bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing Uncertainty in Fish Stock Assessments: the Case of the Southern New England–Mid‐Atlantic Winter Flounder
Authors: Rothschild Brian J. , Jiao Yue 
Published: June 2011

AbstractThe reauthorization of the Magnuson–Stevens Act requires specification of scientific uncertainty associated with stock assessments. The scientific uncertainty associated with stock assessments of southern New England–mid‐Atlantic winter flounderPseudopleuronectes americanusis considered as a case study. Focus is placed upon the uncertainties associated with the assumptions, assertions, and choices (AACs) made in the stock assessment analysis. Two classes of AACs are discussed. The first class involves AACs that characterize the population dynamics of the stock; these AACs include the unit stock assumption, the problem of dealing with retrospective patterns, the method of averaging fishing mortality across cohorts to yield an annual value for fishing mortality, and the equilibrium structure of the stock. The second class of AACs is related to the choice of methods used to determine whether the stock is overfished; these AACs involve focusing on the maximum sustainable yield (MSY) proxy rather than MSY per se to determine overfishing levels. The MSY proxy approach is discussed and compared with heuristic calculations of the MSY approach. Arbitrary choices of instantaneous natural mortality and percent maximum spawning potential in the analysis can lead to an arbitrary decision on whether or not the stock is overfished. We conclude that there is considerable scientific uncertainty on the status of the southern New England–mid‐Atlantic winter flounder stock. The uncertainty identifies critical unknowns in winter flounder population dynamics.
Population Structure and Genetic Divergence of Coastal Rainbow and Redband Trout in the Upper Klamath Basin
Authors: Pearse Devon E. , Gunckel Stephanie L. , Jacobs Steven E. 
Published: June 2011

AbstractFreshwater‐resident coastal rainbow trout Oncorhynchus mykiss irideus and the anadromous form of the subspecies, coastal steelhead (summer and winter runs), are present throughout the lower Klamath River–Trinity River system. Although coastal steelhead and other anadromous salmonids historically migrated into the Upper Klamath Basin (which encompasses the upper Klamath River and Upper Klamath Lake) and associated tributaries, the construction of Copco Dam in 1918 and Iron Gate Dam in 1962 stopped all upstream migration of fish past these barriers. In the Upper Klamath Lake basin, native Upper Klamath Lake redband trout O. mykiss newberrii are found along with coastal rainbow trout that were trapped above the dams or stocked from hatchery sources. However, relatively little is known about the genetic relationships among the O. mykiss populations within the Upper Klamath Basin. A population genetic analysis based on data from 17 variable microsatellite loci was conducted for samples collected in the Upper Klamath Basin, including rainbow trout and Upper Klamath Lake redband trout (presumably representative of the ancestral coastal and inland lineages) as well as samples of O. mykiss from neighboring inland lake basins. In addition, the Upper Klamath Basin samples were compared with data from O. mykiss populations below Iron Gate Dam. Results demonstrate the presence of distinct inland and coastal genetic lineages as well as divergent lineages represented by samples from the inland lake basins; these results have significant implications for future restoration of O. mykiss in the greater Klamath River–Trinity River system.
‘I never talked about, ever’: A comprehensive process analysis of a significant client disclosure event in therapy
Authors: Balmforth Jane , Elliott Robert 
Published: May 2011

AbstractAims: The present study was intended to examine how a particular client disclosure came about and what made it important to the client. Method: A client‐identified significant therapy event involving disclosure of childhood abuse was analysed using Comprehensive Process Analysis (CPA), a qualitative interpretive method for examining the process, effects and context of significant events in therapy. Results: The analysis identified therapist invitation and client universalisation as the key elements of the disclosure event. The context analysis showed how the event linked to the client's symbolisation of her fear earlier in the session and in the previous session. The client gained insight into how the earlier abuse had affected her life, linking it to the victimisation that was her primary reason for seeking therapy, and to her relationship with her mother. The therapist facilitated the event by following up the client's hints, trusting the strength of the alliance, and staying close to the client's frame of reference. Conclusion: The findings suggest that the initial significance of an invited disclosure event may diminish for a client over the course of therapy.
A thematic analysis of young people's experience of counselling in five secondary schools in the UK
Authors: Lynass Rosemarie , Pykhtina Olga , Cooper Mick 
Published: May 2011

AbstractAim: To investigate young people's views on the effects of school‐based counselling, and what they found helpful and unhelpful. Method: Eleven semi‐structured interviews were conducted and thematically analysed. Findings: Participants expressed predominantly positive views of school‐based counselling with changes in three main domains: emotional, interpersonal and behavioural. Participants viewed these changes as having had an important effect on their lives. The most commonly cited helpful aspects of counselling were related to talking or getting things out, and counsellor qualities. Conclusions: School‐based counselling is viewed positively by those who have experienced it, and appears to be an appropriate and valuable intervention for young people.
‘The third person in the room’: Recording the counselling interview for the purpose of counsellor training – barrier to relationship building or effective tool for professional development?
Authors: Gossman Marion , Miller Judi H. 
Published: May 2011

AbstractObjective: Audio and videotape interview recording for training and supervision in counsellor education is commonplace within New Zealand, yet researchers have paid little attention to its value perceived by students. This study explores counselling students’ perceptions of the effects of recording counselling interviews on themselves, their clients and on the counselling process. Design: Counselling students from five tertiary educational settings in New Zealand participated in individual or focus group interviews to discuss their experiences of recording counselling interviews. Findings: All interviewees indicated that recording initially curtailed their ability to be completely present in the counselling interview. Some thought this may have negatively influenced their clients’ ability to use the counselling session effectively. Most noted their own increased confidence over time. Almost all considered recording to be extremely beneficial to the development of effective counselling skills. Conclusion: Most students considered the benefits of recording to outweigh the drawbacks. Implications for continuing the practice of recording and playing back interviews in counsellor‐education programmes are considered.
Fuel retention in impurity seeded discharges in JET after Be evaporation
Authors: Brezinsek S. , Loarer T. , Krieger K. , Jachmich S. , Tsalas M. , Coffey I. , Esser H.G. , Eich T. , Fundamenski W. , Giroud C. , Grünhagen S. , Huber A. , Kruezi U. , Knipe S. , Maddison G.P. , McCormick K. , Meigs A.G. , Morgan Ph. , Philipps V. , Sergienko G. , Stagg R. , Stamp M.F. , Tabares F.L. 
Published: May 2011

Preparatory experiments for the ITER-Like Wall in JET were carried out to simulate the massive Be first wall by a thin Be layer, induced by evaporation of about 2.0 g Be, and to study its impact on fuel retention and divertor radiation with reduced C content and N seeding. Residual gas analysis reveals a reduction of hydrocarbons by one order of magnitude and of O by a factor of 5 in the partial pressure owing to the evaporation. The evolution of wall conditions, impurity fluxes and divertor radiation have been studied in ELMy H-mode plasmas (B
t = 2.7 T, I
p = 2.5 MA, P
aux = 16 MW) whereas a non-seeded reference discharge was executed prior to the evaporation.
The in situ measured Be flux at the midplane increased by about a factor of 40 whereas the C flux decreased by ∼50% in the limiter phase of the first discharge with respect to the reference, but erosion of the Be layer and partial coverage with C takes place quickly. To make best use of the protective Be layer, only the first four discharges were employed for a gas balance analysis providing a D retention rate of 1.94 × 1021 D s−1 which is comparable to rates with C walls. But the Be evaporation provides a non-saturated surface with respect to D and short term retention is not negligible in the balance; the measured retention is overestimated with respect to steady-state conditions like that of the ILW. Moreover, C was only moderately reduced and co-deposition of fuel with eroded Be and C occurs.
The lower C content leads to a minor reduction in divertor radiation as the reference phase prior to seeding indicates. N adds to the radiation of D and the remaining C, and the N content rises due to the legacy effect which has been quantified by gas balance to be 30% of the injected N. C radiation increases with exposure time, and both contributors cause an increase in the radiated fraction in the divertor from 50% to 70%. The radiation pattern suggests that N dominates the increase in the first discharges though C is still the dominating radiator. Therefore, the validity of a proxy of the Be first wall by a thin Be layer is limited and restricted to plasma operation directly after the Be evaporation.
RightField: embedding ontology annotation in spreadsheets
Authors: Wolstencroft Katy , Owen Stuart , Horridge Matthew , Krebs Olga , Mueller Wolfgang , Snoep Jacky L. , du Preez Franco , Goble Carole 
Published: May 2011

Abstract
Motivation: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, may have little experience in the use of such standards and require tools to support this form of data annotation.
Results: RightField is an open source application that provides a mechanism for embedding ontology annotation support for Life Science data in Excel spreadsheets. Individual cells, columns or rows can be restricted to particular ranges of allowed classes or instances from chosen ontologies. The RightField-enabled spreadsheet presents selected ontology terms to the users as a simple drop-down list, enabling scientists to consistently annotate their data. The result is ‘semantic annotation by stealth’, with an annotation process that is less error-prone, more efficient, and more consistent with community standards.
Availability and implementation: RightField is open source under a BSD license and freely available from http://www.rightfield.org.uk
Contact: kwolstencroft@cs.man.ac.uk
Computational discovery of human coding and non-coding transcripts with conserved splice sites
Authors: Rose Dominic , Hiller Michael , Schutt Katharina , Hackermüller Jörg , Backofen Rolf , Stadler Peter F. 
Published: May 2011

Abstract
Motivation: Long non-coding RNAs (lncRNAs) resemble protein-coding mRNAs but do not encode proteins. Most lncRNAs are under lower sequence constraints than protein-coding genes and lack conserved secondary structures, making it hard to predict them computationally.
Results: We introduce an approach to predict spliced lncRNAs in vertebrate genomes combining comparative genomics and machine learning. It is based on detecting signatures of characteristic splice site evolution in vertebrate whole genome alignments. First, we predict individual splice sites, then assemble compatible sites into exon candidates, and finally predict multi-exon transcripts. Using a novel method to evaluate typical splice site substitution patterns that explicitly takes the species phylogeny into account, we show that individual splice sites can be accurately predicted. Since our approach relies only on predicted splice sites, it can uncover both coding and non-coding exons. We show that our predicted exons and partial transcripts are mostly non-coding and lack conserved secondary structures. These exons are of particular interest, since existing computational approaches cannot detect them. Transcriptome sequencing data indicate tissue-specific expression patterns of predicted exons and there is evidence that increasing sequencing depth and breadth will validate additional predictions. We also found a significant enrichment of predicted exons that form multi-exon transcript parts, and we experimentally validate such a novel multi-exon gene. Overall, we obtain 336 novel multi-exon transcript predictions from human intergenic regions. Our results indicate the existence of novel human transcripts that are conserved in evolution and our approach contributes to the completion of the human transcript catalog.
Availability and Implementation: Predicted human splice sites, exons and gene structures together with a Perl implementation of the tree-based log-odds scoring and a supplementary PDF file containing additional figures and tables are available at: http://www.bioinf.uni-leipzig.de/publications/supplements/10-010. The five experimentally confirmed partial transcript isoforms have been deposited in GenBank under accession numbers HM587422-HM587426.
Contact: dominic@bioinf.uni-leipzig.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
TimeTree2: species divergence times on the iPhone
Authors: Kumar Sudhir , Hedges S. Blair 
Published: May 2011

AbstractSummary: Scientists, educators and the general public often need to know times of divergence between species. But they rarely can locate that information because it is buried in the scientific literature, usually in a format that is inaccessible to text search engines. We have developed a public knowledgebase that enables data-driven access to the collection of peer-reviewed publications in molecular evolution and phylogenetics that have reported estimates of time of divergence between species. Users can query the TimeTree resource by providing two names of organisms (common or scientific) that can correspond to species or groups of species. The current TimeTree web resource (TimeTree2) contains timetrees reported from molecular clock analyses in 910 published studies and 17 341 species that span the diversity of life. TimeTree2 interprets complex and hierarchical data from these studies for each user query, which can be launched using an iPhone application, in addition to the website. Published time estimates are now readily accessible to the scientific community, K–12 and college educators, and the general public, without requiring knowledge of evolutionary nomenclature.Availability: TimeTree2 is accessible from the URL http://www.timetree.org, with an iPhone app available from iTunes (http://itunes.apple.com/us/app/timetree/id372842500?mt=8) and a YouTube tutorial (http://www.youtube.com/watch?v=CxmshZQciwo).Contact: sbh1@psu.eduSupplementary information:Supplementary data are available at Bioinformatics online.
Aligning short reads to reference alignments and trees
Authors: Berger Simon A. , Stamatakis Alexandros 
Published: June 2011

Abstract
Motivation: Likelihood-based methods for placing short read sequences from metagenomic samples into reference phylogenies have been recently introduced. At present, it is unclear how to align those reads with respect to the reference alignment that was deployed to infer the reference phylogeny. Moreover, the adaptability of such alignment methods with respect to the underlying reference alignment strategies/philosophies has not been explored. It has also not been assessed if the reference phylogeny can be deployed in conjunction with the reference alignment to improve alignment accuracy in this context.
Results: We assess different strategies for short read alignment and propose a novel phylogeny-aware alignment procedure. Our alignment method can improve the accuracy of subsequent phylogenetic placement of the reads into a reference phylogeny by up to 5.8 times compared with phylogeny-agnostic methods. It can be deployed to align reads to alignments generated by using fundamentally different alignment strategies (e.g. PRANK+F versus MUSCLE).
Availability: http://www.exelixis-lab.org/software.html
Contact: simon.berger@h-its.org; alexandros.stamatakis@h-its.org
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Leaf Blight Caused by Nigrospora sphaerica on Curcuma in China
Authors: Zhang L. X. , Song J. H. , Tan G. J. , Li S. S. 
Published: June 2011

Curcuma (family Zingiberaceae) is commonly cultivated for the use of rhizomes within traditional Chinese medicines. In October 2009 and 2010, severe leaf blight was observed on Curcuma wenyujin Y.H. Chen & C. Ling (4) in fields located in Ruian, China. The area of cultivation in Ruian encompasses 90% of the production in Zhejiang Province. Disease incidence was approximately 90% of plants observed in affected fields. Early symptoms were yellow-to-brown, irregular-shaped lesions on the leaf margin or tip. After several days, lesions expanded along the mid-vein until the entire leaf was destroyed. Blighted leaves turned grayish to dark brown and withered, and severely affected plants died. Eight fungal isolates were recovered from symptomatic C. wenyujin leaves, collected from eight different fields, on potato dextrose agar (PDA). These fungal colonies were initially white, becoming light to dark gray and produced black, spherical to subspherical, single-celled conidia (14 to 17 × 12 to 15 μm), which were borne on a hyaline vesicle at the tip of the conidiophores. On the basis of these morphological features, the isolates appeared to be similar to Nigrospora sphaerica (2). Strain ZJW-1 was selected as a representative for molecular identification. Genomic DNA was extracted from the isolate, and the internal transcribed spacer (ITS) region of the ribosomal DNA (ITS1-5.8S-ITS2) was amplified using ITS1 (5′-TCCGTAGGTGAACCTGCGG-3′) and ITS4 (5′-TCCTCCGCTTATTGATATGC-3′) primers (3). The ITS region was further cloned and sequenced (GenBank Accession No. JF738028) and was 99% identical to N. sphaerica (GenBank Accession No. FJ478134.1). On the basis of morphological data and the ITS rDNA sequence, the isolate was determined to be N. sphaerica. Pathogenicity tests were conducted on four leaves of four C. wenyujin plants by placing agar pieces (5 mm in diameter) from 8-day-old cultures on pushpin-wounded leaves. An equal number of control plants were wounded and inoculated with noncolonized PDA agar pieces. Plants were placed in moist chambers at 25°C with a 12-h photoperiod. Brown-to-black lesions were observed on wounded leaves after 3 days and expanded to an average of 56 × 40 mm 15 days after inoculation. No symptoms developed on the control leaves. The pathogen was reisolated from the margins of necrotic tissues but not from the controls. The pathogen has been reported as a leaf pathogen on several hosts worldwide (1). To our knowledge, this is the first report of N. sphaerica as a leaf pathogen of C. wenyujin in China. Future research will focus primarily on management of this disease. References: (1) D. F. Farr and A. Y. Rossman. Fungal Databases, Systematic Mycology and Microbiology Laboratory, USDA-ARS, Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , March 31, 2011. (2) E. W. Mason. Trans. Brit. Mycol. Soc. 12:152, 1927. (3) T. J. White et al. PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990. (4) J. Zhao et al. Molecules 15:7547, 2010.
Differential Molecular Responses of Rice and Wheat Coleoptiles to Anoxia Reveal Novel Metabolic Adaptations in Amino Acid Metabolism for Tissue Tolerance
Authors: Shingaki-Wells Rachel N. , Huang Shaobai , Taylor Nicolas L. , Carroll Adam J. , Zhou Wenxu , Millar A. Harvey 
Published: May 2011

AbstractRice (Oryza sativa) and wheat (Triticum aestivum) are the most important starch crops in world agriculture. While both germinate with an anatomically similar coleoptile, this tissue defines the early anoxia tolerance of rice and the anoxia intolerance of wheat seedlings. We combined protein and metabolite profiling analysis to compare the differences in response to anoxia between the rice and wheat coleoptiles. Rice coleoptiles responded to anoxia dramatically, not only at the level of protein synthesis but also at the level of altered metabolite pools, while the wheat response to anoxia was slight in comparison. We found significant increases in the abundance of proteins in rice coleoptiles related to protein translation and antioxidant defense and an accumulation of a set of enzymes involved in serine, glycine, and alanine biosynthesis from glyceraldehyde-3-phosphate or pyruvate, which correlates with an observed accumulation of these amino acids in anoxic rice. We show a positive effect on wheat root anoxia tolerance by exogenous addition of these amino acids, indicating that their synthesis could be linked to rice anoxia tolerance. The potential role of amino acid biosynthesis contributing to anoxia tolerance in cells is discussed.
Virus-Induced Necrosis Is a Consequence of Direct Protein-Protein Interaction between a Viral RNA-Silencing Suppressor and a Host Catalase
Authors: Inaba Jun-ichi , Kim Bo Min , Shimura Hanako , Masuta Chikara 
Published: May 2011

AbstractMany plant host factors are known to interact with viral proteins during pathogenesis, but how a plant virus induces a specific disease symptom still needs further research. A lily strain of Cucumber mosaic virus (CMV-HL) can induce discrete necrotic spots on infected Arabidopsis (Arabidopsis thaliana) plants; other CMV strains can induce similar spots, but they are not as distinct as those induced by CMV-HL. The CMV 2b protein (2b), a known RNA-silencing suppressor, is involved in viral movement and symptom induction. Using in situ proximity ligation assay immunostaining and the protoplast assays, we report here that CMV 2b interacts directly with Catalase3 (CAT3) in infected tissues, a key enzyme in the breakdown of toxic hydrogen peroxide. Interestingly, CAT3, normally localized in the cytoplasm (glyoxysome), was recruited to the nucleus by an interaction between 2b and CAT3. Although overexpression of CAT3 in transgenic plants decreased the accumulation of CMV and delayed viral symptom development to some extent, 2b seems to neutralize the cellular catalase contributing to the host defense response, thus favoring viral infection. Our results thus provide evidence that, in addition to altering the type of symptom by disturbing microRNA pathways, 2b can directly bind to a host factor that is important in scavenging cellular hydrogen peroxide and thus interfere specifically with that host factor, leading to the induction of a specific necrosis.