bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome sequence of dwarf birch (Betula nana) and cross‐species RAD markers
Authors: Wang Nian , Thomson Marian , Bodles William J. A. , Crawford Robert M. M. , Hunt Harriet V. , Featherstone Alan Watson , Pellicer Jaume , Buggs Richard J. A. 
Published: November 2012

AbstractNew sequencing technologies allow development of genome‐wide markers for any genus of ecological interest, including plant genera such as Betula (birch) that have previously proved difficult to study due to widespread polyploidy and hybridization. We present a de novo reference genome sequence assembly, from 66× short read coverage, of Betula nana (dwarf birch) – a diploid that is the keystone woody species of subarctic scrub communities but of conservation concern in Britain. We also present 100 bp PstI RAD markers for B. nana and closely related Betula tree species. Assembly of RAD markers in 15 individuals by alignment to the reference B. nana genome yielded 44–86k RAD loci per individual, whereas de novo RAD assembly yielded 64–121k loci per individual. Of the loci assembled by the de novo method, 3k homologous loci were found in all 15 individuals studied, and 35k in 10 or more individuals. Matching of RAD loci to RAD locus catalogues from the B. nana individual used for the reference genome showed similar numbers of matches from both methods of RAD locus assembly but indicated that the de novo RAD assembly method may overassemble some paralogous loci. In 12 individuals hetero‐specific to B. nana 37–47k RAD loci matched a catalogue of RAD loci from the B. nana individual used for the reference genome, whereas 44–60k RAD loci aligned to the B. nana reference genome itself. We present a preliminary study of allele sharing among species, demonstrating the utility of the data for introgression studies and for the identification of species‐specific alleles.
‘Transient’ genetic suppression facilitates generation of hexose transporter null mutants in Leishmania mexicana
Authors: Feng Xiuhong , Rodriguez‐Contreras Dayana , Polley Tamsen , Lye Lon‐Fye , Scott David , Burchmore Richard J.S. , Beverley Stephen M. , Landfear Scott M. 
Published: November 2012

SummaryThe genome of Leishmania mexicana encompasses a cluster of three glucose transporter genes designated LmxGT1, LmxGT2 and LmxGT3. Functional and genetic studies of a cluster null mutant (Δlmxgt1‐3) have dissected the roles of these proteins in Leishmania metabolism and virulence. However, null mutants were recovered at very low frequency, and comparative genome hybridizations revealed that Δlmxgt1‐3 mutants contained a linear extrachromosomal 40 kb amplification of a region on chromosome 29 not amplified in wild type parasites. These data suggested a model where this 29‐40k amplicon encoded a second site suppressor contributing to parasite survival in the absence of GT1‐3 function. To test this, we quantified the frequency of recovery of knockouts in the presence of individual overexpressed open reading frames covering the 29‐40k amplicon. The data mapped the suppressor activity to PIFTC3, encoding a component of the intraflagellar transport pathway. We discuss possible models by which PIFTC3 might act to facilitate loss of GTs specifically. Surprisingly, by plasmid segregation we showed that continued PIFTC3 overexpression was not required for Δlmxgt1‐3 viability. These studies provide the first evidence that genetic suppression can occur by providing critical biological functions transiently. This novel form of genetic suppression may extend to other genes, pathways and organisms.
The response regulator SypE controls biofilm formation and colonization through phosphorylation of the syp‐encoded regulator SypA in Vibrio fischeri
Authors: Morris Andrew R. , Visick Karen L. 
Published: November 2012

SummaryBacteria utilize multiple regulatory systems to modulate gene expression in response to environmental changes, including two‐component signalling systems and partner‐switching networks. We recently identified a novel regulatory protein, SypE, that combines features of both signalling systems. SypE contains a central response regulator receiver domain flanked by putative kinase and phosphatase effector domains with similarity to partner‐switching proteins. SypE was previously shown to exert dual control over biofilm formation through the opposing activities of its terminal effector domains. Here, we demonstrate that SypE controls biofilms in Vibrio fischeri by regulating the activity of SypA, a STAS (sulphate transporter and anti‐sigma antagonist) domain protein. Using biochemical and genetic approaches, we determined that SypE both phosphorylates and dephosphorylates SypA, and that phosphorylation inhibits SypA's activity. Furthermore, we found that biofilm formation and symbiotic colonization required active, unphosphorylated SypA, and thus SypA phosphorylation corresponded with a loss of biofilms and impaired host colonization. Finally, expression of a non‐phosphorylatable mutant of SypA suppressed both the biofilm and symbiosis defects of a constitutively inhibitory SypE mutant strain. This study demonstrates that regulation of SypA activity by SypE is a critical mechanism by which V. fischeri controls biofilm development and symbiotic colonization.
Humpback whale song hierarchical structure: Historical context and discussion of current classification issues
Authors: Cholewiak Danielle M. , Sousa‐Lima Renata S. , Cerchio Salvatore 
Published: November 2012

AbstractConsistent and well‐defined criteria for the classification and measurement of humpback whale song features are essential for robust comparisons between investigators. Song structure terminology has been well‐established and used by many authors, though at times inconsistently. This review discusses the development of the nomenclature describing humpback song and explores the potential significance of the often‐overlooked variation in song patterns. Within the hierarchical definition of humpback song, the most problematic issues arise from the inconsistent delineation of phrase types, and the use of the metric of song duration without regards to variability in thematic sequence. With regards to the former, a set of guidelines is suggested to facilitate consistent delineation of phrases. With regards to the latter, current research demonstrates that the “song duration” metric has resulted in the disregard of variability at this level, which is more widespread than traditionally reported. An exemplar case is used to highlight the problem inherent in defining and measuring song duration. Humpback song is evaluated within the framework of avian songbird research, and a shift in analysis paradigm is recommended, towards phrase‐based analyses in which sequences of phrases are treated as a salient feature of song pattern.
Looking for Candida nivariensis and C. bracarensis among a large Italian collection of C. glabrata isolates: results of the FIMUA working group
Authors: Esposto M. C. , Prigitano A. , Romeo O. , Criseo G. , Trovato L. , Tullio V. , Fadda M. E. , Tortorano A. M. ,   FIMUA Working Group
Published: November 2012

SummaryTwo recently described pathogenic Candida species, C. nivariensis and C. bracarensis, share many phenotypic characteristics with C. glabrata and are easily misidentified as such. The aim of this study was to determine the occurrence of these cryptic species in Italy. One thousand yeast isolates collected in 14 Italian regions and identified as C. glabrata by phenotypic and biochemical methods were included in this study: 928 were screened on CHROMagar and 72 were analysed by a multiplex PCR. None of these cryptic species was identified despite the nationwide distribution and the variety of biological origin of the isolates.
Physical sexual and intimate relationship concerns among Indonesian cervical cancer survivors: A phenomenological study
Authors: Afiyanti Yati , Milanti Ariesta 
Published: November 2012

AbstractCervical cancer often leads to sexuality and intimacy concerns for the affected woman within a marital relationship.This study aimed to explore physical sexual concerns and their impact on the intimate partner relationships experienced by cervical cancer survivors. Using a descriptive phenomenological approach, data were collected through in‐depth interviews with Indonesian women survivors of cervical cancer. Two themes and five sub‐themes were constructed from the thematic analysis. The first theme was the physical sexual concerns following cervical cancer treatment, with the subthemes: red spotting and massive vaginal discharge after having sexual intercourse; narrower, smaller and less lubricated vagina; pain during sexual intercourse; feeling of shortened vagina as if it had been cut. The second theme of impact of sexual concerns on intimate partner had five subthemes of: looking for reasons to refuse sexual intercourse; prejudice towards the spouse; feeling forced to fulfil husband's sexual needs; accepting spouse's anger; willingness to let the spouse marry another woman. The findings provide nurses with a greater understanding on how women adapt to their altered sexuality and intimacy with their partner following cancer treatments.
Phenotypic characterization of the foldase homologue PrsA in Streptococcus mutans
Authors: Guo L. , Wu T. , Hu W. , He X. , Sharma S. , Webster P. , Gimzewski J.K. , Zhou X. , Lux R. , Shi W. 
Published: November 2012

SummaryStreptococcus mutans is generally considered to be the principal etiological agent for dental caries. Many of the proteins necessary for its colonization of the oral cavity and pathogenesis are exported to the cell surface or the extracellular matrix, a process that requires the assistance of the export machineries. Bioinformatic analysis revealed that the S. mutans genome contains a prsA gene, whose counterparts in other gram‐positive bacteria, including Bacillus and Lactococcus, encode functions involved in protein post‐export. In this study, we constructed a PrsA‐deficient derivative of S. mutans and demonstrated that the prsA mutant displayed an altered cell wall/membrane protein profile as well as cell‐surface‐related phenotypes, including auto‐aggregation, increased surface hydrophobicity and abnormal biofilm formation. Further analysis revealed that the disruption of the prsA gene resulted in reduced insoluble glucan production by cell surface localized glucosyltransferases, and mutacin as well as cell surface‐display of a heterologous expressed GFP fusion to the cell surface protein SpaP. Our study suggested that PrsA in S. mutans encodes functions similar to those identified in Bacillus, and so is likely to be involved in protein post‐export.
Metabolic engineering of plant monoterpenes, sesquiterpenes and diterpenes—current status and future opportunities
Authors: Lange B. Markus , Ahkami Amirhossein 
Published: November 2012

SummaryTerpenoids (a.k.a. isoprenoids) represent the most diverse class of natural products found in plants, with tens of thousands of reported structures. Plant‐derived terpenoids have a multitude of pharmaceutical and industrial applications, but the natural resources for their extraction are often limited and, in many cases, synthetic routes are not commercially viable. Some of the most valuable terpenoids are not accumulated in model plants or crops, and genetic resources for breeding of terpenoid natural product traits are thus poorly developed. At present, metabolic engineering, either in the native producer or a heterologous host, is the only realistic alternative to improve yield and accessibility. In this review article, we will evaluate the state of the art of modulating the biosynthetic pathways for the production of mono‐, sesqui‐ and diterpenes in plants.
Spongospora subterranea root infection assessed in two potato cultivars differing in susceptibility to tuber powdery scab
Authors: Hernandez Maldonado M. L. , Falloon R. E. , Butler R. C. , Conner A. J. , Bulman S. R. 
Published: November 2012

Infection by Spongospora subterranea of roots of two potato (Solanum tuberosum) cultivars, either very resistant or very susceptible to powdery scab on their tubers, was studied in a glasshouse experiment. Plants grown in sand/nutrient solution culture were inoculated with S. subterranea sporosori 2 weeks after planting. Plant parameters, the intensity of zoosporangium infection in roots, numbers of Spongospora root galls and amounts of Spongospora DNA in roots, measured using quantitative PCR (qPCR), were assessed at sequential harvests. Inoculation with S. subterranea reduced water use (56 days after planting) by 26% in the tuber resistant cultivar compared with uninoculated plants, and by 60% in the susceptible cultivar. Inoculation did not affect growth of the resistant cultivar, nor shoot mass of the susceptible cultivar, but caused a 38% reduction in root mass of the susceptible cultivar. The intensities of zoosporangium development in both cultivars were similar. The susceptible cultivar had approximately four times more Spongospora root galls g−1 root mass than the resistant cultivar. Quantitative PCR detected S. subterranea DNA in roots 1 week after inoculation, and indicated a twofold greater amount of pathogen DNA in roots of the susceptible than the resistant cultivar. This study suggests that the S. subterranea zoosporangium stage in host roots is affected differently by host resistance factors than the sporosorus (root gall and tuber scab) stages. The study has also demonstrated the usefulness of qPCR for sensitive and consistent detection of S. subterranea across the duration of potato root infection.
Nurses' perceptions of working according to standardized care plans: a questionnaire study
Authors: Jakobsson Jenny , Wann‐Hansson Christine 
Published: November 2012

AimsThe aim of this study was to investigate nurses′ perceptions of working according to standardized care plans (SCPs), regarding usability, documentation, quality of care and the implementation process.BackgroundAdministrative work is an extensive part of nursing practice which leads to decreased time for the near patient‐related care. In addition, the number of very sick patients with short hospital stays has increased. This places new demands on healthcare teams to guarantee a high quality of care. For this reason development and use of standardized care plans has increased in Sweden during recent years.MethodThis was a cross‐sectional survey and 116 registered nurses who had experience of working according SCPs answered a questionnaire with the option of providing written comments.ResultThe nurses reported that the use of SCPs facilitated their daily work, especially for new employees and worked well as a checklist ensuring the quality of care. The documentation was experienced as easy, less time consuming with less redundant information. The implementation process of SCPs was reported as satisfactory but a majority reported that they were not involved in the development of the SCP. However, even though 85.5% reported a positive attitude towards working according to an SCP, it was also sometimes experienced as inflexible.ConclusionThe nurses had overall positive perceptions of working according to an SCP mainly in terms of usability, documentation and quality of care. The implementation process was not optimal and it was doubtful whether the SCP rendered any positive side effects.
Internationally educated nurses’ experiences in a hospital in England: an exploratory study
Authors: Alexis Obrey 
Published: November 2012

BackgroundThe recruiting of internationally educated nurses (IENs) to work in the National Health Service (NHS) in the United Kingdom (UK) is not a new phenomenon. Such practices have its roots in the 1940s when the NHS was first incepted.ObjectiveThe aim of this study was to gain an understanding of IENs’ experiences of working in the NHS in England.MethodsPhenomenology in particular, Heidegger, was the approach adopted, and the study consisted of two phases in which twelve individuals’ interviews were conducted in phase one. The findings from this phase informed the second phase where four focus group interviews were used. The data for both phases were thematically analysed.ResultsSix themes emerged following data analysis, namely Leaving a familiar world, Being thrown into an unfamiliar world, Encountering marginalisation and experiencing inequalities in the world, Surviving in an everyday world, Living in an everyday world and Making a new world.ConclusionInternationally educated nurses encountered a number of challenges to their working practices in an English hospital, and there is a need for both IENs and home‐grown nurses to adapt to each other cultural differences.
Psychological distress and subjective well‐being in partners of somatically ill or physically disabled: The Nord‐Trøndelag Health Study
Authors: BORREN INGRID , TAMBS KRISTIAN , IDSTAD MARIANN , ASK HELGA , SUNDET JON MARTIN 
Published: November 2012

Borren, I., Tambs, K., Idstad, M., Ask, H. & Sundet, J. M. (2012). Psychological distress and subjective well‐being in partners of somatically ill or physically disabled: The Nord‐Trøndelag Health Study. Scandinavian Journal of Psychology 53, 475–482.This study investigated the cross‐sectional associations between various somatic conditions in one partner and the level of distress and well‐being in the spouse. The study is based on survey data from the Norwegian Nord‐Trøndelag Health Study, HUNT II (1995–1997). A sample of 9,797 married or cohabiting couples with valid data on subjective well‐being (SWB), psychological distress (Hopkins Symptom Check List (SCL)‐10) and somatic illness were identified. Regression analyses stratified by sex were conducted with SCL‐10 and SWB scores as dependent variables and a joint somatic score as predictor, including; stroke, cancer, angina, myocardial infarction and physical disability (PD). The contribution of each somatic condition was also explored. Spouses of persons previously diagnosed with at least one somatic condition scored significantly lower on SWB and significantly higher on SCL‐10 than spouses of healthy persons, though effect sizes were small. The effect seems to be at least partly mediated by the ill partner’s psychological distress. Of the specific conditions, PD had the most significant contribution for both genders, though an association between male angina and spousal distress/SWB was also demonstrated.
Information processing in patients with first episode major depression
Authors: HAMMAR ÅSA , KILDAL ANNA B. , SCHMID MARIT 
Published: November 2012

Hammar, Å., Kildal, A. B. & Schmid, M. (2012). Information processing in patients with first episode major depression. Scandinavian Journal of Psychology 53, 445–449.Few studies have investigated cognitive functioning in a group of patients experiencing a first episode of depression. The aim of this study was to investigate how patients diagnosed with a first episode of depression perform in effortful and non‐effortful information processing compared to healthy controls. An experimental paradigm based on a visual search test was applied. Thirty‐one patients and thirty‐one healthy controls were included in the study. All patients experienced a severe level of symptom load at the time of testing. Results showed no significant differences between groups under any of the conditions. Findings in the present study indicate that patients with a first episode of depression perform equally to healthy controls in tasks requiring visual attention in both effortful and non‐effortful information processing.
Self‐esteem and emotional health in adolescents – gender and age as potential moderators
Authors: MOKSNES UNNI K. , ESPNES GEIR A. 
Published: November 2012

Moksnes, U. K. & Espnes, G. A. (2012). Self‐esteem and emotional health in adolescents – gender and age as a potential moderators. Scandinavian Journal of Psychology 53, 483–489.The present paper investigates possible gender and age differences on emotional states (depression and anxiety) and self‐esteem as well as the association between self‐esteem and emotional states. The cross‐sectional sectional sample consists of 1,209 adolescents 13–18 years from public elementary and secondary schools in mid‐Norway. The results showed that girls reported higher scores on state anxiety and state depression, whereas boys consistently scored higher on self‐esteem in all age groups. Self‐esteem was strongly and inversely associated with both state depression and state anxiety. An interaction effect of gender by self‐esteem was found on state depression, where the association was stronger for girls than for boys. The associations found give support for the positive role of self‐esteem in relation to adolescents’ emotional health and well‐being.
Costs of inpatient treatment for multi‐drug‐resistant tuberculosis in South Africa
Authors: Schnippel Kathryn , Rosen Sydney , Shearer Kate , Martinson Neil , Long Lawrence , Sanne Ian , Variava Ebrahim 
Published: November 2012

AbstractBackgroundIn South Africa, patients with multi‐drug‐resistant tuberculosis (MDR‐TB) are hospitalised from MDR‐TB treatment initiation until culture conversion. Although MDR‐TB accounts for <3% of incident TB in South Africa, 55% of the public sector TB budget is spent on MDR‐TB. To inform new strategies for MDR‐TB management, we estimated the per‐patient cost (USD 2011) of inpatient MDR‐TB treatment.MethodsAll resources used by patients admitted to the MDR‐TB hospital with confirmed MDR‐TB from March 2009 to February 2010 were abstracted from patient records for up to 12 months after initial admission or until the earliest of final discharge, abscondment or death. Costs of hospital stay/day were estimated from hospital expenditure records and costs for drugs, laboratory tests, radiography and surgery from public sector sources. 133 patients met study inclusion criteria of whom 121 had complete cost records.ResultsBy 12 months, 86% were discharged with culture conversion, 8% died in hospital, 2% were still admitted, and 3% had absconded. The mean hospital stay was 105 days. The mean total cost per patient was $17 164, of which 95% were hospitalisation costs (buildings, staff, etc.) and ≤ 2% each for MDR‐TB drugs ($380); TB laboratory tests, including drug susceptibility testing ($236); and other costs.ConclusionsThe inpatient cost per patient treated for MDR‐TB is more than 40 times the cost of treating drug‐susceptible TB in South Africa. There is potential for substantial cost savings from improved management of drug‐susceptible TB and shifting to a model of decentralised, outpatient MDR‐treatment.