treatment in HIV disease
Authors: Qurashi Saima , Mynarcik Dennis C. , McNurlan Margaret A. , Ahn Hongshik , Ferris Robert , Gelato Marie C. 
Published: May 2008

The present study was designed to investigate the relationship of isoforms of adiponectin to insulin sensitivity in subjects with HIV-associated insulin resistance in response to treatment with the thiazolidinedione, rosiglitazone. The two isoforms of adiponectin, HMW (high-molecular-mass) and LMW (low-molecular-mass), were separated by sucrose-gradient-density centrifugation. The amount of adiponectin in gradient fractions was determined by ELISA. Peripheral insulin sensitivity (Rd) was determined with hyperinsulinaemic–euglycaemic clamp, whereas hepatic sensitivity [HOMA (Homoeostasis Model Assessment) %S] was based on basal glucose and insulin values. Treatment with rosiglitazone for 3 months resulted in a significant improvement in the index of hepatic insulin sensitivity (86.4±15% compared with 139±23; P=0.007) as well as peripheral insulin sensitivity (4.04±0.23 compared with 6.17±0.66 mg of glucose/kg of lean body mass per min; P&lt;0.001). Improvement in HOMA was associated with increased levels of HMW adiponectin (r=0.541, P=0.045), but not LMW adiponectin. The present study suggests that the HMW isoform of adiponectin is important in the regulation of rosiglitazone-mediated improvement in insulin sensitivity in individuals with HIV-associated insulin resistance, particularly in the liver.
Impairment of arginine metabolism in rats after massive intestinal resection: effect of parenteral nutrition supplemented with citrulline compared with arginine
Authors: Osowska Sylwia , Neveux Nathalie , Nakib Samir , Lasserre Virginie , Cynober Luc , Moinard Christophe 
Published: May 2008

Arginine homoeostasis is impaired in short bowel syndrome, but its supplementation in short bowel syndrome patients remains controversial. Recently, we demonstrated the benefits of citrulline supplementation by the enteral route in resected rats. Since the first step in managing short bowel syndrome is to initiate total parenteral nutrition, we hypothesized that parenteral citrulline supplementation would be more appropriate in this situation than arginine supplementation. In the present study, 24 rats were assigned to four groups. The sham group underwent transection whereas the three other groups underwent resection (R) of 80% of the small intestine. All rats were then fed exclusively by total parenteral nutrition as follows: supplementation with citrulline (R+CIT), with arginine (R+ARG) or no supplementation (R). All of the rats received isocaloric and isonitrogenous nutrition for 4 days. Nitrogen balance was measured daily. Rats were then killed and the blood was collected and the intestinal mucosa and extensor digitorum longus muscle were removed for amino acid and protein analysis. Citrulline and arginine increased mucosal protein content in the ileum (compared with sham and R, P&lt;0.05). However, only citrulline prevented extensor digitorum longus atrophy (R+CIT, 130±3 mg compared with R, 100±6 mg and R+ARG, 110±2 mg, P&lt;0.05). In addition, arginine worsened nitrogen balance (R+ARG, 104±46 mg/72 h compared with R, 249±69 mg/72 h, P&lt;0.05). Only citrulline was able to prevent muscle atrophy and it was achieved independently from any noticeable effect on the gut in particular because citrulline and arginine share the same effect on mucosal ileal protein content. These results suggest that citrulline should be considered as a potential supplement for total parenteral nutrition of short bowel syndrome patients.
Microbial genotype–phenotype mapping by class association rule mining
Authors: Tamura Makio , D'haeseleer Patrik 
Published: May 2008

AbstractMotivation: Microbial phenotypes are typically due to the concerted action of multiple gene functions, yet the presence of each gene may have only a weak correlation with the observed phenotype. Hence, it may be more appropriate to examine co-occurrence between sets of genes and a phenotype (multiple-to-one) instead of pairwise relations between a single gene and the phenotype. Here, we propose an efficient class association rule mining algorithm, netCAR, in order to extract sets of COGs (clusters of orthologous groups of proteins) associated with a phenotype from COG phylogenetic profiles and a phenotype profile. netCAR takes into account the phylogenetic co-occurrence graph between COGs to restrict hypothesis space, and uses mutual information to evaluate the biconditional relation.Results: We examined the mining capability of pairwise and multiple-to-one association by using netCAR to extract COGs relevant to six microbial phenotypes (aerobic, anaerobic, facultative, endospore, motility and Gram negative) from 11 969 unique COG profiles across 155 prokaryotic organisms. With the same level of false discovery rate, multiple-to-one association can extract about 10 times more relevant COGs than one-to-one association. We also reveal various topologies of association networks among COGs (modules) from extracted multiple-to-one correlation rules relevant with the six phenotypes; including a well-connected network for motility, a star-shaped network for aerobic and intermediate topologies for the other phenotypes. netCAR outperforms a standard CAR mining algorithm, CARapriori, while requiring several orders of magnitude less computational time for extracting 3-COG sets.Availability: Source code of the Java implementation is available as Supplementary Material at the Bioinformatics online website, or upon request to the author.Contact: makio323@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
HSEpred: predict half-sphere exposure from protein sequences
Authors: Song Jiangning , Tan Hao , Takemoto Kazuhiro , Akutsu Tatsuya 
Published: May 2008

Abstract
Motivation: Half-sphere exposure (HSE) is a newly developed two-dimensional solvent exposure measure. By conceptually separating an amino acid's sphere in a protein structure into two half spheres which represent its distinct spatial neighborhoods in the upward and downward directions, the HSE-up and HSE-down measures show superior performance compared with other measures such as accessible surface area, residue depth and contact number. However, currently there is no existing method for the prediction of HSE measures from sequence data.
Results: In this article, we propose a novel approach to predict the HSE measures and infer residue contact numbers using the predicted HSE values, based on a well-prepared non-homologous protein structure dataset. In particular, we employ support vector regression (SVR) to quantify the relationship between HSE measures and protein sequences and evaluate its prediction performance. We extensively explore five sequence-encoding schemes to examine their effects on the prediction performance. Our method could achieve the correlation coefficients of 0.72 and 0.68 between the predicted and observed HSE-up and HSE-down measures, respectively. Moreover, contact number can be accurately predicted by the summation of the predicted HSE-up and HSE-down values, which has further enlarged the application of this method. The successful application of SVR approach in this study suggests that it should be more useful in quantifying the protein sequence–structure relationship and predicting the structural property profiles from protein sequences.
Availability: The prediction webserver and supplementary materials are accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/hse/
Contact: sjn@kuicr.kyoto-u.ac.jp; takutsu@kuicr.kyoto-u.ac.jp
Supplementary Information: Supplementary data are available at Bioinformatics online.
PatMaN: rapid alignment of short sequences to large databases
Authors: Prüfer Kay , Stenzel Udo , Dannemann Michael , Green Richard E. , Lachmann Michael , Kelso Janet 
Published: May 2008

Abstract
Summary: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched. Search time is short for perfect matches, and retrieval time rises exponentially with the number of edits allowed.
Availability: The C++ source code for PatMaN is distributed under the GNU General Public License and has been tested on the GNU/Linux operating system. It is available from http://bioinf.eva.mpg.de/patman.
Contact: pruefer@eva.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
lumi: a pipeline for processing Illumina microarray
Authors: Du Pan , Kibbe Warren A. , Lin Simon M. 
Published: May 2008

Abstract
Summary: Illumina microarray is becoming a popular microarray platform. The BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray technologies. Unfortunately, most other analyses have not taken advantage of the unique properties of the BeadArray system, and have just incorporated preprocessing methods originally designed for Affymetrix microarrays. lumi is a Bioconductor package especially designed to process the Illumina microarray data. It includes data input, quality control, variance stabilization, normalization and gene annotation portions. In specific, the lumi package includes a variance-stabilizing transformation (VST) algorithm that takes advantage of the technical replicates available on every Illumina microarray. Different normalization method options and multiple quality control plots are provided in the package. To better annotate the Illumina data, a vendor independent nucleotide universal identifier (nuID) was devised to identify the probes of Illumina microarray. The nuID annotation packages and output of lumi processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data.
Availability: The lumi Bioconductor package, www.bioconductor.org
Contact: dupan@northwestern.edu
Effects of gear characteristics on the presence of bigeye tuna (Thunnus obesus) in the catches of the purse-seine fishery of the eastern Pacific Ocean
Authors: Lennert-Cody Cleridy E. , Roberts Jason J. , Stephenson Richard J. 
Published: May 2008

Abstract
Lennert-Cody, C. E., Roberts, J. J., and Stephenson, R. J. 2008. Effects of gear characteristics on the presence of bigeye tuna (Thunnus obesus) in the catches of the purse-seine fishery of the eastern Pacific Ocean. – ICES Journal of Marine Science, 65: 970–978. Overfishing of bigeye tuna in the eastern Pacific Ocean has motivated a search for a practical means of reducing the catch of bigeye tuna in mixed species aggregations. To explore the effects of gear characteristics on the catch of bigeye tuna, a classification algorithm for the presence/absence of bigeye tuna catch in purse-seine sets on floating objects is developed, using the tree-based method, random forests. Although the location of the set was the strongest determinant of bigeye tuna catch with these data, bigeye tuna in some areas were more likely to be caught on floating objects with greater underwater depths and with deeper purse-seines. Misclassified sets that caught bigeye tuna were concentrated within certain vessels, suggesting the existence of additional vessel effects. Results indicate that fishers may avoid catching bigeye tuna in some areas by changing the depth of the material hanging from the floating object and the actual fishing depth of the purse-seine, or by moving to other fishing areas. Nonetheless, given the complexity of configuring a purse-seine, and the difficulties associated with monitoring compliance with gear regulations, fishery-wide gear restrictions would be problematic.
Functional Characterization of HFR1, a High-MannoseN-Glycan-Specific Wheat Lectin Induced by Hessian Fly Larvae
Authors: Subramanyam Subhashree , Smith David F. , Clemens James C. , Webb Mary A. , Sardesai Nagesh , Williams Christie E. 
Published: May 2008

AbstractWe previously cloned and characterized a novel jacalin-like lectin gene from wheat (Triticum aestivum) plants that responds to infestation by Hessian fly (Mayetiola destructor) larvae, a major dipteran pest of this crop. The infested resistant plants accumulated higher levels of Hfr-1 (for Hessian fly-responsive gene 1) transcripts compared with uninfested or susceptible plants. Here, we characterize the soluble and active recombinant His6-HFR1 protein isolated from Escherichia coli. Functional characterization of the protein using hemagglutination assays revealed lectin activity. Glycan microarray-binding assays indicated strong affinity of His6-HFR1 to Manα1-6(Manα1-3)Man trisaccharide structures. Resistant wheat plants accumulated high levels of HFR1 at the larval feeding sites, as revealed by immunodetection, but the avirulent larvae were deterred from feeding and consumed only small amounts of the lectin. Behavioral studies revealed that avirulent Hessian fly larvae on resistant plants exhibited prolonged searching and writhing behaviors as they unsuccessfully attempted to establish feeding sites. During His6-HFR1 feeding bioassays, Drosophila melanogaster larvae experienced significant delays in growth and pupation, while percentage mortality increased with progressively higher concentrations of His6-HFR1 in the diet. Thus, HFR1 is an antinutrient to dipteran larvae and may play a significant role in deterring Hessian fly larvae from feeding on resistant wheat plants.
An External δ-Carbonic Anhydrase in a Free-Living Marine Dinoflagellate May Circumvent Diffusion-Limited Carbon Acquisition
Authors: Lapointe Mathieu , MacKenzie Tyler D.B. , Morse David 
Published: May 2008

Abstract
The oceans globally constitute an important sink for carbon dioxide (CO2) due to phytoplankton photosynthesis. However, the marine environment imposes serious restraints to carbon fixation. First, the equilibrium between CO2 and bicarbonate (HCO3 −) is pH dependent, and, in normal, slightly alkaline seawater, [CO2] is typically low (approximately 10 μ m). Second, the rate of CO2 diffusion in seawater is slow, so, for any cells unable to take up bicarbonate efficiently, photosynthesis could become carbon limited due to depletion of CO2 from their immediate vicinity. This may be especially problematic for those dinoflagellates using a form II Rubisco because this form is less oxygen tolerant than the usually found form I enzyme. We have identified a carbonic anhydrase (CA) from the free-living marine dinoflagellate Lingulodinium polyedrum that appears to play a role in carbon acquisition. This CA shares 60% sequence identity with δ-class CAs, isoforms so far found only in marine algae. Immunoelectron microscopy indicates that this enzyme is associated exclusively with the plasma membrane. Furthermore, this enzyme appears to be exposed to the external medium as determined by whole-cell CA assays and vectorial labeling of cell surface proteins with 125I. The fixation of 14CO2 is strongly pH dependent, suggesting preferential uptake of CO2 rather than HCO3 −, and photosynthetic rates decrease in the presence of 1 mm acetazolamide, a non-membrane-permeable CA inhibitor. This constitutes the first CA identified in the dinoflagellates, and, taken together, our results suggest that this enzyme may help to increase CO2 availability at the cell surface.
Involvement of CBF Transcription Factors in Winter Hardiness in Birch
Authors: Welling Annikki , Palva E. Tapio 
Published: May 2008

AbstractCold acclimation of plants involves extensive reprogramming of gene expression. In Arabidopsis (Arabidopsis thaliana), three cold-inducible transcriptional activators designated CBF1 to -3/DREB1a to -c have been shown to play an important regulatory role in this acclimation process. Similarly to Arabidopsis, boreal zone trees can increase their freezing tolerance (FT) in response to low temperature during the growing season. However, maximal FT of these trees requires short daylength-induced dormancy development followed by exposure to both low and freezing temperatures. To elucidate the molecular basis of FT in overwintering trees, we characterized the role of birch (Betula pendula) CBF transcription factors in the cold acclimation process. We identified four putative CBF orthologs in a birch expressed sequence tag collection designated BpCBF1 to -4. Ectopic expression of birch CBFs in Arabidopsis resulted in constitutive expression of endogenous CBF target genes and increased FT of nonacclimated transgenic plants. In addition, these plants showed stunted growth and delayed flowering, typical features for CBF-overexpressing plants. Expression analysis in birch showed that BpCBF1 to -4 are low temperature responsive but differentially regulated in dormant and growing plants, the expression being delayed in dormant tissues. Freeze-thaw treatment, simulating wintertime conditions in nature, resulted in strong induction of BpCBF genes during thawing, followed by induction of a CBF target gene, BpLTI36. These results suggest that in addition to their role in cold acclimation during the growing season, birch CBFs appear to contribute to control of winter hardiness in birch.
The Arabidopsis Halophytic RelativeThellungiella halophilaTolerates Nitrogen-Limiting Conditions by Maintaining Growth, Nitrogen Uptake, and Assimilation
Authors: Kant Surya , Bi Yong-Mei , Weretilnyk Elizabeth , Barak Simon , Rothstein Steven J. 
Published: May 2008

AbstractA comprehensive knowledge of mechanisms regulating nitrogen (N) use efficiency is required to reduce excessive input of N fertilizers while maintaining acceptable crop yields under limited N supply. Studying plant species that are naturally adapted to low N conditions could facilitate the identification of novel regulatory genes conferring better N use efficiency. Here, we show that Thellungiella halophila, a halophytic relative of Arabidopsis (Arabidopsis thaliana), grows better than Arabidopsis under moderate (1 mm nitrate) and severe (0.4 mm nitrate) N-limiting conditions. Thellungiella exhibited a lower carbon to N ratio than Arabidopsis under N limitation, which was due to Thellungiella plants possessing higher N content, total amino acids, total soluble protein, and lower starch content compared with Arabidopsis. Furthermore, Thellungiella had higher amounts of several metabolites, such as soluble sugars and organic acids, under N-sufficient conditions (4 mm nitrate). Nitrate reductase activity and NR2 gene expression in Thellungiella displayed less of a reduction in response to N limitation than in Arabidopsis. Thellungiella shoot GS1 expression was more induced by low N than in Arabidopsis, while in roots, Thellungiella GS2 expression was maintained under N limitation but was decreased in Arabidopsis. Up-regulation of NRT2.1 and NRT3.1 expression was higher and repression of NRT1.1 was lower in Thellungiella roots under N-limiting conditions compared with Arabidopsis. Differential transporter gene expression was correlated with higher nitrate influx in Thellungiella at low 15NO3 − supply. Taken together, our results suggest that Thellungiella is tolerant to N-limited conditions and could act as a model system to unravel the mechanisms for low N tolerance.
A Pathogenic Fungi Diphenyl Ether Phytotoxin Targets Plant Enoyl (Acyl Carrier Protein) Reductase
Authors: Dayan Franck E. , Ferreira Daneel , Wang Yan-Hong , Khan Ikhlas A. , McInroy John A. , Pan Zhiqiang 
Published: May 2008

AbstractCyperin is a natural diphenyl ether phytotoxin produced by several fungal plant pathogens. At high concentrations, this metabolite inhibits protoporphyrinogen oxidase, a key enzyme in porphyrin synthesis. However, unlike its herbicide structural analogs, the mode of action of cyperin is not light dependent, causing loss of membrane integrity in the dark. We report that this natural diphenyl ether inhibits Arabidopsis (Arabidopsis thaliana) enoyl (acyl carrier protein) reductase (ENR). This enzyme is also sensitive to triclosan, a synthetic antimicrobial diphenyl ether. Whereas cyperin was much less potent than triclosan on this target site, their ability to cause light-independent disruption of membrane integrity and inhibition of ENR is similar at their respective phytotoxic concentrations. The sequence of ENR is highly conserved within higher plants and a homology model of Arabidopsis ENR was derived from the crystal structure of the protein from Brassica napus. Cyperin mimicked the binding of triclosan in the binding pocket of ENR. Both molecules were stabilized by the π-π stacking interaction between one of their phenyl rings and the nicotinamide ring of the NAD+. Furthermore, the side chain of tyrosine is involved in hydrogen bonding with a phenolic hydroxy group of cyperin. Therefore, cyperin may contribute to the virulence of the pathogens by inhibiting ENR and destabilizing the membrane integrity of the cells surrounding the point of infection.