bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sound-scattering spectra of steelhead (Oncorhynchus mykiss), coho (O. kisutch), and Chinook (O. tshawytscha) salmonids
Authors: Renfree Josiah S. , Hayes Sean A. , Demer David A. 
Published: April 2009

Abstract
Renfree, J. S., Hayes, S. A., and Demer, D. A. 2009. Sound-scattering spectra of steelhead (Oncorhynchus mykiss), coho (O. kisutch), and Chinook (O. tshawytscha) salmonids. – ICES Journal of Marine Science, 66: 1091–1099. A recently developed method for measuring total target strength (TTS) allows calculation of the absolute scattered energy from fish over a broad-bandwidth signal. This technique uses the ratio of coherent and incoherent sound fields reflected off fish swimming in tanks. In stark contrast to other acoustic methods, this technique works best in reverberant conditions, is self-calibrating, and conveniently provides measurements of sound-scattering spectra for possible target identification. It has been used to successfully characterize the scattering spectra of marine life such as anchovy, sardine, and krill. In this experiment, the broad-bandwidth scattering spectra are characterized for the salmonids steelhead (Oncorhynchus mykiss), coho (Oncorhynchus kisutch), and Chinook (Oncorhynchus tshawytscha). The TTS measurements demonstrate that the scattering spectra for these species are similar, yet discernible. These unique scattering spectra may provide means for acoustically identifying and enumerating such targets in rivers or streams. Having effective acoustic methods for assessing salmon abundance could become a major addition to currently available measurement tools and provide a new, low-impact assessment technique for both commercial and endangered populations.
Using acoustic technology to improve the modelling of the transportation and distribution of juvenile gadoids in the Barents Sea
Authors: Johansen Geir O. , Godø Olav R. , Skogen Morten D. , Torkelsen Terje 
Published: April 2009

Abstract
Johansen, G. O., Godø, O. R., Skogen, M. D., and Torkelsen, T. 2009. Using acoustic technology to improve the modelling of the transportation and distribution of juvenile gadoids in the Barents Sea. – ICES Journal of Marine Science, 66: 1048–1054. Transport of the juvenile stages of gadoids by oceanic currents in the Barents Sea is governed by interactions between the vertical positioning of the fish and the horizontal movement of the water masses. The resulting geographical distribution is important for growth and survival. There is need for observations at proper temporal and spatial scales to improve the representation of vertical distribution in models of the transport process. Stationary acoustic systems are suitable for this purpose. We use such a system to quantify the vertical dynamics of 0-group gadoids with reference to a conceptual model of the temporal variation. The vertical distribution from the conceptual model is applied within a Lagrangian, particle-tracking model. This approach performs better in predicting the geographic distribution of the 0-group during the first 10 months after hatching than a model with random, vertical distribution. The potential of stationary acoustic systems to provide high-quality vertical distributions that improve the predictive power of the transport model is demonstrated. Extensive sampling programmes based on the principles presented here can provide the observations needed to obtain more realistic recruitment–prediction models.
A New Leaf Spot Disease of Calotropis gigantean Caused by Alternaria alternata in Rajasthan, India
Authors: Sain Satish K. , Gour H. N. , Sharma P. , Chowdhry P. N. 
Published: April 2009

Madar (Calotropis gigantea) is a medicinally important wild shrub native to India. The seed floss is used for furniture stuffing and the bark for nets and twine. In early 2005, we observed a leaf spot epidemic of madar growing on wasteland sites near the Sikar district of Rajasthan, India. Koch's Postulates were completed. This is the first record of the disease from the Sikar district of the Rajasthan state of India. Accepted for publication 6 February 2009. Published 31 March 2009.
The Soybean Resistance Gene Rag1 Does Not Protect Against Soybean Cyst and Root-knot Nematodes
Authors: Studham Matthew , MacIntosh Gustavo C. , Avendaño Felicitas , Soh David , Tylka Gregory L. 
Published: April 2009

The only well-characterized gene controlling soybean aphid (SBA) resistance is Mi-1.2, a tomato gene that also confers resistance to root-knot nematodes (RKN). Based on similarities between Mi-1.2 and Rag1, which produces a strong antibiosis-type resistance, the authors hypothesized that Rag1 could also provide resistance to nematodes. They evaluated two soybean lines, one carrying the Rag1 gene, and one with no resistance gene, for susceptibility or resistance to soybean cyst nematode (SCN) and RKN. Accepted for publication 4 March 2009. Published 1 April 2009.
Control of Helicoverpa zea in Tomatoes with Chlorantraniliprole Applied Through Drip Chemigation
Authors: Kuhar Thomas P. , Walgenbach James F. , Doughty Hélène B. 
Published: April 2009

Chlorantraniliprole (=Rynaxypyr) is a novel anthranilic diamide insecticide that is of interest to vegetable growers because of its low mammalian toxicity and systemic properties. Field trials were conducted between 2006 and 2008 in North Carolina and Virginia to test the efficacy of chlorantraniliprole as a drip chemigation treatment on tomatoes. Drip chemigation of chlorantraniliprole at various rates and intervals significantly reduced the percentage of tomatoes damaged by tomato fruitworm (Helicoverpa zea) comparable to that typically achieved from multiple foliar applications of insecticides. The best control was achieved with two applications of chlorantraniliprole at 0.074 kg ai/ha, or a single application at 0.099 kg ai/ha. Residual ingestion bioassays showed that chlorantraniliprole was effectively taken up by the roots and was active in leaves up to 66 days after treatment (DAT), active in blossoms up to 22 DAT, but was not active in fruit. Drip chemigation of chlorantraniliprole may offer several advantages over foliar applications, including ease of application, reduced pesticide input into the environment, reduced worker exposure to pesticides, and reduced risk to beneficial arthropods. Accepted for publication 14 January 2010. Published 7 April 2010.
Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks
Authors: Vandepoele Klaas , Quimbaya Mauricio , Casneuf Tine , De Veylder Lieven , Van de Peer Yves 
Published: April 2009

Abstract
Analysis of gene expression data generated by high-throughput microarray transcript profiling experiments has demonstrated that genes with an overall similar expression pattern are often enriched for similar functions. This guilt-by-association principle can be applied to define modular gene programs, identify cis-regulatory elements, or predict gene functions for unknown genes based on their coexpression neighborhood. We evaluated the potential to use Gene Ontology (GO) enrichment of a gene's coexpression neighborhood as a tool to predict its function but found overall low sensitivity scores (13%–34%). This indicates that for many functional categories, coexpression alone performs poorly to infer known biological gene functions. However, integration of cis-regulatory elements shows that 46% of the gene coexpression neighborhoods are enriched for one or more motifs, providing a valuable complementary source to functionally annotate genes. Through the integration of coexpression data, GO annotations, and a set of known cis-regulatory elements combined with a novel set of evolutionarily conserved plant motifs, we could link many genes and motifs to specific biological functions. Application of our coexpression framework extended with cis-regulatory element analysis on transcriptome data from the cell cycle-related transcription factor OBP1 yielded several coexpressed modules associated with specific cis-regulatory elements. Moreover, our analysis strongly suggests a feed-forward regulatory interaction between OBP1 and the E2F pathway. The ATCOECIS resource (http://bioinformatics.psb.ugent.be/ATCOECIS/) makes it possible to query coexpression data and GO and cis-regulatory element annotations and to submit user-defined gene sets for motif analysis, providing an access point to unravel the regulatory code underlying transcriptional control in Arabidopsis (Arabidopsis thaliana).
Ethyl glucuronide in hair. A sensitive and specific marker of chronic heavy drinking
Authors: Morini Luca , Politi Lucia , Polettini Aldo 
Published: April 2009

ABSTRACTAims  This study aims to define a cut‐off concentration for ethyl glucuronide in hair to determine if there was a history of heavy drinking.Settings  Pavia, Italy.Participants  We analysed hair samples from 98 volunteers among teetotallers, social drinkers and heavy drinkers, whose ethanol daily intake (EDI) was estimated by means of a written questionnaire.Measurements  Ethyl glucuronide hair concentration (HEtG) was measured by liquid chromatography‐tandem mass spectrometry (lower limit of quantification: 3 pg/mg) using a fully validated method.Findings  The HEtG level providing the best compromise between sensitivity (0.92) and specificity (0.96) at detecting an EDI of 60 g or higher during the last 3 months was 27 pg/mg. None of the factors examined among those known to affect ethanol metabolism and/or the diagnostic power of other markers of ethanol use or hair analyses, including age, gender, body mass index, tobacco smoke, prevalent beverage, hair colour, cosmetic treatments and hygienic habits was found to influence marker performance significantly. However, the slight differences in HEtG performance observed for some factors (e.g. body mass index, smoke and hair treatments) require further studies on larger groups of individuals in order to assess their influence more precisely.Conclusions  Our results confirm further that HEtG is a sensitive and specific marker of chronic heavy drinking.
Association of tobacco dependence and quit attempt duration with Rasch‐modeled withdrawal sensitivity using retrospective measures
Authors: Javitz Harold S. , Brigham Janet , Lessov‐Schlaggar Christina N. , Krasnow Ruth E. , Swan Gary E. 
Published: April 2009

ABSTRACTAim  To examine whether Rasch modeling would yield a unidimensional withdrawal sensitivity measure correlating with factors associated with successful smoking cessation.Design  The psychometric Rasch modeling approach was applied to estimate an underlying latent construct (withdrawal sensitivity) in retrospective responses from 1644 smokers who reported quitting for 3 or more months at least once.Setting  Web‐based, passcode‐controlled self‐administered computerized questionnaire.Participants  Randomly selected convenience sample of 1644 adult members of an e‐mail invitation‐only web panel drawn from consumer databases.Measurements  Lifetime Tobacco Use Questionnaire, assessing tobacco use across the life‐span, including demographics and respondent ratings of the severity of withdrawal symptoms experienced in respondents' first and most recent quit attempts lasting 3 or more months.Findings  Rasch‐modeled withdrawal sensitivity was generally unidimensional and was associated with longer periods of smoking cessation. One latent variable accounted for 74% of the variability in symptom scores. Rasch modeling with a single latent factor fitted withdrawal symptoms well, except for increased appetite, for which the fit was marginal. Demographic variables of education, gender and ethnicity were not related to changes in sensitivity. Correlates of greater withdrawal sensitivity in cessation attempts of at least 3 months included younger age at first quit attempt and indicators of tobacco dependence.Conclusion  The relationship between tobacco dependence symptoms and Rasch‐model withdrawal sensitivity defines further the relationship between sensitivity and dependence. The findings demonstrate the utility of modeling to create an individual‐specific sensitivity measure as a tool for exploring the relationships among sensitivity, dependence and cessation.
Parents who quit smoking and their adult children's smoking cessation: a 20‐year follow‐up study
Authors: Bricker Jonathan B. , Otten Roy , Liu Jingmin L. , Peterson, Jr Arthur V. 
Published: April 2009

ABSTRACTAims  Extending our earlier findings from a longitudinal cohort study, this study examines parents' early and late smoking cessation as predictors of their young adult children's smoking cessation.Design  Parents' early smoking cessation status was assessed when their children were aged 8 years; parents' late smoking cessation was assessed when their children were aged 17 years. Young adult children's smoking cessation, of at least 6 months duration, was assessed at age 28 years.Setting  Forty Washington State school districts.Participants and measurements  Participants were 991 at least weekly smokers at age 17 whose parents were ever regular smokers and who also reported their smoking status at age 28. Questionnaire data were gathered on parents and their children (49% female and 91% Caucasian) in a longitudinal cohort (84% retention).Findings  Among children who smoked daily at age 17, parents' quitting early (i.e. by the time their children were aged 8) was associated with a 1.7 times higher odds of these children quitting by age 28 compared to those whose parents did not quit [odds ratio (OR) 1.70; 95% confidence interval (CI) 1.23, 2.36]. Results were similar among children who smoked weekly at age 17 (OR 1.91; 95% CI 1.41, 2.58). There was a similar, but non‐significant, pattern of results among those whose parents quit late.Conclusions  Supporting our earlier findings, results suggest that parents' early smoking cessation has a long‐term influence on their adult children's smoking cessation. Parents who smoke should be encouraged to quit when their children are young.
A radiation hybrid comparative map of ovine chromosome 1 aligned to the virtual sheep genome
Authors: Wu C. H. , Jin W. , Nomura K. , Goldammer T. , Hadfield T. , Dalrymple B. P. , McWilliam S. , Maddox J. F. , Cockett N. E. 
Published: April 2009

Summary Ovis aries chromosome one (OAR1) is the largest submetacentric chromosome in the sheep genome and is homologous to regions on human chromosomes 1, 2, 3 and 21. Using the USUoRH5000 ovine whole‐genome radiation hybrid (RH) panel, we have constructed a RH map of OAR1 comprising 102 framework and 75 placed/binned markers across five linkage groups spanning 3759.43 cR5000, with an average marker density of 21.2 cR5000/marker. The alignment of our OAR1 RH map shows good concordance with the recently developed virtual sheep genome, with fewer than 1.86% discrepancies. A comparative map of OAR1 was constructed by examining the location of RH‐mapped orthologues in sheep within the genomes of cow, human, horse and dog. Analysis of the comparative map indicates that conserved syntenies within the five ovine RH linkage groups underwent internal chromosomal rearrangements which, in general, reflect the evolutionary distances between sheep and each of these four species. The ovine RH map presented here integrates all available mapping data and includes new genomic information for ovine chromosome 1.
Genetic diversity of Hungarian indigenous chicken breeds based on microsatellite markers
Authors: Bodzsar N. , Eding H. , Revay T. , Hidas A. , Weigend S. 
Published: April 2009

SummarySix local chicken breeds are registered in Hungary and are regarded as Hungarian national treasures: Hungarian White, Yellow and Speckled, and Transylvanian Naked Neck White, Black and Speckled. Three Hungarian academic institutes have maintained these genetic resources for more than 30 years. The Hungarian Yellow, the Hungarian Speckled and the Transylvanian Naked Neck Speckled breeds were kept as duplicates in two separate subpopulations since time of formation of conservation flocks at different institutes. In this study, we investigated genetic diversity of these nine Hungarian chicken populations using 29 microsatellite markers. We assessed degree of polymorphism and relationships within and between Hungarian breeds on the basis of molecular markers, and compared the Hungarian chicken populations with commercial lines and European local breeds. In total, 168 alleles were observed in the nine Hungarian populations. The FST estimate indicated that about 22% of the total variation originated from variation between the Hungarian breeds. Clustering using structure software showed clear separation between the Hungarian populations. The most frequent solutions were found at K = 5 and K = 6, respectively, classifying the Transylvanian Naked Neck breeds as a separate group of populations. To identify genetic resources unique to Hungary, marker estimated kinships were estimated and a safe set analysis was performed. We show that the contribution of all Hungarian breeds together to the total diversity of a given set of populations was lower when added to the commercial lines than when added to the European set of breeds.
Whole genome scan to detect quantitative trait loci for bovine milk protein composition
Authors: Schopen G. C. B. , Koks P. D. , Van Arendonk J. A. M. , Bovenhuis H. , Visker M. H. P. W. 
Published: April 2009

SummaryThe objective of this study was to perform a whole genome scan to detect quantitative trait loci (QTL) for milk protein composition in 849 Holstein–Friesian cows originating from seven sires. One morning milk sample was analysed for the major milk proteins using capillary zone electrophoresis. A genetic map was constructed with 1341 single nucleotide polymorphisms, covering 2829 centimorgans (cM) and 95% of the cattle genome. The chromosomal regions most significantly related to milk protein composition (Pgenome < 0.05) were found on Bos taurus autosomes (BTA) 6, 11 and 14. The QTL on BTA6 was found at about 80 cM, and affected αS1‐casein, αS2‐casein, β‐casein and κ‐casein. The QTL on BTA11 was found at 124 cM, and affected β‐lactoglobulin, and the QTL on BTA14 was found at 0 cM, and affected protein percentage. The proportion of phenotypic variance explained by the QTL was 3.6% for β‐casein and 7.9% for κ‐casein on BTA6, 28.3% for β‐lactoglobulin on BTA11, and 8.6% for protein percentage on BTA14. The QTL affecting αS2‐casein on BTA6 and 17 showed a significant interaction. We investigated the extent to which the detected QTL affecting milk protein composition could be explained by known polymorphisms in β‐casein, κ‐casein, β‐lactoglobulin and DGAT1 genes. Correction for these polymorphisms decreased the proportion of phenotypic variance explained by the QTL previously found on BTA6, 11 and 14. Thus, several significant QTL affecting milk protein composition were found, of which some QTL could partially be explained by polymorphisms in milk protein genes.
Epithelial stem cell‐related alterations in Trichinella spiralis‐infected small intestine
Authors: Walsh R. , Seth R. , Behnke J. , Potten C. S. , Mahida Y. R. 
Published: April 2009

AbstractObjectives:  Infection of mice with the parasite Trichinella spiralis leads to small intestinal inflammation, characterized by changes in mucosal architecture and subpopulations of epithelial cells. This model has been used to explore changes in the epithelial proliferative cell population and expression of transforming growth factor‐beta (TGF‐β).Materials and methods:  Histochemical and immunohistochemical studies were undertaken in duodenal samples. Location and number of Ki‐67‐positive cells were assessed using Score and Wincrypts program. Changes in mRNA transcripts were studied by real‐time RT‐PCR.Results:  T. spiralis infection induced an increase in total number of proliferative (Ki‐67‐positive) cells per half crypt on day 2 post‐infection. Transcription of Math1, a transcription factor required for secretory cell differentiation in the intestine, was up‐regulated on days 6–18 post‐infection. At these time points, numbers of Paneth cells at the crypt base were also increased and the epithelial proliferative zone was shifted up the crypt‐villus axis. Transcription of TGF‐β isoforms within the small intestine was up‐regulated on days 6 and 12 post‐infection, but anti‐TGF‐β antibody treatment had no effect on T. spiralis‐induced changes in mucosal architecture or increase in Paneth/intermediate cells.Conclusions:  T. spiralis infection promotes an initial increase in small intestinal epithelial proliferation and subsequent cell differentiation along the secretory cell lineage. The resulting increase in numbers of Paneth cells at the crypt base causes the proliferative zone to move up the crypt‐villus axis. Further studies are required to determine the significance of an increase in the expression of TGF‐β transcripts.
Low‐grade inflammation can partly explain the association between the metabolic syndrome and either coronary artery disease or severity of peripheral arterial disease: the CODAM study
Authors: Jacobs M. , Van Greevenbroek M. M. J. , Van Der Kallen C. J. H. , Ferreira I. , Blaak E. E. , Feskens E. J. M. , Jansen E. H. J. M. , Schalkwijk C. G. , Stehouwer C. D. A. 
Published: April 2009

AbstractBackground  Low‐grade inflammation has been hypothesized to underlie the coronary artery disease (CAD) risk associated with the metabolic syndrome, but the evidence is not conclusive. For peripheral arterial disease (PAD; as measured by the ankle‐arm index), this association has not been studied before. The aim was to study whether the association between the metabolic syndrome and CAD or the severity of PAD can be explained by low‐grade inflammation.Methods  The Cohort study Diabetes and Atherosclerosis Maastricht population includes 574 subjects, with an increased risk of type 2 diabetes, of whom 560 were included in the analyses (343 males; age: 59·5 ± 7·0 years). The inflammation markers that were measured were C‐reactive protein, interleukin 6, soluble vascular cell adhesion molecule‐1, soluble intercellular adhesion molecule‐1 and serum amyloid A. All analyses were adjusted for age, sex and smoking.Results  Logistic regression showed that the metabolic syndrome was significantly associated with CAD [odds ratio (OR) = 1·86, 95% CI: 1·21; 2·84, P = 0·004]. Further adjustment for inflammatory status, as captured in a combination of the inflammation markers (using an averaged Z‐score), resulted in significant associations of both the metabolic syndrome and inflammatory status with CAD [ORmetabolic syndrome (95% CI) = 1·58 (1·01; 2·46), P = 0·044; ORinflammation (95% CI) = 1·59 (1·14; 2·21), P = 0·007]. Linear regression analysis showed similar results for the ankle‐arm index.Conclusions  The association between the metabolic syndrome, on the one hand, and prevalence of CAD or the severity of PAD, on the other, can be partly but not completely, 26% and 29% respectively, explained by low‐grade inflammation.