bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abiotic mosaics affect seasonal variation of plant resources and influence the performance and mortality of a leaf‐miner in Gambel's oak (Quercus gambelii, Nutt.)
Authors: Yarnes Christopher T. , Boecklen William J. 
Published: November 2005

AbstractConceptual models of terrestrial trophic dynamics have emphasized the potential influence of various abiotic factors, though empirical studies have found generalities to be scarce. Progress may result through an increased use of experimental gradients in tandem with existing, natural gradients of abiotic factors that are more difficult to manipulate. Along an elevation/climatic gradient, a fertilization experiment was conducted to examine the impact of environmentally induced variation in foliar nitrogen on tri‐trophic interactions for Phyllonorycter sp., a leaf‐miner (Lepidoptera: Gracillariidae), in Rocky Mountain white oak, Quercus gambelii. Microclimate determined the relative effect of host‐plant and natural‐enemy effects for Phyllonorycter sp. Cooler, more humid microclimates resulted in a higher biomass payoff (total biomass/density). Further, increased seasonal variation in foliar nitrogen content at warmer, drier sites significantly increased parasitism rates. Fertilization treatments increased foliar nitrogen content and resulted in increased early‐instar mortality. Fertilization treatment also acted in a non‐linear fashion with microclimate to influence spatial patterns in parasitism rates. Overall, microclimate was found to affect characteristics of each trophic level, including host‐plant nitrogen dynamics, Phyllonorycter sp. performance, and parasitism rates. Additionally, nutrient availability altered patterns of parasitoid‐related mortality in Phyllonorycter sp. within microclimates. These results suggest that local topographic variation in combinations of abiotic factors, or abiotic mosaics, has important effects for spatial patterns of tri‐trophic interactions.
The effects of understorey dwarf bamboo (Sasa kurilensis) removal on soil fertility in a Betulaermanii forest of northern Japan
Authors: Tripathi Shri Kant , Sumida Akihiro , Ono Kiyomi , Shibata Hideaki , Uemura Shigeru , Takahashi Koichi , Hara Toshihiko 
Published: November 2005

AbstractWe investigated the changes in soil microbial biomass C (MBC), microbial biomass N (MBN) and N mineralization in Sasa kurilensis‐present (SP) and S. kurilensis‐removed (SR) stands in a Betula ermanii forest. The mean levels of MBC and MBN were significantly higher in the SR stand than in the SP, which may have positively influenced the N‐mineralization rate as depicted by a significant positive correlation between these variables and the N‐mineralization rate. N immobilization and subsequent N release along with decreased use of available soil N due to S. kurilensis removal may have ensured greater N availability in the SR stand.
PCP: a program for supervised classification of gene expression profiles
Authors: Buturović Ljubomir J. 
Published: November 2005

Abstract
Summary: PCP (Pattern Classification Program) is an open-source machine learning program for supervised classification of patterns (vectors of measurements). The principal use of PCP in bioinformatics is design and evaluation of classifiers for use in clinical diagnostic tests based on measurements of gene expression. PCP implements leading pattern classification and gene selection algorithms and incorporates cross-validation estimation of classifier performance. Importantly, the implementation integrates gene selection and class prediction stages, which is vital for computing reliable performance estimates in small-sample scenarios. Additionally, the program includes automated and efficient model selection (optimization of parameters) for support vector machine (SVM) classifier. The distribution includes Linux and Windows/Cygwin binaries. The program can easily be ported to other platforms.
Availability: Free download at
Contact: ljubomir@sfsu.edu
Pathway recognition and augmentation by computational analysis of microarray expression data
Authors: Novak Barbara A. , Jain Ajay N. 
Published: November 2005

Abstract
Motivation: We present a system, QPACA (Quantitative Pathway Analysis in Cancer) for analysis of biological data in the context of pathways. QPACA supports data visualization and both fine- and coarse-grained specifications, but, more importantly, addresses the problems of pathway recognition and pathway augmentation.
Results: Given a set of genes hypothesized to be part of a pathway or a coordinated process, QPACA is able to reliably distinguish true pathways from non-pathways using microarray expression data. Relying on the observation that only some of the experiments within a dataset are relevant to a specific biochemical pathway, QPACA automates selection of this subset using an optimization procedure. We present data on all human and yeast pathways found in the KEGG pathway database. In 117 out of 191 cases (61%), QPACA was able to correctly identify these positive cases as bona fide pathways with p-values measured using rigorous permutation analysis. Success in recognizing pathways was dependent on pathway size, with the largest quartile of pathways yielding 83% success. In cross-validation tests of pathway membership prediction, QPACA was able to yield enrichments for predicted pathway genes over random genes at rates of 2-fold or better the majority of the time, with rates of 10-fold or better 10–20% of the time.
Availability: The software is available for academic research use free of charge by email request.
Contact: ajain@jainlab.org
Supplementary information: Data used in the paper may be downloaded from
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios
Authors: Pei Jimin , Cai Wei , Kinch Lisa N. , Grishin Nick V. 
Published: November 2005

Abstract
Motivation: A number of methods have been developed to predict functional specificity determinants in protein families based on sequence information. Most of these methods rely on pre-defined functional subgroups. Manual subgroup definition is difficult because of the limited number of experimentally characterized subfamilies with differing specificity, while automatic subgroup partitioning using computational tools is a non-trivial task and does not always yield ideal results.
Results: We propose a new approach SPEL (specificity positions by evolutionary likelihood) to detect positions that are likely to be functional specificity determinants. SPEL, which does not require subgroup definition, takes a multiple sequence alignment of a protein family as the only input, and assigns a P-value to every position in the alignment. Positions with low P-values are likely to be important for functional specificity. An evolutionary tree is reconstructed during the calculation, and P-value estimation is based on a random model that involves evolutionary simulations. Evolutionary log-likelihood is chosen as a measure of amino acid distribution at a position. To illustrate the performance of the method, we carried out a detailed analysis of two protein families (LacI/PurR and G protein α subunit), and compared our method with two existing methods (evolutionary trace and mutual information based). All three methods were also compared on a set of protein families with known ligand-bound structures.
Availability: SPEL is freely available for non-commercial use. Its pre-compiled versions for several platforms and alignments used in this work are available at
Contact: grishin@chop.swmed.edu.
Supplementary information: Supplementary materials are available at
Distinct and Cooperative Functions of Phytochromes A, B, and C in the Control of Deetiolation and Flowering in Rice
Authors: Takano Makoto , Inagaki Noritoshi , Xie Xianzhi , Yuzurihara Natsu , Hihara Fukiko , Ishizuka Toru , Yano Masahiro , Nishimura Minoru , Miyao Akio , Hirochika Hirohiko , Shinomura Tomoko 
Published: November 2005

AbstractWe have isolated phytochrome B (phyB) and phyC mutants from rice (Oryza sativa) and have produced all combinations of double mutants. Seedlings of phyB and phyB phyC mutants exhibited a partial loss of sensitivity to continuous red light (Rc) but still showed significant deetiolation responses. The responses to Rc were completely canceled in phyA phyB double mutants. These results indicate that phyA and phyB act in a highly redundant manner to control deetiolation under Rc. Under continuous far-red light (FRc), phyA mutants showed partially impaired deetiolation, and phyA phyC double mutants showed no significant residual phytochrome responses, indicating that not only phyA but also phyC is involved in the photoperception of FRc in rice. Interestingly, the phyB phyC double mutant displayed clear R/FR reversibility in the pulse irradiation experiments, indicating that both phyA and phyB can mediate the low-fluence response for gene expression. Rice is a short-day plant, and we found that mutation in either phyB or phyC caused moderate early flowering under the long-day photoperiod, while monogenic phyA mutation had little effect on the flowering time. The phyA mutation, however, in combination with phyB or phyC mutation caused dramatic early flowering.
Caesarean section delivery and the risk of allergic disorders in childhood
Authors: Renz‐Polster H. , David M. R. , Buist A. S. , Vollmer W. M. , O'Connor E. A. , Frazier E. A. , Wall M. A. 
Published: November 2005

SummaryBackground
The composition of the intestinal flora in young children, if unfavourable, may increase the susceptibility to allergic disorders. Beneficial intestinal microbes originate from the maternal vaginal tract and thus are more likely to be transferred during vaginal births than during Caesarean sections (C‐sections).Objective
To determine whether children born by C‐section have a different risk of allergic disorders compared with those delivered vaginally. We also tested the hypothesis that the risk of allergic disorders is highest for children born after ‘repeat C‐sections’.Methods
A retrospective cohort study of 8953 children aged 3–10 years. Children diagnosed with allergic rhinoconjunctivitis (AR), asthma, atopic dermatitis (AD), or food allergies were identified from the Kaiser Permanente Northwest Region electronic records. The children's sex, birth weight, birth order, postnatal exposure to antibiotics as well as the mothers' age, ethnicity, education, marital status, smoking status during pregnancy, and use of asthma or hayfever medications were identified through the mothers' medical records or through the Oregon Birth Registry.Results
The risk of being diagnosed with AR was significantly higher in the children born by C‐section than in those delivered vaginally: adjusted odds ratio (OR)=1.37%, 95% confidence interval (CI)=1.14–1.63. Delivery by C‐section was also associated with the subsequent diagnosis of asthma (OR=1.24%, 95% CI=1.01–1.53); this association was gender specific, with a positive association restricted to girls (OR for asthma in girls: OR=1.53%, 95% CI=1.11–2.10; in boys: OR=1.08%, 95% CI=0.81–1.43). There was no significant association between mode of delivery and AD.If children born in a ‘repeat C‐section’ were considered separately the risk of being diagnosed with AR increased further (OR=1.78%, 95% CI=1.34–2.37). The same increase was noted for asthma in girls (OR=1.83%, 95% CI=1.13–2.97) but not in boys.Conclusion
Caesarean sections may be associated with an increased risk of developing AR in childhood.
A case–control study of bronchial asthma associated with ulcerative colitis: role of airway microvascular permeability
Authors: Kanazawa H. , Yoshikawa J. 
Published: November 2005

SummaryBackground
Recent attention has been devoted to the respiratory manifestations that may be associated with diseases of distant organs. The most prevalent and distinctive pattern of respiratory involvement in ulcerative colitis (UC) is airway inflammation.Objective
This study was designed to examine the contribution of airway microvascular permeability to the pathophysiological association of asthma with UC.Methods
Sputum induction and methacholine provocation test were performed in 27 asthmatic patients (15 without UC and 12 with UC), nine patients with UC and 15 normal controls. Inflammatory indexes, vascular endothelial growth factor (VEGF) levels in induced sputum, airway vascular permeability index and exhaled nitric oxide (NO) levels were examined in all subjects.Results
The percentage of eosinophils and concentration of eosinophil cationic protein in induced sputum were similar in all four groups. Though exhaled NO levels were significantly higher in asthmatics with or without UC than in normal controls or UC patients, these levels were comparable in asthmatics with and without UC. VEGF levels in induced sputum and airway vascular permeability index were significantly higher in asthmatics without UC (VEGF: 1920 (990) pg/mL; airway vascular permeability index: 0.018 (0.008)) and asthmatics with UC (6570 (1000) pg/mL; 0.040 (0.006)) than in normal controls (950 (700) pg/mL; 0.009 (0.003)), whose levels were comparable to those of UC patients (900 (600) pg/mL; 0.011 (0.003)). In particular, these parameters were markedly increased in asthmatics with UC than in asthmatics without UC. VEGF level was significantly correlated with airway vascular permeability index in asthmatics with UC. Moreover, VEGF level and airway vascular permeability index was inversely correlated with degree of airway obstruction and airway hyper‐reactivity to methacholine in these asthmatics.Conclusion
Airway microvascular hyper‐permeability induced by VEGF may have a profound effect on airway function and can explain the heightened airway hyper‐responsiveness characteristic of asthma associated with UC.
Vascular endothelial growth factor up‐regulation and bronchial wall remodelling in asthma
Authors: Chetta A. , Zanini A. , Foresi A. , D'Ippolito R. , Tipa A. , Castagnaro A. , Baraldo S. , Neri M. , Saetta M. , Olivieri D. 
Published: November 2005

SummaryBackground
There is increasing in vitro evidence to support a role for vascular endothelial growth factor (VEGF), a major regulator of angiogenesis, as a mediator of fibrosis associated with neovascularization.Objective
We tested the hypothesis that VEGF is involved both in increased airway mucosal vascularity and in the subepithelial fibrosis of asthmatic patients.Methods
Bronchial biopsies were performed in 24 asthmatic patients and eight healthy controls. Immunostaining, using computerized image analysis, was performed using monoclonal antibodies against VEGF+ cells, type IV collagen, to outline the basement membrane thickness, and tryptase and EG2, to identify mast cells and eosinophils, respectively.Results
The counts of VEGF+ cells (P<0.05), mast cells and EG2+ cells (both P<0.01) were higher in asthmatics than in controls. The number of vessels, the vascular area in the lamina propria, and the basement membrane thickness were significantly higher in asthmatics than in healthy volunteers (P<0.01). Moreover, in asthmatic patients, the number of VEGF+ cells was significantly related to the number of vessels (P<0.01), to mast cells (P<0.01) and to basement membrane thickness (P<0.01). A colocalization study also revealed that mast cells were a relevant cellular source of VEGF. High doses of inhaled fluticasone propionate significantly reduced VEGF+ cells (P<0.05), vessel number (P<0.05), vascular area (P<0.05) and basement membrane thickness (P<0.05) in a subgroup of asthmatic patients.Conclusions
This study shows that VEGF, in addition to being involved in the vascular component of airway remodelling, may play a role in the thickening of the basement membrane in asthma.
Molecular cloning and immunoglobulin E reactivity of a natural rubber latex lecithinase homologue, the major allergenic component of Hev b 4
Authors: Sunderasan E. , Bahari A. , Arif S. A. M. , Zainal Z. , Hamilton R. G. , Yeang H. Y. 
Published: November 2005

SummaryBackground
Hev b 4 is an allergenic natural rubber latex (NRL) protein complex that is reactive in skin prick tests and in vitro immunoassays. On SDS‐polyacrylamide gel electrophoresis (SDS‐PAGE), Hev b 4 is discerned predominantly at 53–55 kDa together with a 57 kDa minor component previously identified as a cyanogenic glucosidase. Of the 13 NRL allergens recognized by the International Union of Immunological Societies, the 53–55 kDa Hev b 4 major protein is the only candidate that lacks complete cDNA and protein sequence information.Objective
We sought to clone the transcript encoding the Hev b 4 major protein, and characterize the native protein and its recombinant form in relation to IgE binding.Methods
The 5′/3′ rapid amplification of cDNA ends method was employed to obtain the complete cDNA of the Hev b 4 major protein. A recombinant form of the protein was over‐expressed in Escherichia coli. The native Hev b 4 major protein was deglycosylated by trifluoromethane sulphonic acid. Western immunoblots of the native, deglycosylated and recombinant proteins were performed using both polyclonal antibodies and sera from latex‐allergic patients.Results
The cDNA encoding the Hev b 4 major protein was cloned. Its open reading frame matched lecithinases in the conserved domain database and contained 10 predicted glycosylation sites. Detection of glycans on the Hev b 4 lecithinase homologue confirmed it to be a glycoprotein. The deglycosylated lecithinase homologue was discerned at 40 kDa on SDS‐PAGE, this being comparable to the 38.53 kDa mass predicted by its cDNA. Deglycosylation of the lecithinase homologue resulted in the loss of IgE recognition, although reactivity to polyclonal rabbit anti‐Hev b 4 was retained. IgE from latex‐allergic patients also failed to recognize the non‐glycosylated E. coli recombinant lecithinase homologue.Conclusion
The IgE epitopes of the Hev b 4 lecithinase homologue reside mainly in its carbohydrate moiety, which also account for the discrepancy between the observed molecular weight of the protein and the value calculated from its cDNA.
Long‐term seasonal variation in the biological traits of benthic‐macroinvertebrates in two Mediterranean‐climate streams in California, U.S.A.
Authors: BÊCHE LEAH A. , MCELRAVY ERIC P. , RESH VINCENT H. 
Published: November 2005

Summary1. We investigated the seasonal variation of biological traits and the influence of interannual rainfall variability on this pattern. Using long‐term survey data (6–19 years) from an intermittent and a perennial stream in the Mediterranean‐climate region of northern California, we examined 16 fuzzy‐coded biological traits (e.g. maximum size, life cycle duration, and mode of respiration).2. Seasonal habitat variability is higher in the intermittent stream than in the perennial stream. During the winter and spring wet‐season both streams flood; however, during the summer dry‐season, the intermittent stream forms isolated pools in (occasionally drying completely).3. Seasonal habitat variability influenced both taxonomic and biological trait composition. Distinct taxonomic communities were present in each season, particularly in the intermittent stream. The intermittent stream also exhibited more seasonal variation in biological traits than the perennial stream.4. Despite statistically significant seasonal variation, trait composition was relatively stable among seasons in comparison with taxonomic composition and abundance. Taxonomic composition varied considerably between seasons, because of high seasonal and interannual replacement of taxa resulting from seasonal habitat changes.5. The seasonality of taxonomic composition and abundance was sensitive to interannual rainfall variability. In dry years, the taxonomic composition of communities was more similar between seasons than in wet years, while trait composition was relatively insensitive to rainfall variability.6. Despite high seasonal variation in abundance and taxonomic composition, biological traits of aquatic macroinvertebrates varied less and exhibited seasonal stability, which may be a result of the unpredictability and harshness of stream environments.
Effect of landscape factors on fish distribution in arctic Alaskan lakes
Authors: HERSHEY A. E. , BEATY S. , FORTINO K. , KEYSE M. , MOU P. P. , O'BRIEN W. J. , ULSETH A. J. , GETTEL G. A. , LIENESCH P. W. , LUECKE C. , MCDONALD M. E. , MAYER C. H. , MILLER M. C. , RICHARDS C. , SCHULDT J. A. , WHALEN S. C. 
Published: November 2005

Summary1. The distribution of species is affected by many factors operating at a variety of temporal and spatial scales in a heterogeneous landscape. In lakes, fish communities are dynamic, influenced by landscape‐level factors that control colonisation and extinction.2. We used classification and regression tree (CART) analyses to quantify the importance of landscape‐level factors in determining the distribution of fish species in 168 arctic Alaskan lakes. Factors including lake size, depth, outflow gradient, distance to other lakes, lake order, altitude, river drainage and age of glacial surface were analysed. These factors could affect either access of fish to a lake (colonisation variables), or their survival in a lake that already had been colonised (extinction variables).3. The presence of a species was predicted accurately in 78.4% ± 10.5% (mean ± SD) of cases, and absence in 75.0% ± 6.1% of cases. The relative importance of extinction versus colonisation variables varied with species. Extinction variables were most important for lake trout (Salvelinus namaycush) and slimy sculpin (Cottus cognatus), a mixture of extinction and colonisation variables was important for arctic char (Salvelinus alpinus), and colonisation variables were most important for arctic grayling (Thymallus arcticus) and round whitefish (Prosopium cylindraceum).4. Ecological differences among species account for much of the difference in relative importance of colonisation versus extinction variables. In addition, stream piracy events have occurred over geologic time scales, which have resulted in lakes that are currently inaccessible but support relict fish populations.5. Climate warming, currently occurring in the arctic, is likely to alter further the stream network, which could have dramatic effects on fish distributions by affecting access to isolated lakes or isolating lakes that are currently accessible.