bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linking Fish and Angler Dynamics to Assess Stocking Strategies for Hatchery-Dependent, Open-Access Recreational Fisheries
Authors: Askey Paul J. , Parkinson Eric A. , Post John R. 
Published: May 2013

Abstract
Optimization of stocking practices regarding release size and density requires an understanding of how dynamic ecological and angler effort processes interact. We used experimental data on size and density-dependent fish recruitment processes and combined these with empirical fishery data to model the outcome of different stocking strategies. The model is based on the British Columbia Rainbow Trout Oncorhynchus mykiss fishery, which is an open-access recreational fishery where fish recruitment is entirely derived from hatchery production. Under this scenario, changes to stocking practices primarily influence angler effort densities, whereas angling quality, defined as a function of catch rate and fish size, remain relatively constant. In light of this, we suggest that the primary performance measure for open-access recreational fisheries management be sustainable angler effort. We modeled the effort response to stocking changes under contrasting biological (lake productivity) and fishery (remoteness, harvest regulations) characteristics. Lake-specific effort is maximized by stocking larger fish into productive lakes that are harvested. However, the strategy to maximize regional effort across multiple lakes was dependent on the ratio of hatchery production to total lake area and the mix of individual lake productivities within the total lake area.
Received July 10, 2012; accepted March 10, 2013
Capabilities and Childbearing Intentions in Europe
Authors: Fahlén Susanne 
Published: May 2013

ABSTRACT
This article investigates the association between economic uncertainties, work–family reconciliation policies and women's short-term childbearing intentions in 10 European countries. I introduce the capability approach to this issue and argue that short-term childbearing intentions are an indicator of women's capabilities to start a family or to have additional children. Using data from the European Social Survey, the analysis reveals that the association between economic uncertainties and short-term childbearing intentions varies by the number of children already born, education and institutional contexts. In some countries, having a job have a positive impact on childless women's short-term intentions, while in other countries, low educated childless women out of the labour market are those most likely to intend to have a child in the near future. Other aspects of economic uncertainties, namely perceived job and income insecurity, have a negative impact on short-term childbearing intentions, regardless of motherhood status. The analysis also shows that the combination of weaker institutional support for work–family reconciliation, perceived job and income insecurity and low educational skills are associated with lower childbearing intentions, and the pattern across the 10 countries is slightly stronger for childless women. This study underscores the importance of embedding individual decision processes in a broader societal context.
Acute Hepatitis B Outbreaks in 2 Skilled Nursing Facilities and Possible Sources of Transmission: North Carolina, 2009–2010
Authors: Seña Arlene C. , Moorman Anne , Njord Levi , Williams Roxanne E. , Colborn James , Khudyakov Yury , Drobenuic Jan , Xia Guo-Liang , Wood Hattie , Moore Zack 
Published: May 2013

Objective.Acute hepatitis B virus (HBV) infections have been reported in long-term care facilities (LTCFs), primarily associated with infection control breaks during assisted blood glucose monitoring. We investigated HBV outbreaks that occurred in separate skilled nursing facilities (SNFs) to determine factors associated with transmission.Design.Outbreak investigation with case-control studies.Setting.Two SNFs (facilities A and B) in Durham, North Carolina, during 2009–2010.Patients.Residents with acute HBV infection and controls randomly selected from HBV-susceptible residents during the outbreak period.Methods.After initial cases were identified, screening was offered to all residents, with repeat testing 3 months later for HBV-susceptible residents. Molecular testing was performed to assess viral relatedness. Infection control practices were observed. Case-control studies were conducted to evaluate associations between exposures and acute HBV infection in each facility.Results.Six acute HBV cases were identified in each SNF. Viral phylogenetic analysis revealed a high degree of HBV relatedness within, but not between, facilities. No evaluated exposures were significantly associated with acute HBV infection in facility A; those associated with infection in facility B (all odds ratios >20) included injections, hospital or emergency room visits, and daily blood glucose monitoring. Observations revealed absence of trained infection control staff at facility A and suboptimal hand hygiene practices during blood glucose monitoring and insulin injections at facility B.Conclusions.These outbreaks underscore the vulnerability of LTCF residents to acute HBV infection, the importance of surveillance and prompt investigation of incident cases, and the need for improved infection control education to prevent transmission.
Codazzi tensors with two eigenvalue functions
Authors: Merton Gabe 
Published: May 2013

This paper addresses a gap in the classification of Codazzi tensors with exactly two eigenfunctions on a Riemannian manifold of dimension three or higher. Derdzinski proved that if the trace of such a tensor is constant and the dimension of one of the eigenspaces is

n
−
1

n-1

, then the metric is a warped product where the base is an open interval, a conclusion we will show to be true under a milder trace condition. Furthermore, we construct examples of Codazzi tensors having two eigenvalue functions, one of which has eigenspace dimension

n
−
1

n-1

, where the metric is not a warped product with interval base, refuting a claim by A. L. Besse that the warped product conclusion holds without any restriction on the trace.
Updating RNA-Seq analyses after re-annotation
Authors: Roberts Adam , Schaeffer Lorian , Pachter Lior 
Published: May 2013

Abstract
The estimation of isoform abundances from RNA-Seq data requires a time-intensive step of mapping reads to either an assembled or previously annotated transcriptome, followed by an optimization procedure for deconvolution of multi-mapping reads. These procedures are essential for downstream analysis such as differential expression. In cases where it is desirable to adjust the underlying annotation, for example, on the discovery of novel isoforms or errors in existing annotations, current pipelines must be rerun from scratch. This makes it difficult to update abundance estimates after re-annotation, or to explore the effect of changes in the transcriptome on analyses. We present a novel efficient algorithm for updating abundance estimates from RNA-Seq experiments on re-annotation that does not require re-analysis of the entire dataset. Our approach is based on a fast partitioning algorithm for identifying transcripts whose abundances may depend on the added or deleted isoforms, and on a fast follow-up approach to re-estimating abundances for all transcripts. We demonstrate the effectiveness of our methods by showing how to synchronize RNA-Seq abundance estimates with the daily RefSeq incremental updates. Thus, we provide a practical approach to maintaining relevant databases of RNA-Seq derived abundance estimates even as annotations are being constantly revised.
Availability and implementation: Our methods are implemented in software called ReXpress and are freely available, together with source code, at http://bio.math.berkeley.edu/ReXpress/.
Contact: lpachter@math.berkeley.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats
Authors: Tae Hongseok , McMahon Kevin W. , Settlage Robert E. , Bavarva Jasmin H. , Garner Harold R. 
Published: May 2013

AbstractMotivation: Simple tandem repeats are highly variable genetic elements and widespread in genomes of many organisms. Next-generation sequencing technologies have enabled a robust comparison of large numbers of simple tandem repeat loci; however, analysis of their variation using traditional sequence analysis approaches still remains limiting and problematic due to variants occurring in repeat sequences confusing alignment programs into mapping sequence reads to incorrect loci when the sequence reads are significantly different from the reference sequence.Results: We have developed a program, ReviSTER, which is an automated pipeline using a ‘local mapping reference reconstruction method’ to revise mismapped or partially misaligned reads at simple tandem repeat loci. RevisSTER estimates alleles of repeat loci using a local alignment method and creates temporary local mapping reference sequences, and finally remaps reads to the local mapping references. Using this approach, ReviSTER was able to successfully revise reads misaligned to repeat loci from both simulated data and real data.Availability: ReviSTER is open-source software available at http://revister.sourceforge.net.Contact: garner@vbi.vt.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Teleseismic correlations of ambient seismic noise for deep global imaging of the Earth
Authors: Boué P. , Poli P. , Campillo M. , Pedersen H. , Briand X. , Roux P. 
Published: May 2013

Abstract
We present here a global analysis showing that wave paths probing the deepest part of the Earth can be obtained from ambient noise records. Correlations of seismic noise recorded at sensors located various distances apart provide new virtual seismograms for paths that are not present in earthquake data. The main arrivals already known for earthquake data are also present in teleseismic correlations sections, including waves that have propagated through the Earth's core. We present examples of applications of such teleseismic correlations to lithospheric imaging, study of the core mantle boundary or of the anisotropy of the inner core.
Naming the problem: a membership categorization analysis study of family therapy
Authors: O'Neill Katherine , LeCouteur Amanda 
Published: May 2013

Discursive research has examined family therapy as a process of collaboratively negotiating a preferable account of the problem. The present study uses membership categorization analysis to examine how this process occurs in a sequence of family therapy sessions with the family of a 15‐year‐old boy diagnosed with high‐functioning autism and experiencing conflict with his school. The analysis focuses on the deployment of the membership categorization device ‘disability’ in the construction of the problem and the use of the devices ‘family’ and ‘stages‐of‐life’ to construct a new, problem‐dissolving account. Conclusions are drawn about the potential usefulness of recategorization via naturally occurring membership categorization devices in constructing solutions in family therapy.Practitioner points
Therapy is the collaborative negotiation of an account of the family situation in which the problem does not exist.
Naturally occurring groups of categories (MCDs) supply resources for such renegotiation.
Where a problem has been constructed in the MCD ‘disability’ it can be ‘dis‐solved’ using the MCDs ‘family’ and ‘stages‐of‐life’.
More generally, the use of higher order and highly naturalized MCDs may be effective in displacing problem‐generating constructions.
Protective vigilance: a parental strategy in caring for a child diagnosed with ADHD
Authors: Goodwillie Gill 
Published: May 2013

This article describes a key finding that emerged from a small‐scale qualitative study that explored parental views of the impact of having a child diagnosed with attention deficit hyperactivity disorder (ADHD) on family relationships. The term, protective vigilance, describes a strategy used by parents to manage the risk that children can present to themselves and to others with whom they might come in contact, such as their siblings or peers. The term draws attention to the challenges parents face in supervising their children in a manner that others might describe as overprotective or over‐controlling. In this article the parents' voice is heard describing their dilemmas and the article invites professionals working with families, with a child diagnosed with ADHD to consider protective vigilance as an inevitable aspect of the parental role and incorporate this idea into their clinical practice.Practitioner points
Explore with parents how concerns for their child's safety might impact on their parenting style
Recognize that a child's behaviour shapes and influences parental style in a recursive manner
Note that early intervention with a relational focus may improve future outcomes for the child diagnosed with ADHD
Adopt a systemic approach based on a ‘both and’ stance to free the practitioner from the polarized discourses that surround the diagnosis of ADHD and help to avoid the dialectics of blame
Note that parental aspirations and hopes for a child diagnosed with ADHD may be affected by negative cultural views about the diagnosis
Explore practitioners' own prejudices about the diagnosis before they set about helping parents.
Implementation of the INTERGROWTH‐21st Project in the UK
Authors: Roseman F , Knight HE , Giuliani F , Lloyd S , Di Nicola P , Laister A , Roseman S , Kennedy K , Burnham O , Patel B , Puglia F , Blakey I , Cheikh Ismail L ,   for the International Fetal and Newborn Growth Consortium for the 21 Century (INTERGROWTH‐21)
Published: May 2013

Please cite this paper as: Roseman F, Knight H, Giuliani F, Lloyd S, Di Nicola P, Laister A, Roseman S, Kennedy K, Burnham O, Patel B, Puglia F, Blakey I, Cheikh Ismail L, for the International Fetal and Newborn Growth Consortium for the 21st Century (INTERGROWTH‐21st). Implementation of the INTERGROWTH‐21st Project in the UK. BJOG 2013; 120 (Suppl. 2): 117–122.There are approximately 10 000 births per year in the county of Oxfordshire in the UK, which is one of the two European sites for the International Fetal and Newborn Growth Consortium for the 21st Century (INTERGROWTH‐21st) Project. The samples for both components of the project – the Fetal Growth Longitudinal Study (FGLS) and Newborn Cross‐Sectional Study (NCSS) – were drawn from the John Radcliffe Hospital, a major university hospital with a large regional role that covers more than 75% of deliveries in the county. Special activities to encourage participation in this population included the formation of a research coalition to streamline recruitment in the Maternity Unit and the distribution of study information leaflets to women using the hospital’s antenatal care service. This was a demanding project and several challenges were overcome to reach recruitment targets and to maintain high standards of data quality. Amongst the major challenges for FGLS at this study site was the level of ineligibility because of maternal age, smoking and body mass index (BMI) ≥ 30. The major challenge for the NCSS field teams was to ensure that all anthropometric data were collected before the early discharge of uncomplicated deliveries, often within 6 hours of birth. It is evident from our experience in implementing this project that, when large‐scale clinical studies are meticulously planned and avoid major disruption to routine clinical care, they are well received by hospital staff and can contribute to the improvement of the overall standard of clinical care.
Prevalence and predictors of alanine aminotransferase elevation among normal weight, overweight and obese youth in Mexico
Authors: Purcell Maura , Flores Yvonne N , Zhang Zuo‐Feng , Denova‐Gutiérrez Edgar , Salmeron Jorge 
Published: May 2013

ObjectiveThis study aimed to determine the prevalence of and risk factors associated with elevated alanine aminotransferase (ALT) levels among a sample of normal weight, overweight and obese youth from two urban populations in Central Mexico.MethodsBaseline data from 1262 youth aged 8–19 years who participated in the Mexican Health Worker Cohort Study from March 2004 to April 2006 were reviewed, including 680 girls and 582 boys, with a total of 83 participants with elevated ALT level (>40 U/L). Information was obtained from self‐administered questionnaires, anthropometric results and clinical measurements. Associations of interest were examined using multivariate logistic regression models.ResultsA total of 3.8% of girls and 9.8% of boys had elevated ALT levels. Elevated ALT was observed in 28.9% of the obese and 14.2% of the overweight participants. Metabolic syndrome (MS) occurred in 6.1% of the study population and those with MS had a high percentage of elevated ALT (14.5% of girls and 40.0% of boys, respectively). Abdominal obesity and insulin resistance were also associated with a greater risk of elevated ALT.ConclusionsObesity and certain metabolic risk factors are important predictors for elevated ALT. Screening for ALT levels in obese youth could help to identify those at risk and reduce the possibility of future liver diseases.
Perceived pubertal timing and recent substance use among adolescents: a longitudinal perspective
Authors: Cance Jessica Duncan , Ennett Susan T. , Morgan‐Lopez Antonio A. , Foshee Vangie A. , Talley Anna E. 
Published: May 2013

AbstractAimsTo determine the longitudinal associations between perceived pubertal timing and recent substance use between the ages of 11 and 17 years.Design, setting and participantsA school‐based cohort sequential study of adolescents in rural North Carolina, USA (n = 6892, 50% female) in the 6–8th grades at baseline and interviewed across five consecutive semesters.MeasurementsSelf‐administered questionnaires in a group setting measured perceived pubertal development using the Pubertal Development Scale and adolescents reported past 3‐month use of cigarettes, alcohol and marijuana. Latent class growth analysis determined the longitudinal relationships between perceived pubertal timing (early, on‐time and late) and use of the three substances.FindingsA negative quadratic model was the best‐fitting model for all three substances. Higher proportions of early developers had used cigarettes and marijuana within the past 3 months at age 11 compared with on‐time (P < 0.001 and P = 0.013) and late developers (P = 0.010 and P = 0.014) and a higher proportion of early developers had recently used alcohol at age 11 compared with on‐time adolescents (P < 0.001). However, the proportion of recent cigarette and marijuana users increased more across adolescence for on‐time adolescents compared with early developers (P = 0.020 and P = 0.037). Desistance in the proportion of substance users was similar for all adolescents (all P > 0.050).ConclusionsAdolescents who believe they are more advanced in puberty than their peers are more likely to have used cigarettes, alcohol and marijuana recently compared with adolescents who believe they are on‐time or late developing; these findings are mainly due to differences in use at age 11.
Pregnancy outcomes in a cohort of women with a preconception body mass index >50 kg/m2
Authors: Bonnesen Barbara , Secher Niels J. , Møller Lars K. , Rasmussen Steen , Andreasen Kirsten R. , Renault Kristina 
Published: May 2013

AbstractWe describe characteristics and risk factors regarding pregnancy outcome in women with a preconception body mass index (BMI) >50 kg/m2 compared with women with BMI ≤50 kg/m2 in a retrospective population cohort study in singleton pregnancies from the Danish Medical Birth Registry. Results were analyzed as relative risks by a two‐proportion z‐test. Women with preconception BMI >50 kg/m2 smoked, developed gestational diabetes and pre‐eclampsia, and needed induction of labor more frequently than mothers with BMI ≤50 kg/m2. Examination of the case records showed that many attempted vaginal delivery without epidural analgesia, 21% needed an emergency cesarean section (compared with 12% among women with BMI ≤50 kg/m2), and 25% underwent general anesthesia in this context. Many neonates were macrosomic and 34% needed neonatal intensive care and early feeding compared with 6% of neonates from women with BMI ≤50 kg/m2. Women with an extremely high preconception BMI develop more pregnancy complications and their neonates appear affected by this as well.
Long‐term follow‐up of children exposed intrauterine to maternal thiopurine therapy during pregnancy in females with inflammatory bowel disease
Authors: de Meij T. G. J. , Jharap B. , Kneepkens C. M. F. , van Bodegraven A. A. , de Boer N. K. H. ,   The Dutch Initiative on Crohn and Colitis
Published: May 2013

SummaryBackgroundInflammatory bowel disease (IBD) affects a substantial number of female patients in their reproductive years. Therefore, many physicians face the dilemma whether thiopurines, prescribed to maintain remission, can be taken safely during pregnancy. Data on long‐term development outcome of children exposed to maternal thiopurine therapy are very limited.AimTo assess the long‐term effects of in utero exposure to thiopurines during pregnancy on infant health status.MethodsA prospective multicentre follow‐up study was performed in children exposed intrauterine to maternal thiopurine therapy. Physical, cognitive and social aspects of infant health status were assessed with the 43‐item TNO‐AZL Preschool Children Quality of Life Questionnaire (TAPQOL). Furthermore, information on visits to general practitioner and medical specialists, and physician's advice regarding lactation was evaluated. Data were compared with normative data from a control group consisting of 340 children.ResultsThirty children were included in this study [median 3.8 years (IQR 2.9–4.7)]. No differences on global medical and psychosocial health status were found between children exposed to intrauterine thiopurines and the reference group. Exposure to intrauterine thiopurines was not associated with increased susceptibility to infection or immunodeficiency in childhood. Twenty‐one of 30 children were exclusively formula‐fed based on a negative advice of medical specialists directed at thiopurine use during lactation.ConclusionsThiopurine use during pregnancy did not affect long‐term development or immune function of children up to 6 years of age. Our results underscore the present notion that mothers, even those using thiopurines, should be encouraged to breastfeed their infants.