bluuebunny/crossref_metadata_2025_split huggingface dataset:
Traders’ preference for goat characteristics in selected markets of Pangasinan, Philippines
Authors: ORDEN Maria Excelsis M. , JAMANDRE Wilfred E. , BROWN Ernesto O. , ORDEN Edgar A. , CRUZ Emilio M. , ALO Ana Marie P. , VILLAR Edwin C. 
Published: March 2005

ABSTRACTPreference for goat characteristics was determined from 42 traders in six markets in Pangasinan, an important trading center for goats in Luzon, the Philippines, and analyzed using a hedonic price model to determine whether these characteristics are important price determinants of goats. This information is important to goat raisers to respond to the needs of the local market, and thus to achieve a better price and higher income in goat raising. Meatiness, size, breed, sex and age (in descending order) were the dominant goat characteristics preferred by traders. Meatiness had the largest positive influence on price, with a price premium of US$6.24 (US$1.00 = PhP 53), whereas the age of the animal had the smallest influence at US$3.72. However, size and meatiness are manifestations of good breeds. Therefore, continued efforts to improve breeds in order to produce good quality goats are imperative to cater to market needs. Different characteristics implied different price premiums. Traders offered a higher price premium for better goat characteristics; thus, the improvement of these characteristics could result in higher returns for goat raisers.
The nutrient intakes of mothers of low birth weight babies – a comparison of ethnic groups in East London, UK
Authors: Rees G. A. , Doyle W. , Srivastava A. , Brooke Z. M. , Crawford M. A. , Costeloe K. L. 
Published: March 2005

AbstractThe objective of this paper was to compare the nutrient intakes of mothers of different ethnic origins after they had given birth to a low birth weight (LBW) baby (<2.5 kg). A total of 165 participants from East London, UK completed a prospective 7‐day diet diary using household measures, between 8 and 12 weeks post‐partum. The data were originally collected as baseline data prior to two separate nutrition intervention studies and were combined and re‐interrogated for the purpose of this paper. Folate and iron intakes were low in all ethnic groups compared to the Reference Nutrient Intakes (RNI). Half did not meet the RNI for folate and 88% did not meet the RNI for iron. Nearly a quarter of the group did not achieve the Lower Reference Nutrient Intake (LRNI) for iron. The mean vitamin D and calcium intakes were significantly different between the ethnic groups (P = 0.007, P = 0.001, respectively). African women had the highest vitamin D intakes (4.72 µg d−1) and Caucasians and Asians the lowest (2.4 µg d−1). Caucasians had the highest calcium intakes (780 mg d−1) and Africans the lowest (565 mg d−1). Over two‐thirds of African, Asian and African‐Caribbean women did not meet the RNI for calcium. Thirty‐one per cent of Africans did not meet the LRNI for calcium. Our data show a high prevalence of inadequate nutrition among women who deliver LBW babies with differences in nutrient intake between ethnic groups. This information can be used to target specific appropriate dietary advice to ethnic minorities for the prevention or repetition of LBW.
Maternal nutritional knowledge and child nutritional status in the Volta Region of Ghana
Authors: Appoh Lily Yaa , Krekling Sturla 
Published: March 2005

AbstractThe relationship between mother's nutritional knowledge, maternal education, and child nutritional status (weight‐for‐age) was the subject of investigation in this study. The data were collected in Ghana on 55 well nourished and 55 malnourished mother–child pairs. A questionnaire designed to collect data on mother's knowledge and practices related to child care and nutrition was administered to the mothers. Data on mother's demographic and socio‐economic characteristics as well as child anthropometric data were also collected. A nutrition knowledge score was calculated based on mother's responses to the nutrition related items. Bivariate analysis gave significant associations between child nutritional status and the following variables: time of initiating of breastfeeding, mother's knowledge of importance of colostrum and whether colostrum was given to child, age of introduction of supplementary food, and mother's knowledge about causes of kwashiorkor. The two groups also showed significant differences in their nutrition knowledge scores. Maternal formal education, and marital status were also found to be associated with child nutritional status in bivariate analyses. Further analysis with logistic regression revealed that maternal nutrition knowledge was independently associated with nutritional status after the effects of other significant variables were controlled for. Maternal education on the other hand was not found to be independently associated with nutritional status. These results imply that mother's practical knowledge about nutrition may be more important than formal maternal education for child nutrition outcome.
Identification of a TcpC-TcpQ Outer Membrane Complex Involved in the Biogenesis of the Toxin-Coregulated Pilus of
Vibrio cholerae
Authors: Bose Niranjan , Taylor Ronald K. 
Published: March 2005

ABSTRACT

The toxin-coregulated pilus (TCP) of
Vibrio cholerae
and the soluble TcpF protein that is secreted via the TCP biogenesis apparatus are essential for intestinal colonization. The TCP biogenesis apparatus is composed of at least nine proteins but is largely uncharacterized. TcpC is an outer membrane lipoprotein required for TCP biogenesis that is a member of the secretin protein superfamily. In the present study, analysis of TcpC in a series of strains deficient in each of the TCP biogenesis proteins revealed that TcpC was absent specifically in a
tcpQ
mutant. TcpQ is a predicted periplasmic protein required for TCP biogenesis. Fractionation studies revealed that the protein is not localized to the periplasm but is associated predominantly with the outer membrane fraction. An analysis of the amount of TcpQ present in the series of
tcp
mutants demonstrated the inverse of the TcpC result (absence of TcpQ in a
tcpC
deletion strain). Complementation of the
tcpQ
deletion restored TcpC levels and TCP formation, and similarly, complementation of
tcpC
restored TcpQ. Metal affinity pull-down experiments performed using His-tagged TcpC or TcpQ demonstrated a direct interaction between TcpC and TcpQ. In the presence of TcpQ, TcpC was found to form a high-molecular-weight complex that is stable in 2% sodium dodecyl sulfate and at temperatures below 65°C, a characteristic of secretin complexes. Fractionation studies in which TcpC was overexpressed in the absence of TcpQ showed that TcpQ is also required for proper localization of TcpC to the outer membrane.
Identification of New Protein-Protein Interactions Involving the Products of the Chromosome- and Plasmid-Encoded Type IV Secretion Loci of the PhytopathogenXanthomonas axonopodispv. citri
Authors: Alegria Marcos C. , Souza Diorge P. , Andrade Maxuel O. , Docena Cassia , Khater Leticia , Ramos Carlos H. I. , da Silva Ana C. R. , Farah Chuck S. 
Published: March 2005

ABSTRACTThe recently sequenced genome of the bacterial plant pathogenXanthomonas axonopodispv. citri contains twovirBgene clusters, one on the chromosome and one on a 64-kb plasmid, each of which codes for a previously uncharacterized type IV secretion system (T4SS). Here we used a yeast two-hybrid assay to identify protein-protein interactions in these two systems. Our results revealed interactions between known T4SS components as well as previously uncharacterized interactions involving hypothetical proteins coded by open reading frames in the twoX. axonopodispv. citrivirBloci. Our results indicate that both loci may code for previously unidentified VirB7 proteins, which we show interact with either VirB6 or VirB9 or with a hypothetical protein coded by the same locus. Furthermore, a set of previously uncharacterizedXanthomonasproteins have been found to interact with VirD4, whose gene is adjacent to the chromosomalvirBlocus. The gene for one member of this family is found within the chromosomalvirBlocus. All these uncharacterized proteins possess a conserved 120-amino-acid domain in their C termini and may represent a family of cofactors or substrates of theXanthomonasT4SS.
Characterization of the Acetate Binding Pocket in theMethanosarcina thermophilaAcetate Kinase
Authors: Ingram-Smith Cheryl , Gorrell Andrea , Lawrence Sarah H. , Iyer Prabha , Smith Kerry , Ferry James G. 
Published: March 2005

ABSTRACTAcetate kinase catalyzes the reversible magnesium-dependent synthesis of acetyl phosphate by transfer of the ATP γ-phosphoryl group to acetate. Inspection of the crystal structure of theMethanosarcina thermophilaenzyme containing only ADP revealed a solvent-accessible hydrophobic pocket formed by residues Val93, Leu122, Phe179, and Pro232in the active site cleft, which identified a potential acetate binding site. The hypothesis that this was a binding site was further supported by alignment of all acetate kinase sequences available from databases, which showed strict conservation of all four residues, and the recent crystal structure of theM. thermophilaenzyme with acetate bound in this pocket. Replacement of each residue in the pocket produced variants withKmvalues for acetate that were 7- to 26-fold greater than that of the wild type, and perturbations of this binding pocket also altered the specificity for longer-chain carboxylic acids and acetyl phosphate. The kinetic analyses of variants combined with structural modeling indicated that the pocket has roles in binding the methyl group of acetate, influencing substrate specificity, and orienting the carboxyl group. The kinetic analyses also indicated that binding of acetyl phosphate is more dependent on interactions of the phosphate group with an unidentified residue than on interactions between the methyl group and the hydrophobic pocket. The analyses also indicated that Phe179is essential for catalysis, possibly for domain closure. Alignments of acetate kinase, propionate kinase, and butyrate kinase sequences obtained from databases suggested that these enzymes have similar catalytic mechanisms and carboxylic acid substrate binding sites.
The Presumptive Magnetosome Protein Mms16 Is a Poly(3-Hydroxybutyrate) Granule-Bound Protein (Phasin) in
Magnetospirillum gryphiswaldense
Authors: Schultheiss Daniel , Handrick René , Jendrossek Dieter , Hanzlik Marianne , Schüler Dirk 
Published: March 2005

ABSTRACT

The Mms16 protein has been previously found to be associated with isolated magnetosomes from two
Magnetospirillum
strains. A function of this protein as a magnetosome-specific GTPase involved in the formation of intracellular magnetosome membrane vesicles was suggested (Y. Okamura, H. Takeyama, and T. Matsunaga, J. Biol. Chem.
276:
48183-48188, 2001). Here we present a study of the Mms16 protein from
Magnetospirillum gryphiswaldense
to clarify its function. Insertion-duplication mutagenesis of the
mms16
gene did not affect the formation of magnetosome particles but resulted in the loss of the ability of
M. gryphiswaldense
cell extracts to activate poly(3-hydroxybutyrate) (PHB) depolymerization in vitro, which was coincident with loss of the most abundant 16-kDa polypeptide from preparations of PHB granule-bound proteins. The
mms16
mutation could be functionally complemented by enhanced yellow fluorescent protein (EYFP) fused to ApdA, which is a PHB granule-bound protein (phasin) in
Rhodospirillum rubrum
sharing 55% identity to Mms16. Fusions of Mms16 and ApdA to enhanced green fluorescent protein (EGFP) or EYFP were colocalized in vivo with the PHB granules but not with the magnetosome particles after conjugative transfer to
M. gryphiswaldense
. Although the Mms16-EGFP fusion protein became detectable by Western analysis in all cell fractions upon cell disruption, it was predominantly associated with isolated PHB granules. Contrary to previous suggestions, our results argue against an essential role of Mms16 in magnetosome formation, and the previously observed magnetosome localization is likely an artifact due to unspecific adsorption during preparation. Instead, we conclude that Mms16 in vivo is a PHB granule-bound protein (phasin) and acts in vitro as an activator of PHB hydrolysis by
R. rubrum
PHB depolymerase PhaZ1. Accordingly, we suggest renaming the Mms16 protein of
Magnetospirillum
species to ApdA, as in
R. rubrum
.
Analysis of the Hypervariable Region of the
Salmonella enterica
Genome Associated with tRNA

leuX
Authors: Bishop Anne L. , Baker Stephen , Jenks Sara , Fookes Maria , Gaora Peadar Ó , Pickard Derek , Anjum Muna , Farrar Jeremy , Hien Tran T. , Ivens Al , Dougan Gordon 
Published: March 2005

ABSTRACT

The divergence of
Salmonella enterica
and
Escherichia coli
is estimated to have occurred approximately 140 million years ago. Despite this evolutionary distance, the genomes of these two species still share extensive synteny and homology. However, there are significant differences between the two species in terms of genes putatively acquired via various horizontal transfer events. Here we report on the composition and distribution across the
Salmonella
genus of a chromosomal region designated SPI-10 in
Salmonella enterica
serovar Typhi and located adjacent to tRNA

leuX

. We find that across the
Salmonella
genus the tRNA

leuX

region is a hypervariable hot spot for horizontal gene transfer; different isolates from the same
S. enterica
serovar can exhibit significant variation in this region. Many P4 phage, plasmid, and transposable element-associated genes are found adjacent to tRNA

leuX

in both
Salmonella
and
E. coli
, suggesting that these mobile genetic elements have played a major role in driving the variability of this region.
Genotyping of
Ochrobactrum
spp. by AFLP Analysis
Authors: Leal-Klevezas Diana Sara , Martínez-de-la-Vega Octavio , Ramírez-Barba Ector Jaime , Osterman Björn , Martínez-Soriano Juan Pablo , Simpson June 
Published: March 2005

ABSTRACT

AFLP was used to analyze the genetic diversity among
Ochrobactrum
strains. AFLP patterns showed a great genomic variability that separated the samples into three distinct clusters.
Ochrobactrum intermedium
was found to be closely related to
Brucella abortus
S99.
Transcriptional Analysis of the Principal Cell Division Gene,
ftsZ
, of
Mycobacterium tuberculosis
Authors: Roy Sougata , Ajitkumar Parthasarathi 
Published: March 2005

ABSTRACT

Multiple promoters drive the expression of the principal cell division gene,
ftsZ
, in bacterial systems. Primer extension analysis of total RNA from
Mycobacterium tuberculosis
and a
Mycobacterium smegmatis
transformant containing 1.117 kb of the upstream region of
M. tuberculosis ftsZ
and promoter fusion studies identified six
ftsZ
transcripts and their promoters in the
ftsQ
open reading frame and
ftsQ
-
ftsZ
intergenic region. The presence of multiple promoters reflects the requirement to maintain a high basal level of, or to differentially regulate, FtsZ expression during different growth conditions of the pathogen in vivo.
X- and Y-chromosome specific variants of the amelogenin gene allow sex determination in sheep (Ovis aries) and European red deer (Cervus elaphus)
Authors: Pfeiffer I , Brenig B 
Published: March 2005

Abstract
Background
Simple and precise methods for sex determination in animals are a pre-requisite for a number of applications in animal production and forensics. However, some of the existing methods depend only on the detection of Y-chromosome specific sequences. Therefore, the abscence of a signal does not necessarily mean that the sample is of female origin, because experimental errors can also lead to negative results. Thus, the detection of Y- and X-chromosome specific sequences is advantageous.

Results
A novel method for sex identification in mammals (sheep, Ovis aries and European red deer, Cervus elaphus) is described, using a polymerase chain reaction (PCR) and sequencing of a part of the amelogenin gene. A partial sequence of the amelogenin gene of sheep and red deer was obtained, which exists on both X and Y chromosomes with a deletion region on the Y chromosome. With a specific pair of primers a DNA fragment of different length between the male and female mammal was amplified.

Conclusion
PCR amplification using the amelogenin gene primers is useful in sex identification of samples from sheep and red deer and can be applied to DNA analysis of micro samples with small amounts of DNA such as hair roots as well as bones or embryo biopsies.
Efficacy of acupuncture for cocaine dependence: a systematic review & meta-analysis
Authors: Mills Edward J , Wu Ping , Gagnier Joel , Ebbert Jon O 
Published: March 2005

BackgroundAcupuncture is a commonly used treatment option for the treatment of addictions such as alcohol, nicotine and drug dependence. We systematically reviewed and meta-analyzed the randomized controlled trials of acupuncture for the treatment of cocaine addiction.
Methods
Two reviewers independently searched 10 databases. Unpublished studies were sought using Clinicaltrials.gov, the UK National Research Register and contacting content experts. Eligible studies enrolled patients with the diagnosis of cocaine dependence of any duration or severity randomly allocated to either acupuncture or sham or other control. We excluded studies of acupuncture methods and trials enrolling patients with polysubstance use or dependence. We abstracted data on study methodology and outcomes. We pooled the studies providing biochemical confirmation of cocaine abstinence.

Results
Nine studies enrolling 1747 participants met inclusion criteria; 7 provided details for biochemical confirmation of cocaine abstinence. On average, trials lost 50% of enrolled participants (range 0–63%). The pooled odds ratio estimating the effect of acupuncture on cocaine abstinence at the last reported time-point was 0.76 (95% CI, 0.45 to 1.27, P = 0.30, I2 = 30%, HeterogeneityP = 0.19).

Conclusion
This systematic review and meta-analysis does not support the use of acupuncture for the treatment of cocaine dependence. However, most trials were hampered by large loss to follow up and the strength of the inference is consequently weakened.
Influence of immunomagnetic enrichment on gene expression of tumor cells
Authors: Woelfle Ute , Breit Elisabeth , Pantel Klaus 
Published: March 2005

Abstract
Background
Metastasis is the leading cause of cancer-related death. Bone marrow (BM) is a frequent site for the settlement of disseminated tumor cells which occurs years before overt metastases signal incurability.

Methods
Here we describe a new method to assess the initial stage of metastasis development in cancer patients. By immunomagnetic selection with HER2/neu and EpCAM as catcher antigens single disseminated tumor cells can be enriched from BM samples. To examine whether the immunomagnetic enrichment technique may change gene expression in the selected tumor cells, we performed differential expression profiling with the breast cancer cell lines MCF-7 and BT474 as models. The profiles were performed using 1.2 Cancer Arrays (Clontech) containing 1176 cDNAs that can be grouped into different functional categories, such as signal transduction, cell cycle, adhesion, cytoskeleton plasticity, growth factors and others.

Results
The reproducibility of the gene expression profiling between duplicate cDNA-array experiments was assessed by two independent experiments with MCF-7 breast cancer cells. Scatter blot analysis revealed a good reproducibility of the cDNA array analysis (i.e. less than 10% difference in the gene expression between the arrays). Subsequent comparative cDNA-array analyses of immunobead-selected and unselected MCF-7 and BT474 cancer cells indicated that the antibody incubation during the immunomagnetic selection procedure did not considerably alter the gene expression profile.

Conclusion
The described method offers an excellent tool for the enrichment of micrometastatic tumor cells in BM without largely changing the gene expression pattern of these cells.
ZIRLO™ — An Alloy Development Success
Authors: Sabol GP 
Published: March 2005

AbstractSignificant data and milestones in the development of the ZIRLO alloy for PWR applications are reviewed. From humble beginnings as an R&D program, an approach to improving the corrosion resistance of zirconium-based alloys was developed. The corrosion resistance of dilute alloys is controlled by the microstructure, and both solid solution and precipitate effects impact corrosion performance. Several transition metals are beneficial for corrosion at low concentrations, but the most favorable alloy system is zirconium-niobium, because it offers flexibility in processing options. Strength of the binary alloys can be improved by additions of tin, which, in combination with low levels of iron, provide corrosion resistance in lithium hydroxide solutions. Numerous experimental ingots, thermo-mechanical processing routes, corrosion tests, and materials characterizations were performed along the path to the final alloy composition. The resulting material, ZIRLO, has proven itself as a successful alloy for PWR fuel cladding and structural applications.
Using Simulation Techniques to Estimate Management Parameters on Snake River Steelhead: Declines in Productivity Make Rebuilding Difficult
Authors: Yuen Henry , Sharma Rishi 
Published: March 2005

Abstract
We collected adult and juvenile spawner recruit data on wild summer steelhead Oncorhynchus mykiss for the Snake River and estimated parameters for fisheries management by partitioning the data into predam and postdam periods and fitting the Ricker and Beverton–Holt models to those time series. The results showed a decline in productivity irrespective of the model chosen and the way in which the pre- and postdam periods were defined. However, the data were noisy and the confidence bounds on parameter estimates were fairly large. To reconcile the different management goals derived from the different data sources (adult or juvenile data) or model choice (Ricker or Beverton–Holt), we used simulation techniques and Bayesian algorithms. The combined approach suggests a recovery management goal (i.e., spawning stock associated with the maximum sustainable yield) of 60,000 steelhead above Lower Granite Dam. At current smolt-to-adult survival rates, the data indicate optimal escapement of between 20,000 and 27,000 adults. We note that Snake River steelhead stocks cannot be managed for recovery escapement levels given current estimates of smolt-to-adult survival rates, and we discuss alternatives for present-day management and rebuilding over time.