bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanical behaviour of ultrafine grained aluminium containing Al8Fe2Si precipitates
Authors: Korchef A. , Kolsi A. W. , Njah N. 
Published: April 2006

AbstractA 99.1% aluminium was deformed by Equal Channel Angular (ECA) pressing. The material contains a low volume fraction of Al8Fe2Si precipitates located essentially at the grain boundaries. An important increase of the X‐ray diffraction peak broadening was observed after ECA pressings. This is due to grain refinement and enhanced lattice distortions. This was accompanied by a lattice decrease due to compressive stresses and partial dissolution of the Al8Fe2Si precipitates. The grain refinement leads to a significant improvement of the mechanical properties in compression and tension after the first pass through the die. Thereafter, the increase was less significant. The strengthening of the material was accompanied by decreased strain hardening, due to enhanced activities in grain boundaries. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Leading, learning, and unleashing potential: Youth leadership and civic engagement
Authors: Wheeler Wendy , Edlebeck Carolyn 
Published: April 2006

AbstractThe Innovation Center for Community and Youth Development is a Washington, D.C.‐based organization engaged in programming, research, and policy development related to youth civic engagement. Its mission is to unleash the potential of youth, adults, organizations, and communities to engage together in creating a just and equitable society.
Glycolytic sequence and respiration of Debaryomyces hansenii as compared to Saccharomyces cerevisiae
Authors: Sánchez N. S. , Calahorra M. , González‐Hernández J. C. , Peña A. 
Published: April 2006

AbstractThe fermentation and respiration activities of Debaryomyces hansenii were compared with those of Saccharomyces cerevisiae grown to stationary phase with high respiratory activity. It was found that: (a) glucose consumption, fermentation and respiration were lower than for S. cerevisiae; (b) fasting produced a much smaller decrease of respiration; (c) glucose consumed and not transformed to ethanol was higher; (d) in S. cerevisiae, full oxygenation prevented ethanol production but this effect was reversed by CCCP, whereas D. hansenii still showed some ethanol production under aerobiosis, which was moderately increased by CCCP. ATP levels were similar in the two yeasts. Levels of glycolytic intermediaries after glucose addition, and enzyme activities, indicated that the main difference and limiting step to explain the lower fermentation of D. hansenii is phosphofructokinase activity. Respiration and fermentation, which are lower in D. hansenii, compete for the re‐oxidation of reduced nicotinamide adenine nucleotides; this competition, in turn, seems to play a role in defining the fermentation rates of the two yeasts. The effect of CCCP on glucose consumption and ethanol production also indicates a role of ADP in both the Pasteur and Crabtree effects in S. cerevisiae but not in D. hansenii. D. hansenii shows an alternative oxidase, which in our experiments did not appear to be coupled to the production of ATP. Copyright © 2006 John Wiley & Sons, Ltd.
Involvement of yeast YOL151W/GRE2 in ergosterol metabolism
Authors: Warringer Jonas , Blomberg Anders 
Published: April 2006

AbstractThe Saccharomyces cerevisiae gene YOL151W/GRE2 is widely used as a model gene in studies on yeast regulatory responses to osmotic and oxidative stress. Nevertheless, information concerning the physiological role of this enzyme, a distant homologue of mammalian 3‐β‐hydroxysteroid dehydrogenases, is scarce. Combining quantitative phenotypic profiling and protein expression analysis studies, we here report the involvement of yeast Gre2p in ergosterol metabolism. Growth was significantly and exclusively reduced in gre2Δ strains subjected to environmental stress straining the cell membrane. Furthermore, whereas no compensatory mechanisms were activated due to loss of Gre2p during growth in favourable conditions (synthetic defined media, no stress), a striking and highly specific induction of the ergosterol biosynthesis pathway, represented by the enzymes Erg10p, Erg19p and Erg6p, was observed in gre2Δ during growth in a stress condition in which lack of Gre2p significantly affects growth. Involvement of Gre2p in ergosterol metabolism was confirmed by application of an array of selective inhibitors of lipid biosynthesis, as gre2Δ displayed vastly impaired tolerance exclusively to agents targeting the ergosterol biosynthesis. The approach outlined here, combining broad‐spectrum phenotypic profiling, expression analysis during conditions reducing the growth of the mutant and functional confirmation by application of highly selective inhibitors, may prove a valuable tool in gene functional analysis. Copyright © 2006 John Wiley & Sons, Ltd.
PCR‐mediated seamless gene deletion and marker recycling in Saccharomyces cerevisiae
Authors: Akada Rinji , Kitagawa Takao , Kaneko Shohei , Toyonaga Daiso , Ito Sachiko , Kakihara Yoshito , Hoshida Hisashi , Morimura Shigeru , Kondo Akihiko , Kida Kenji 
Published: April 2006

AbstractRepeated gene manipulations can be performed in yeast by excision of an introduced marker. Cassette modules containing a marker flanked by two direct repeat sequences of hisG or loxP have often been used for marker recycling, but these leave one copy of the repeats in the chromosome after excision. Genomic copies of a repeat can cause increased mistargeting of constructs containing the same repeats or unexpected chromosomal rearrangements via intra‐ or interchromosomal recombinations. Here, we describe a novel marker recycling procedure that leaves no scar in the genome, which we have designated seamless gene deletion. A 40 base sequence derived from an adjacent region to the targeted locus was placed in an integrating construct to generate direct repeats after integration. Seamless HIS3 deletion was achieved via a PCR fragment that consisted of a URA3 marker attached to a 40 base repeat‐generating sequence flanked by HIS3 targeting sequences at both ends. Transformation of the designed construct resulted in his3 disruption and the generation of 40 base direct repeats on both sides of URA3 in the targeted locus. The resulting his3::URA3 disruptants were plated on 5‐fluoroorotic acid medium to select for URA3 loss. All the selected colonies had lost URA3 precisely by recombination between the repeats, resulting in his3 deletion without any extraneous sequences left behind in the chromosome. Copyright © 2006 John Wiley & Sons, Ltd.
Different effects of sphingid and noctuid moths on the fecundity of Platanthera metabifolia (Orchidaceae) in Hokkaido
Authors: Inoue Ken 
Published: April 2006

AbstractThe fecundity of Platanthera metabifolia was investigated in relation to different types of behavior and morphology in both noctuid and sphingid pollinator moths. Low capsule set in the native habitats resulted from low activity of pollinating moths. From different patterns of capsule formation on spikes, pollinated spikes could be classified into sphingid‐pollinated and noctuid‐pollinated types. The contributions of sphingids to capsule set were nearly constant at the three study sites. High percentage capsule set at one site was linked with high noctuid activity. Different preferences of sphingids and noctuids as to spike features were detected: sphingids selected spikes with large numbers of flowers in early stages of flowering. Flowers with different spur length were equally pollinated by sphingids. On the other hand, noctuids selected spikes with short and medium‐sized spurs in the late stage of flowering. The size and density of spikes scarcely affected the pollination activity of noctuids. Selection pressure upon spike size and spur length in relation to sphingid pollination was suggested. The possibility of local differentiation in spur length due to activity of noctuids was discussed.
Cycling of soil carbon in a Japanese red pine forest II. Changes occurring in the first year after a clear‐felling
Authors: Nakane Kaneyuki , Tsubota Hiroyuki , Yamamoto Makoto 
Published: April 2006

AbstractCycling of soil carbon in the first year after a clear‐felling was compared with that before the felling in a Japanese red pine forest in Hiroshima Prefecture, west Japan. The daily mean temperature at the soil surface in summer was increased after the felling in comparison to that before felling, and the water content of both the A0 layer and the surface mineral soil was decreased due to the loss of the forest canopy. The rate of weight loss of the A0 layer was reduced after felling. However, accumulation of the A0 layer rapidly decreased because of the lack of litter supply to the forest floor. Low soil respiration after felling was mainly caused by the cessation of root respiration. Analysis of annual soil carbon cycling was then conducted using a compartment model. The relative decomposition rate of the A0 layer decreased whereas that of humus and dead roots in mineral soil increased to some extent after felling. The accumulation of carbon in mineral soil, however, increased slightly due to the supply of humus from roots killed by the felling.
Is intralesional cidofovir worthwhile in juvenile recurrent respiratory papillomatosis?
Authors: Sheahan P , Sexton S , Russell J D 
Published: April 2006

Objective: To investigate the efficacy of intralesional cidofovir in the treatment of recurrent respiratory papillomatosis (RRP) in children.Methods: Prospective observational study of four consecutive children with RRP treated at an academic tertiary children's hospital. Laryngo-bronchoscopy was performed at three- to five-weekly intervals. Photodocumentation was obtained and disease severity assessed using an anatomical RRP severity score. Surgical debulking of large papillomas was then performed, and cidofovir (5 mg/ml) injected into any remaining papillomas as well as submucosally at the sites of resected papillomas. The efficacy of cidofovir was assessed by the change in papilloma severity score over the course of the treatment.Results: Complete disease remission was obtained in one patient, with a partial response seen in two others. One patient showed no significant response. The greatest beneficial effect was seen after the fourth cidofovir injection; however, two patients demonstrated a deterioration in severity scores after treatment was withheld at this point. Both responded well to further cidofovir injections. However, a clear plateau in the response to cidofovir was seen in all patients by the eighth injection.Conclusion: Intralesional cidofovir may help control papilloma regrowth and reduce disease severity in many children with RRP. In most cases, cidofovir would appear to be less efficacious in causing disease eradication. There appears to be little evidence to support prolonged treatment regimes (i.e. more than eight treatments).
ProMAT: protein microarray analysis tool
Authors: White Amanda M. , Daly Don S. , Varnum Susan M. , Anderson Kevin K. , Bollinger Nikki , Zangar Richard C. 
Published: April 2006

Abstract
Summary: ProMAT is a software tool for statistically analyzing data from enzyme-linked immunosorbent assay microarray experiments. The software estimates standard curves, sample protein concentrations and their uncertainties for multiple assays. ProMAT generates a set of comprehensive figures for assessing results and diagnosing process quality. The tool is available for Windows or Mac, and is distributed as open-source Java and R code.
Availability: ProMAT is available at . ProMAT requires Java version 1.5.0 and R version 1.9.1 (or more recent versions). ProMAT requires either Windows XP or Mac OS 10.4 or newer versions.
Contact: amanda.white@pnl.gov
NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures
Authors: Weichenberger Christian X. , Sippl Manfred J. 
Published: April 2006

Abstract
Summary: The error rate of asparagine (Asn) and glutamine (Gln) amide rotamers in protein crystal structures is in the order of 20% and as a consequence the current Protein Database (PDB) contains approximately half a million incorrect Asn and Gln side-chain rotamers. Here we present NQ-Flipper, a web service based on knowledge-based potentials of mean force to automatically detect and correct erroneous rotamers. We achieve excellent agreement with expert curated data.
Availability: The program is accessible freely as a web service at
Contact: sippl@came.sbg.ac.at
ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees
Authors: Bardel Claire , Danjean Vincent , Génin Emmanuelle 
Published: April 2006

Abstract
Summary: Finding the genes involved in complex diseases susceptibility and among those genes, localizing the variant sites explaining this susceptibility is a major goal of genetic epidemiology. In this context, haplotypic methods that use the joint information on several markers may be of particular interest. When the number of haplotypes is large, a grouping may be required. Phylogenetic trees allow such groupings of haplotypes based on their evolutionary history and may help in the detection and localization of disease susceptibility sites. In this paper, we present a new software to perform phylogeny-based association and localization analysis.
Availability: The software package, including all documentation and example files, is freely available at . It is distributed under the GPL license.
Contact: bardel@vjf.inserm.fr
Computational recognition of potassium channel sequences
Authors: Heil Burkhard , Ludwig Jost , Lichtenberg-Fraté Hella , Lengauer Thomas 
Published: April 2006

Abstract
Motivation: Potassium channels are mainly known for their role in regulating and maintaining the membrane potential. Since this is one of the key mechanisms of signal transduction, malfunction of these potassium channels leads to a wide variety of severe diseases. Thus potassium channels are priority targets of research for new drugs, despite the fact that this protein family is highly variable and closely related to other channels, which makes it very difficult to identify new types of potassium channel sequences.
Results: Here we present a new method for identifying potassium channel sequences (PSM, Property Signature Method), which—in contrast to the known methods for protein classification—is directly based on physicochemical properties of amino acids rather than on the amino acids themselves. A signature for the pore region including the selectivity filter has been created, representing the most common physicochemical properties of known potassium channels. This string enables genome-wide screening for sequences with similar features despite a very low degree of amino acid similarity within a protein family.
Availability: The PSM software will be made available on request from the corresponding author.
Contact: Burkhard.Heil@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Pulmonary hypertension in thalassaemia major patients with normal left ventricular systolic function
Authors: Hagar R. W. , Morris C. R. , Vichinsky E. P. 
Published: April 2006

SummaryPulmonary hypertension is common in adults with thalassaemia and other haemolytic anaemias. It was hypothesised that regular transfusions in thalassaemia major should both decrease the chronic haemolytic rate and be protective from pulmonary hypertension (PHT). To reduce the contribution of existing cardiac disease to PHT, the subjects were limited to patients with normal left ventricular shortening fractions. Associations with multiple laboratory markers of haemolysis, serum ferritin levels, chest X‐rays findings and splenectomy status were also considered. We found no biochemical, transfusional, or clinical (except gender) differences in transfused thalassaemia patients with or without pulmonary hyper tension.
Tumours and microbial diseases of marine fishes in Alaskan waters
Authors: McCAIN B. B. , GRONLUND W. D. , MYERS M.S. , WELLINGS S. R. 
Published: April 2006

Abstract. In an effort further to define the current health status of demersal fish in the Bering Sea, 36 618 fish captured by otter trawl during 1976 were examined for pathological conditions. Of the 26 species examined, 22 were found to have no detectable abnormalities. The four species with abnormalities were Pacific cod Gadus macrocephalus Tilesius with pseudobranchial tumours and skin lesions, walleye pollock Theragra chalcogramma (Pallas) with pseudobranchial tumours, yellowfin sole Limanda aspera (Pallas) with lymphocystis, and rock sole Lepidopsetta bilineata (Ayres) with epidermal papillomas. The prevalence, geographical distribution and biological and pathological characteristics of affected individuals were determined.Pseudobranchial tumours of both Pacific cod and walleye pollock were occasionally found to be invasive. Fish bearing these tumours were distributed throughout the sampling area. The epidermal papillomas on rock sole resembled similar tumours found on several flatfish species along the West Coast of North America. The distribution of this disease appeared to be depth related. The virus‐caused lymphocystis growths were located on the ‘blind’ side of yellowfin sole. The highest frequencies of fish with lymphocystis were in the south‐eastern Bering Sea. Two main types of skin lesions were seen on Pacific cod: ulcers and ring‐shaped lesions. Isolates of bacteria (Pseudomonas sp.) were routinely obtained from the cod ulcers and may be the cause of this disease. The ring‐shaped skin lesions, when examined microscopically, contained unidentified epidermal basophilic bodies.
Infectious haematopoietic necrosis in rainbow trout Salmo gairdneri Richardson in a semi‐closed system
Authors: CARLISLE J. C. , SCHAT K. A. , ELSTON R. 
Published: April 2006

Abstract. An outbreak of infectious haematopoietic necrosis causing high mortality in rainbow trout fry occurred in New York State. Despite the fact that the hatchery effluent was recycled, spread of viral infection or of clinical disease was not demonstrated.Endocardial and glomerular endothelial necrosis and fibrinous peritonitis were among the histopathologic changes seen. Many of the signs and lesions were similar to those seen in infectious pancreatic necrosis.
Tissue reactions to microsporidian infections in fish
Authors: DYKOVÁ IVA , LOM JIŘÍ 
Published: April 2006

Abstract. Histopathological studies on natural and experimental infections of nineteen microsporidian species from fishes distinguished two types of tissue reactions.The first type is characteristic of infections with xenoma‐inducing microsporidian species and comprises three successive stages: a weakly reactive stage, a productive stage with the formation of granulomas and a stage of granuloma involution. Following the first stage, tissue reactions are directed towards the isolation of the parasite and result in its complete elimination and host tissue repair. The extent of pathological changes probably depends on the number of parasite cells which initiated the infection.The second type is represented by Pleistophora species infecting muscles or oocytes. Host tissue reaction is surprisingly slight during the schizogony and sporogony and does not tend to isolate the invaded muscle fibres. A slight lymphocytic infiltration of myosepta indicates the first stage of tissue reaction. The tissue reaction only reaches the productive stage when mature spores completely fill the contents of the infected muscle fibre. A thick wall of fibroblasts may be formed to demarcate the parasite mass as soon as it undergoes necrotic changes. The extent of pathological changes probably depends on the ability of early developmental stages of the parasite to spread the infection within the host.In both types of tissue reaction, the spores are destroyed by complete digestion within host phagocytic cells.
Detection of channel catfish virus in channel catfish, Ictalurus punctatus (Rafinesque): use of a nucleic acid probe*
Authors: WISE JANET A. , BOYLE J. A. 
Published: April 2006

AbstractA nucleic acid probe for channel catfish virus (CCV) was constructed using recombinant DNA techniques. This probe consisted of a specific viral DNA fragment generated by digestion of CCV DNA with the restriction enzyme EcoRI. The probe was used to examine DNA isolated from tissues of fish that had been injected with CCV. Viral DNA was detected in some tissues of various injected fish. The sensitivity limit of detection was determined to be one viral DNA per cell.
Serum chemistry of diseased English sole, Parophrys vetulus Girard, from polluted areas of Puget Sound, Washington
Authors: CASILLAS E. , MYERS M. S. , RHODES LINDA D. , McCAIN B. B. 
Published: April 2006

AbstractRelationships between selected serum components and microscopically detected idiopathic liver and kidney lesions were evaluated for English sole, Parophrys vetulus, sampled from urban and non‐urban areas of Puget Sound, Washington. The normal range for each serum chemistry parameter was based on English sole with no lesions, or sole with minor parasitic conditions or with lesions in tissues other than liver and kidney which did not significantly affect serum chemistry values. Generally, sole with idiopathic liver lesions had significantly different haematocrit values and levels of serum albumin, calcium, and bilirubin when compared to sole which were free of idiopathic liver and/or kidney lesions. Serum aspartate aminotransferase and alanine aminotransferase activity and serum levels of glucose, total protein, phosphates and magnesium were also abnormal, but appeared to be associated only with certain types of liver lesions. No association between kidney lesions and abnormal serum chemistry values was identified. In addition, English sole sampled from some urban areas of Puget Sound had particular serum chemistry values and liver lesion prevalences which were significantly different from those of sole sampled from non‐urban areas. These findings support the hypothesis that sole near highly urbanized environments may display other signs of impaired health in addition to high prevalences of tissue lesions. Thus, measurements of serum chemistry parameters, in conjunction with histopathological examination, appear to be useful techniques for evaluating the health of English sole.
Regulation of toxin and bacteriocin gene expression in Clostridium by interchangeable RNA polymerase sigma factors
Authors: Dupuy Bruno , Raffestin Stéphanie , Matamouros Susana , Mani Nagraj , Popoff Michel R. , Sonenshein Abraham L. 
Published: April 2006

SummaryThe production of major extracellular toxins by pathogenic strains of Clostridium botulinum, Clostridium tetani and Clostridium difficile, and a bacteriocin by Clostridium perfringens is dependent on a related group of RNA polymerase σ‐factors. These σ‐factors (BotR, TetR, TcdR and UviA) were shown to be sufficiently similar that they could substitute for one another in in vitro DNA binding and run‐off transcription experiments. In cells, however, the σ‐factors fell into two subclasses. BotR and TetR were able to direct transcription of their target genes in a fully reciprocal manner. Similarly, UviA and TcdR were fully interchangeable. Neither BotR nor TetR could substitute for UviA or TcdR, however, and neither UviA nor TcdR could direct transcription of the natural targets of BotR or TetR. The extent of functional interchangeability of the σ‐factors was attributed to the strong conservation of their subregion 4.2 sequences and the conserved −35 sequences of their target promoters, while restrictions on interchangeability were attributed to variations in their subregion 2.4 sequences and the target site −10 sequences. The four σ‐factors have been assigned to group 5 of the σ70 family and seem to have arisen from a common ancestral protein that may have co‐evolved with the genes whose transcription they direct. A fifth Clostridiumσ‐factor, σY of Clostridium acetobutylicum, resembles the TcdR family, but was not functionally interchangeable with members of this family.