bluuebunny/crossref_metadata_2025_split huggingface dataset:
Health promoting contacts as encountered by individuals with head and neck cancer
Authors: Björklund Margereth , Sarvimäki Anneli , Berg Agneta 
Published: August 2009

Aim.  To describe the characteristics of health promoting contacts with health professionals as encountered by individuals with head and neck cancer.Background.  Head and neck cancer has a profound and chronic impact on the individual’s everyday life, e.g. physical problems that hinder speaking, breathing, eating and drinking. Furthermore, fear and uncertainty can lead to long‐term psychological and psychosocial problems. The National Institute of Public Health in Sweden advocates that all care contacts should improve the quality of the individual’s health.Design.  A qualitative descriptive and explorative design was used. Eight participants were interviewed in the year 2005 and a qualitative thematic content analysis of the data was performed.Findings.  Health promoting contacts were defined as contacts where health care professionals contribute positively to the well‐being of individual patients. Characteristics include being available, engaged, respectful and validating. Three themes were identified: being believed in one’s illness story; having a working relationship with health professionals and receiving individualised, tailored care.Conclusions.  Health promoting contacts were experienced mainly during the treatment phase, when patients had daily contact with specific, qualified health professionals. Although the interview questions focused on health promoting contacts, nearly half of the contacts were experienced as not health promoting. Feelings of abandonment were particularly manifested before and after treatment. The starting point for achieving health promoting contact lies in understanding the patient’s lifeworld in relation to health, illness and suffering and focusing on the individual’s personal strengths and health resources.Relevance to clinical practice.  The findings highlighted the importance of ensuring that patient interests and concerns are core considerations in health care. The participants viewed continuing individualised, tailored care and access to ear, nose and throat healthcare professionals as highly important.
Isolation and characterization of 64 novel microsatellite markers from a fosmid library of female half‐smooth tongue sole (Cynoglossus semilaevis)
Authors: WANG XUBO , ZHANG QUANQI , SUN XIAOHUA , YIN GUOLIANG , QI JIE , WANG ZHIGANG , WANG XINGLIAN 
Published: August 2009

AbstractMicrosatellite markers were developed from a fosmid library of female half‐smooth tongue sole, Cynoglossus semilaevis. Three hundred eighty‐four clones were randomly selected to sequence (double strand reading), and 168 sequences in 143 clones were found to contain microsatellites. Of the 101 primer pairs designed, 64 gave polymorphic polymerase chain reaction products. Based on characterization with 36 individuals, the number of alleles ranged from two to nine. The values of observed and expected heterozygosities varied from 0.06 to 1.00 and from 0.05 to 0.94, respectively. These markers have the potential as tools for population structure evaluation, ecological analyses and linkage map construction.
concatenator: sequence data matrices handling made easy
Authors: PINA‐MARTINS F. , PAULO O. S. 
Published: August 2009

Abstractconcatenator is a simple and user‐friendly software that implements two very useful functions for phylogenetics data analysis. It concatenates NEXUS files of several fragments in a single NEXUS file ready to be used in phylogenetics software, such as paup and mrbayes and it converts FASTA sequence data files to NEXUS and vice‐versa. Additionally, concatenated files can be prepared for partition tests in paup. It is freely available in http://cobig2.fc.ul.pt.
Development of microsatellite markers in the St Lucia anole, Anolis luciae
Authors: JOHANSSON HELENA , SURGET‐GROBA YANN , GOW JENNIFER L. , THORPE ROGER S. 
Published: August 2009

Abstract Anolis lizards are important models in studies of ecology and evolution. Here we describe 13 polymorphic microsatellites for use in population screening in the St Lucia anole, Anolis luciae, that can be used as a natural replicate to Anolis roquet on Martinique to study processes involved in population differentiation and speciation. Genotyping of 32 individuals using M13 tails and FAM‐labelled universal M13 primers showed that all loci were polymorphic with high genetic diversity, averaging at 16.8 alleles per locus. Genotypic frequencies conformed to Hardy–Weinberg expectations, and there were no instances of linkage disequilibrium between loci.
Isolation and characterization of microsatellite markers in the striped hamster (Cricetulus barabensis)
Authors: XU LAIXIANG , SONG MINGJING , ZHANG FEIFEI , XU YANCHAO , GAO QIAN , LI CHUANHAI , LU YUNQI 
Published: August 2009

AbstractA total of 14 polymorphic microsatellite markers were isolated and characterized from the striped hamster, Cricetulus barabensis, a widespread rodent pest in northern China. Two to six alleles per locus were detected in 90 individuals from three locations in Shandong Province, China. The observed and expected heterozygosities ranged from 0.21 to 0.78 and from 0.30 to 0.80, respectively. These microsatellite markers provide new tools for investigating the population structure of this species.
Computation vs. cloning: evaluation of two methods for haplotype determination
Authors: HARRIGAN RYAN J. , MAZZA MAUREEN E. , SORENSON MICHAEL D. 
Published: August 2009

AbstractNuclear sequence data, often from multiple loci, are increasingly being employed in analyses of population structure and history, yet there has been relatively little evaluation of methods for accurately and efficiently separating the alleles or haplotypes in heterozygous individuals. We compared the performance of a computational method of haplotype reconstruction and standard cloning methods using a highly variable intron (ornithine decarboxylase, intron 6) in three closely related species of dabbling ducks (genus Anas). Cloned sequences from 32 individuals were compared to results obtained from phase 2.1.1 . phase correctly identified haplotypes in 28 of 30 heterozygous individuals when the underlying model assumed no recombination. Haplotypes of the remaining two individuals were also inferred correctly except for unique polymorphisms, the phase of which was appropriately indicated as uncertain (phase probability = 0.5). For a larger set of 232 individuals, results were essentially identical regardless of the recombination model used and haplotypes for all 30 of the tested heterozygotes were correctly inferred, with the exception of uncertain phase for unique polymorphisms in one individual. In contrast, initial sequences of one clone per sample yielded accurate haplotype determination in only 26 of 30 individuals; polymerase chain reaction (PCR)/cloning errors resulting from misincorporation of individual nucleotides could be recognized and avoided by comparison to direct sequences, but errors due to PCR recombination resulted in incorrect haplotype reconstruction in four individuals. The accuracy of haplotypes reconstructed by phase, even when dealing with a relatively small number of samples and numerous variable sites, suggests broad utility of computational approaches for reducing the cost and improving the efficiency of data collection from nuclear sequence loci.
Development of microsatellite markers for the wood cricket, Nemobius sylvestris (Orthoptera: Gryllidae)
Authors: VANHALA TYTTI , COTTRELL JOAN 
Published: August 2009

AbstractThirty‐four novel microsatellite markers developed for wood cricket (Nemobius sylvestris) were tested and optimized. Twenty‐five microsatellite loci were polymorphic, exhibiting between two and nine alleles. Observed heterozygosities ranged from 0.038 to 0.925. The microsatellites were also tested in a species belonging to another genus of the Gryllidae family (Gryllus bimaculatus). Two markers produced clear banding patterns with the expected product size. These markers will be used to study the effects of forest fragmentation on genetic connectivity using wood cricket as a model species.
Development of simple sequence repeat markers for the soybean rust fungus, Phakopsora pachyrhizi
Authors: ANDERSON SHARON J. , STONE CHRISTINE L. , POSADA‐BUITRAGO MARTHA LUCIA , BOORE JEFFREY L. , NEELAM BEENA A. , STEPHENS ROBERT M. , LUSTER DOUGLAS G. , FREDERICK REID D. , PEDLEY KERRY F. 
Published: August 2009

AbstractTwenty‐four simple sequence repeat markers were developed for Phakopsora pachyrhizi, a fungal pathogen of soybean (Glycine max) and other legumes. All 24 of the loci were evaluated on 28 isolates of P. pachyrhizi. Twenty‐one loci were polymorphic, with allelic diversity ranging from two to eight alleles, and null alleles were observed for eight of the 24 loci. A preliminary screen with the closely related species, P. meibomiae, indicated that these primer pairs are specific to P. pachyrhizi.
Microsatellite loci for two East African tree species, Leptonychia usambarensis (Sterculiaceae) and Sorindeia madagascariensis (Anacardiaceae)
Authors: CORDEIRO N. J. , FELDHEIM K. A. , IKEJIMBA E. , NDANGALASI H. J. 
Published: August 2009

AbstractWe isolated 20 trinucleotide microsatellites from two African tree species: Sorindeia madagascariensis (nine microsatellites) and Leptonychia usambarensis (11 microsatellites). Number of alleles ranged from three to seven in Sorindeia and two to 10 in Leptonychia. Observed heterozygosity ranged from 0.025 to 0.829 for Sorindeia and from 0.226 to 0.933 for Leptonychia. Two loci from each species departed from Hardy–Weinberg equilibrium. These microsatellite markers will be used to study how forest fragmentation affects pollination and seed dispersal processes of these tree species.
Development of simple sequence repeat markers from expressed sequence tags of the black tiger shrimp (Penaeus monodon)
Authors: WHANKAEW SUKHUMAN , TANGPHATSORNRUANG SITHICHOKE , TRIWITAYAKORN KANOKPORN 
Published: August 2009

AbstractIn this study, we describe the development of expressed sequence tag–simple sequence repeat markers from expressed sequence tags of the black tiger shrimp (Penaeus monodon) deposited in public sequence databases. A total of 46 primer pairs were designed and screened on 26 individuals of P. monodon from a natural population. Of these, 16 primer pairs showed polymorphic profiles with between two and five alleles per locus. The average unbiased and direct count heterozygosities were 0.4662 and 0.3516, respectively. Cross‐amplification was tested with five individuals of Penaeus vannamei and polymorphic products were detected at five loci.
Species identification of aphids (Insecta: Hemiptera: Aphididae) through DNA barcodes
Authors: FOOTTIT R. G. , MAW H. E. L. , VON DOHLEN C. D. , HEBERT P. D. N. 
Published: August 2009

AbstractA 658‐bp fragment of mitochondrial DNA from the 5′ region of the mitochondrial cytochrome c oxidase 1 (COI) gene has been adopted as the standard DNA barcode region for animal life. In this study, we test its effectiveness in the discrimination of over 300 species of aphids from more than 130 genera. Most (96%) species were well differentiated, and sequence variation within species was low, averaging just 0.2%. Despite the complex life cycles and parthenogenetic reproduction of aphids, DNA barcodes are an effective tool for identification.
Eleven polymorphic microsatellite markers forOedaleus decorus(Orthoptera, Acrididae), an endangered grasshopper in Central Europe
Authors: BERTHIER K. , LOISEAU A. , STREIFF R. , ARLETTAZ R. 
Published: August 2009

AbstractWe isolated and characterized 11 microsatellite loci in the grasshopperOedaleus decorus(Orthoptera: Acrididae), an endangered species in Central Europe. Polymorphism was studied from two populations, one out of two populations known from Switzerland (n = 20 individuals) and one site from south of France (n = 20). The number of alleles and the expected heterozygosity ranged from five to 12 and from 0.559 to 0.898, respectively, in the Swiss population, and from 14 to 23 and from 0.895 to 0.974, respectively, in the French population. These microsatellite markers are suitable for further conservation genetic studies ofO. decorus.
Non‐invasive genetic identification of small mammal species using real‐time polymerase chain reaction
Authors: MORAN S. , TURNER P. D. , O’REILLY C. 
Published: August 2009

AbstractDNA identification of non‐invasive samples is a potentially useful tool for monitoring small mammal species. Here we describe a novel method for identifying five small mammal species: wood mouse, bank vole, common shrew, pygmy shrew and water shrew. Species‐specific real‐time polymerase chain reaction primers were designed to amplify fragments of the mitochondrial cytochrome b gene from hair and scat samples. We also amplified nuclear DNA from scats, demonstrating their potential as a source of DNA for population genetic studies.
Development of 11 polymorphic microsatellite loci in the small abalone (Haliotis diversicolor Reeve)
Authors: REN PENG , WANG ZHIYONG , YAO CUILUAN , LIU YING , KE CAIHUAN 
Published: August 2009

AbstractEleven polymorphic microsatellite loci for Haliotis diversicolor were isolated and characterized from (CT)n‐ and (AC)n‐enriched library. They were tested in 24 individuals from a natural population. All of them were polymorphic, with the number of alleles varying between three and 10. The observed heterozygosities and expected heterozygosities ranged from 0.083 to 0.913 and from 0.159 to 0.856, respectively. The 11 isolated microsatellite loci, except SA‐JMU6 and SA‐JMU12, followed Hardy–Weinberg expectations. Seven sets of primers also amplify in closely related species, H. ovina and H. asinine. These 11 polymorphic microsatellites will be useful for analysing the population structure and genetic diversity in H. diversicolor.
DNA barcoding discriminates echinoderm species
Authors: WARD ROBERT D. , HOLMES BRONWYN H. , O’HARA TIM D. 
Published: August 2009

AbstractDNA barcode sequences (a 657‐bp segment of the mtDNA cytochrome oxidase I gene, COI) were collected from 191 species (503 specimens) of Echinodermata. All five classes were represented: Ophiuroidea, Asteroidea, Echinoidea, Holothuroidea and Crinoidea. About 30% of sequences were collected specifically for this study, the remainder came from GenBank. Fifty‐one species were represented by multiple samples, with a mean intraspecific divergence of 0.62%. Several possible instances of cryptic speciation were noted. Thirty‐two genera were represented by multiple species, with a mean congeneric divergence of 15.33%. One hundred and eighty‐seven of the 191 species (97.9%) could be distinguished by their COI barcodes. Those that could not were from the echinoid genusAmblypneustes. Neighbour‐joining trees of COI sequences generally showed low bootstrap support for anything other than shallow splits, although with very rare exceptions, members of the same class clustered together. Two ophiuran species, in both nucleotide and amino acid neighbour‐joining trees, grouped loosely as sister taxa to Crinoidea rather than Ophiuroidea; sequences of these two species appear to have evolved very quickly. Results suggest that DNA barcoding is likely to be an effective, accurate and useful method of species diagnosis for all five classes of Echinodermata.
Characterization of polymorphic microsatellite DNA markers in Banksia nivea, formerly Dryandra nivea
Authors: MILLAR M. A. , BYRNE M. 
Published: August 2009

AbstractA genomic library was constructed and 10 novel polymorphic microsatellite markers were developed for Banksia nivea subsp. uliginosa, a woody shrub endemic to the southwest of Western Australia. Polymorphism was investigated for these markers in 30 individuals from one population located in restricted habitat at the base of the Whicher Range east of Busselton. Expected heterozygosity ranged from 0.124 to 0.898 and averaged 0.570. Observed heterozygosity ranged from 0.133 to 0.933 and averaged 0.544. The number of alleles per locus ranged from 2.0 to 16.0 and averaged 7.3. These markers also produced amplification products in three other Banksia species and will be used to assay genetic diversity in these species.
Development and characterization of novel, polymorphic microsatellite markers for oat crown rust, Puccinia coronata
Authors: DAMBROSKI HATTIE R , CARSON MARTIN L 
Published: August 2009

AbstractWe report the development of 37 novel and polymorphic microsatellite markers for oat crown rust, Puccinia coronata f.sp. avenae. The allelic diversity ranged from two to 16 alleles per locus. Observed heterozygosity ranged from 0.000 to 0.971, and expected heterozygosity from 0.057 to 0.848. Thirteen of the loci were not in Hardy‐Weinberg equilibrium, due to either the presence of null alleles, small sample size, or the effects of population subdivision (Wahlund's effect). All 37 primer pairs were tested with P. graminis and P. triticina showing that they are specific to P. coronata.
Isolation and characterization of microsatellite marker loci in the greylag goose (Anser anser)
Authors: WEIß B. M. , POGGEMANN K. , OLEK K. , FOERSTER K. , HIRSCHENHAUSER K. 
Published: August 2009

AbstractTen novel polymorphic microsatellite loci were isolated and characterized from the greylag goose, Anser anser, a long‐term monogamous and biparental bird. Additionally, five new primers pairs were designed based on previously published microsatellite locus sequences from closely related species. Multiplex polymerase chain reactions conditions were optimized for all 15 primer pairs. The number of alleles ranged from two to 12 per locus with an observed heterozygosity ranging from 0.07 to 0.85. This marker set will be used to determine rates and origins of extra‐pair and parasitic young in a population of individually banded greylag geese with known life histories.
Improving the reliability of molecular sexing of birds using a W‐specific marker
Authors: SHIZUKA DAIZABURO , LYON BRUCE E. 
Published: August 2009

AbstractMolecular techniques for identifying sex of birds utilize length differences between CHD‐Z and CHD‐W introns, but in some cases these methods can lead to sexing errors. Here we show that an additional W‐specific primer can be used in conjunction with a pre‐existing sexing primer pair to dramatically improve the reliability of molecular sexing methods. We illustrate the approach with American coots (Fulica americana), a species with CHD‐Z polymorphism that could not be accurately sexed using traditional methods. We developed a reverse primer GWR2 designed to sit within the intron of the W chromosome and amplify a distinctively small DNA fragment that serves as a W‐specific marker. Analysis of known‐sex individuals indicates that this W‐specific primer provides an efficient and reliable protocol to identify the sex of F. americana. The development of such sex‐specific primers will likely increase the reliability of molecular sexing methods in other birds as well. Comparisons between CHD‐Z alleles of coots and common moorhens (Gallinula chloropus) revealed that CHD‐Z polymorphism evolved separately in these two closely related species. We discuss the implications of repeated evolution of CHD‐Z polymorphisms among birds.
Eight variable microsatellite loci for a Neotropical tree, Jacaranda copaia (Aubl.) D.Don (Bignoniaceae)
Authors: VINSON C. C. , SAMPAIO I. , CIAMPI A. Y 
Published: August 2009

AbstractThe Dendrogene Project (Genetic Conservation within Managed Forests in Amazonia) aims to understand the genetic and ecological processes that underpin tree species survival and in particular their response to forest management regimes. As part of the project, we developed eight microsatellite markers for Jacaranda copaia to be used for genetic structure, gene flow and reproductive biology studies. Polymorphism was evaluated using 96 adult trees from the Tapajos National Forest in the Eastern Brazilian Amazon. An average of 22 alleles per locus were detected, with expected heterozygosity ranging from 0.731 to 0.94.
The influence of family groups on inferences made with the program Structure
Authors: ANDERSON E. C. , DUNHAM K. K. 
Published: August 2009

AbstractUnsupervised clustering algorithms, like the program Structure, are increasingly used to infer the presence of population structure from a sample of genotyped individuals. We evaluate the extent to which the presence of related individuals can lead such algorithms to the false inference that there is population structure. First, we demonstrate this problem using a real data set from a rainbow trout (Oncorhynchus mykiss) population. Then we perform an extensive series of simulations involving the program Structure. Our simulations encompass both a simple scenario with fixed numbers of full‐ and half‐siblings in the sample, and a more complicated scenario in which we investigate 360 combinations of population divergence, fraction of population sampled, variance in family size, mating system and number of loci. We find that the inclusion of family members in a sample may produce very strong evidence of population structure, even when population structure is absent. This problem becomes more pronounced when more loci are genotyped, and it is particularly likely in studies of monogamous species, especially if variance in family size is high and a large fraction of a small population has been sampled. Researchers working in such situations should test observed clusters for the presence of family members to distinguish family‐induced structure from real population structure. Additionally, this work shows that Structure's ability to estimate the number of subpopulations may be influenced by a number of factors, and therefore should be interpreted guardedly.
STORM: software for testing hypotheses of relatedness and mating patterns
Authors: FRASIER TIMOTHY R. 
Published: August 2009

AbstractStorm is a software package that allows users to test a variety of hypotheses regarding patterns of relatedness and patterns of mate choice and/or mate compatibility within a population. These functions are based on four main calculations that can be conducted either independently or in the hypothesis‐testing framework: internal relatedness; homozygosity by loci; pairwise relatedness; and a new metric called allele inheritance, which calculates the proportion of loci at which an offspring inherits a paternal allele different from that inherited from its mother. STORM allows users to test four hypotheses based on these calculations and Monte Carlo simulations: (i) are individuals within observed associations or groupings more/less related than expected; (ii) do observed offspring have more/less genetic variability (based on internal relatedness or homozygosity by loci) than expected from the gene pool; (iii) are observed mating pairs more/less related than expected if mating is random with respect to relatedness; and (iv) do observed offspring inherit paternal alleles different from those inherited from the mother more/less often than expected based on Mendelian inheritance.