bluuebunny/crossref_metadata_2025_split huggingface dataset:
hzar: hybrid zone analysis using an R software package
Authors: Derryberry Elizabeth P. , Derryberry Graham E. , Maley James M. , Brumfield Robb T. 
Published: December 2013

AbstractWe present a new software package (hzar) that provides functions for fitting molecular genetic and morphological data from hybrid zones to classic equilibrium cline models using the Metropolis–Hastings Markov chain Monte Carlo (MCMC) algorithm. The software applies likelihood functions appropriate for different types of data, including diploid and haploid genetic markers and quantitative morphological traits. The modular design allows flexibility in fitting cline models of varying complexity. To facilitate hypothesis testing, an autofit function is included that allows automated model selection from a set of nested cline models. Cline parameter values, such as cline centre and cline width, are estimated and may be compared statistically across clines. The package is written in the R language and is available through the Comprehensive R Archive Network (CRAN;http://cran.r-project.org/). Here, we describehzarand demonstrate its use with a sample data set from a well‐studied hybrid zone in western Panama between white‐collared (Manacus candei) and golden‐collared manakins (M. vitellinus). Comparisons of our results with previously published results for this hybrid zone validate thehzarsoftware. We extend analysis of this hybrid zone by fitting additional models to molecular data where appropriate.
Parentage and sibship inference from markers in polyploids
Authors: Wang Jinliang , Scribner Kim T. 
Published: December 2013

AbstractMany plants and some animal species are polyploids. Nondisomically inherited markers (e.g. microsatellites) in such species cannot be analysed directly by standard population genetics methods developed for diploid species. One solution is to transform the polyploid codominant genotypes to pseudodiploid‐dominant genotypes, which can then be analysed by standard methods for various purposes such as spatial genetic structure, individual relatedness and relationship. Although this data transformation approach has been used repeatedly in the literature, no systematic study has been conducted to investigate how efficient it is, how much marker information is lost and thus how much analysis accuracy is reduced. More specifically, it is unknown whether or not the transformed data can be used to infer parentage and sibship jointly, and how different sampling schemes (number and polymorphism of markers, number of individuals) and ploidy level affect the inference accuracy. This study analyses both simulated and empirical data to examine the effects of polyploid levels, actual pedigree structures and marker number and polymorphism on the accuracy of joint parentage and sibship assignments in polyploid species. We show that sibship, parentage and selfing rates in polyploids can be inferred accurately from a typical set of microsatellite loci. We also show that inferences can be substantially improved by allowing for a small genotyping error rate to accommodate the distortion in assumed Mendelian inheritance of the converted markers when large sibship groups are involved. The results are discussed in the context of polyploid data analysis in molecular ecology.
Content Validation of the Operational Definitions of the Nursing Diagnoses of Activity Intolerance, Excess Fluid Volume, and Decreased Cardiac Output in Patients With Heart Failure
Authors: de Souza Vanessa , Zeitoun Sandra Salloum , Lopes Camila Takao , de Oliveira Ana Paula Dias , Lopes Juliana de Lima , de Barros Alba Lucia Botura Leite 
Published: December 2013

ObjectivesTo consensually validate the operational definitions of the nursing diagnoses activity intolerance, excessive fluid volume, and decreased cardiac output in patients with decompensated heart failure.MethodConsensual validation was performed in two stages: analogy by similarity of defining characteristics, and development of operational definitions and validation with experts.ResultsA total of 38 defining characteristics were found. Operational definitions were developed and content‐validated. One hundred percent of agreement was achieved among the seven experts after five rounds. “Ascites” was added in the nursing diagnosis excessive fluid volume.ConclusionThe consensual validation improves interpretation of human response, grounding the selection of nursing interventions and contributing to improved nursing outcomes.Implications for PracticeSupport the assessment of patients with decompensated heart failure.ObjetivosRealizar a validação consensual das definições operacionais dos diagnósticos de enfermagem Intolerância à atividade, Volume de líquidos excessivo e Débito cardíaco diminuído em pacientes com insuficiência cardíaca descompensada.MétodoValidação consensual em duas etapas: Analogia de semelhança das características definidoras e desenvolvimento de definições operacionais e validação com expertst.ResultadosForam encontradas 38 características definidoras para os diagnósticos de enfermagem. Suas definições operacionais foram desenvolvidas e seu conteúdo validado. Os resultados mostram que houve 100% de concordância entre os sete experts após cinco rodada. As definições operacionais foram classificadas com base no nível de concordânica. “Ascite” foi acrescentada ao diagnóstico Volume de líquidos excessivo.ConclusãoA validação consensual melhora a interpretação das respostas humanas, embasando a seleção de intervenções de enfermagem e contribuindo para melhorar os resultados.Implicações Para A PráticaApoio à avaliação dos pacientes com insuficiência cardíaca descompensada.
Prevalence and Predictors of Maternal Alcohol Consumption in 2 Regions of Ukraine
Authors: Chambers Christina D. , Yevtushok Lyubov , Zymak‐Zakutnya Natalya , Korzhynskyy Yuriy , Ostapchuk Lyubov , Akhmedzhanova Diana , Chan Priscilla H. , Xu Ronghui , Wertelecki Wladimir 
Published: December 2013

BackgroundFetal alcohol spectrum disorders are thought to be a leading cause of developmental disabilities worldwide. However, data are lacking on alcohol use among pregnant women in many countries. The purpose of this study was to evaluate the prevalence and predictors of alcohol consumption by pregnant women in Ukraine.MethodsCross‐sectional screening of pregnant women was conducted in 2 regions of Ukraine during the recruitment phase of an ongoing clinical study that is part of the Collaborative Initiative on Fetal Alcohol Spectrum Disorders. Women attending a routine prenatal visit at 1 of 2 participating regional centers were asked about alcohol consumption. Quantity and frequency of alcoholic beverages consumed in the month around conception and in the most recent month of pregnancy were measured using a standard interview instrument.ResultsBetween 2007 and 2012, 11,909 pregnant women were screened on average in the second trimester of pregnancy. Of these, 92.7% reported being ever‐drinkers. Among ever‐drinkers, 54.8% reported drinking alcohol in the month around conception and 12.9% consumed at least 3 drinks on at least 1 day in that time period. In the most recent month of pregnancy, 46.3% continued to report alcohol use and 9.2% consumed at least 3 drinks per day. Significant predictors of average number of drinks or heavier drinking per day in either time period in pregnancy included lower gravidity, being single, unmarried/living with a partner, or separated, lower maternal education, smoking, younger age at initiation of drinking, and higher score on the TWEAK screening test for harmful drinking.ConclusionsThese findings support the need for education/intervention in women of childbearing age in Ukraine and can help inform targeted interventions for women at risk of an alcohol‐exposed pregnancy. The initiation of a standard screening protocol in pregnancy is a step in the right direction.
Discontinuation of clozapine: a 15‐year naturalistic retrospective study of 320 patients
Authors: Davis M. C. , Fuller M. A. , Strauss M. E. , Konicki P. E. , Jaskiw G. E. 
Published: December 2013

ObjectiveClozapine is underutilized in the management of treatment‐resistant schizophrenia. To understand contributing factors, we analyzed the frequency and causes of clozapine discontinuations that occurred over a 15‐year period in a clinical setting.MethodData were extracted from computerized records and from mandatory termination reports for discontinuation events 1993–2007. The reasons for termination were analyzed.ResultsOver half of the patients (n = 183/320; 57%) had at least one discontinuation (median time 609 days). The two most common causes for discontinuation were non‐adherence (35%) and side‐effects (28%). Hematological side‐effects accounted for 45% of all side‐effect associated discontinuations; most such patients remained eligible for clozapine treatment, and a significant fraction remained on clozapine after rechallenge. Central nervous system side‐effects accounted for 35% of side‐effect induced discontinuations. General factors significantly associated with discontinuation were African American race, older age at initiation of clozapine and less improvement in psychiatric symptoms.ConclusionIn addition to anticipating and addressing causes of non‐adherence, psychiatrists should consider clozapine rechallenge in eligible patients and implement measures to mitigate clozapine‐associated sedation, seizures, and other side‐effects. Future studies should particularly address why African American and older patients may be more likely to discontinue clozapine.
Improving osteoporosis management following minimal trauma fracture in a regional setting: The Coffs Fracture Card Project
Authors: Tulk Cheryl , Lane Pam , Gilbey Anne , Johnston Helena , Chia Karen , Mitchell Lee , Bagga Hanish , Wong Peter K.K. 
Published: December 2013

AbstractObjectivesTo improve osteoporosis (OSP) management following minimal trauma fracture (MTF) with few additional resources.DesignPopulation intervention with serial cross‐sectional analysis.SettingRegional setting involving primary care, base hospital and private hospital.ParticipantsPatients with MTF.InterventionA ‘Fracture Card’ prompting OSP management was provided to all patients post‐MTF. Patients were encouraged to attend their general practitioner (GP) with this to discuss bone health issues. The 2‐year intervention was supported by a public health education campaign.Main outcome measuresNumber of (i) serum 25‐OH vitamin D assays, (ii) dual‐energy X‐ray absorptiometry (DXA) scans, and (iii) new Pharmaceutical Benefits Scheme (PBS)‐subsidised prescriptions for bone protective therapy (bisphosphonates, raloxifene, strontium, teriparatide, denosumab).ResultsThe number of serum 25‐OH vitamin D assays ordered in Coffs Harbour increased from 329 ± 15 per month (July 2009–June 2010) to 568 ± 21 (July 2010–June 2012; P < 0.001). The number of DXA scans performed per month increased from 192 ± 14 (July 2009–June 2010) to 296 ± 12 (July 2010–June 2012; P < 0.001). There was no difference in the number of new PBS‐subsidised prescriptions for bone protective therapy in the Coffs statistical subdivision over that time (176 ± 3.8 per month, July 2009–June 2010 versus 180 ± 3.5, July 2010–June 2012, P > 0.05).ConclusionsThe intervention was associated with an increased number of 25‐OH vitamin D assays and DXA scans but not with more prescriptions for bone protective therapy. This suggests that a public health education campaign and provision of a ‘prompt’ for GPs was only partially successful at improving OSP management post‐MTF. This has driven establishment of a Fracture Liaison Service.
Glycated haemoglobin variations in paediatric type 1 diabetes: the impact of season, gender and age
Authors: Hanberger L , Åkesson K , Samuelsson U 
Published: December 2013

AbstractAimTo study whether monthly variations in type 1 diabetes incidence are related to monthly glycated haemoglobin (HbA1c) levels at diagnosis and if high HbA1c at diagnosis is related to certain clinical variables at diagnosis and during the clinical course of the disease.MethodsData from 4430 boys and 3590 girls registered in the Swedish paediatric diabetes quality registry, Swedish paediatric diabetes quality registry, from 2000 to 2010 were analysed.ResultsMonth of onset varied (p < 0.001), with 53% diagnosed during September to February, and mean HbA1c at diagnosis was highest in May (10.9%, 96 mmol/mol) and lowest in (October 9.4%, 88 mmol/mol) (p < 0.001). Girls showed higher HbA1c at onset than boys (p < 0.001). More than half (53%) with an annual mean HbA1c of >9.3% (78 mmol/mol) and 4% of those with an annual mean of <7.4% (57 mmol/mol) in 2007 had >9.3% (78 mmol/mol) in 2010.ConclusionPatients with high HbA1c levels during a certain period have the same high levels several years later. This group, perhaps including those with high HbA1c level at diagnosis, may need more intensive care, including extra support from the diabetes teams and other forms of medical treatment.
Does tagging improve the navigation of online recorded lectures by students?
Authors: Gorissen Pierre , van Bruggen Jan , Jochems Wim 
Published: December 2013

AbstractStudents more and more have access to online recordings of the lectures they attend at universities. The volume and length of these recorded lectures however make them difficult to navigate. Research shows that students primarily watch the recorded lectures while preparing for their exams. They do watch the full recorded lectures, but review only the parts that are relevant to them. While doing so, they often lack the required mechanisms to locate efficiently those parts of the recorded lecture that they want to view. In this paper, we describe an experiment where expert tagging is used as a means to facilitate the students' search. In the experiment, 255 students had the option to use tags to navigate 18 recorded lectures. We used the data tracked by the lecture capture system to analyze the use of the tags by the students. We compared these data to students who did not use the tagging interface (TI). Results show that the use of the TI increases in time. Students use the TI more actively over time while reducing the amount of video that they view. The experiment also shows that students who use the TI score higher grades when compared with students who use the regular interface.
Radiographic progression by Prostate Cancer Working Group (PCWG)‐2 criteria as an intermediate endpoint for drug development in metastatic castration‐resistant prostate cancer
Authors: Sonpavde Guru , Pond Gregory R. , Armstrong Andrew J. , Galsky Matthew D. , Leopold Lance , Wood Brian A. , Wang Shaw‐Ling , Paolini Jolanda , Chen Isan , Chow‐Maneval Edna , Mooney David J. , Lechuga Mariajose , Smith Matthew R. , Michaelson M. Dror 
Published: December 2013

ObjectiveTo investigate the association of radiographic progression defined by Prostate Cancer Working Group (PCWG)‐2 guidelines and overall survival (OS) in men with metastatic castration‐resistant prostate cancer (mCRPC).Patients and MethodsTwo trials that used PCWG‐2 guidelines to define progression were analysed: a randomized phase II trial (n = 221) comparing first‐line docetaxel‐prednisone plus AT‐101 or placebo, and a phase III trial (n = 873) comparing prednisone plus sunitinib or placebo after docetaxel‐based chemotherapy. Cox proportional hazards regression models were used to estimate the association of radiographic progression with OS. Landmark analyses compared progressing patients with those who had not progressed. Sub‐analyses compared patients removed from trial for progression vs other reasons.ResultsAn increased risk of death was seen for radiographic progression at landmark times from 6 to 12 months with docetaxel‐based therapy (hazard ratio [HR] >1.7 at all time‐points). An increased risk of death was also seen with post‐docetaxel prednisone alone or with sunitinib for progression at landmark times from 2 to 8 months (HR >2.7 at all time‐points). Kendall's τ was 0.50 (P < 0.001) in the setting of docetaxel‐based therapy and 0.34 (P < 0.001) in the post‐docetaxel setting for association between radiographic progression and death amongst patients with both events. Removal from study due to radiographic progression was associated with a significantly lower OS compared with removal for other reasons in both trials. Limitations of a retrospective analysis apply and there was no central radiology review.ConclusionsRadiographic progression by PCWG‐2 criteria was significantly associated with OS in patients with mCRPC receiving first‐line docetaxel‐based chemotherapy or post‐docetaxel therapy. With external validation as a surrogate endpoint in trials showing survival benefits, the use of radiographic progression‐free survival may expedite drug development in mCRPC, which has been hampered by the lack of intermediate endpoints.
Tissue engineering of diseased bladder using a collagen scaffold in a bladder exstrophy model
Authors: Roelofs Luc A.J. , Kortmann Barbara B.M. , Oosterwijk Egbert , Eggink Alex J. , Tiemessen Dorien M. , Crevels A. Jane , Wijnen Rene M.H. , Daamen Willeke F. , van Kuppevelt Toin H. , Geutjes Paul J. , Feitz Wout F.J. 
Published: December 2013

ObjectiveTo compare the regenerative capacity of diseased bladder in a large animal model of bladder exstrophy with regeneration in healthy bladder using a highly porous collagen scaffold.Materials and MethodsHighly porous bovine typeIcollagen scaffolds with a diameter of 32 mm were prepared. In 12 fetal sheep a bladder exstrophy was surgically created at 79 days’ gestation. Lambs were born at full term (140 days’ gestation). After 1 week the bladder lesion was reconstructed and augmented with a collagen scaffold (group 1). In nine normal newborn lambs the bladder was augmented with a collagen scaffold 1 week after birth (group 2). Functional (video‐urodynamics) and histological evaluation was performed at 1 and 6 months after surgery.ResultsThe survival rate was 58% in group 1 and 100% in group 2. Cystograms were normal in all lambs, besides low‐grade reflux in both groups. Urodynamics showed comparable capacity between both groups and a trend to lower compliance in group 1. Histological evaluation at 1 month revealed a non‐confluent urothelial layer, an immature submucosa, and initial ingrowth of smooth muscle cells. At 6 months both groups showed normal urothelial lining, standard extracellular matrix development, and smooth muscle cell ingrowth.ConclusionsBladder tissue regeneration with a collagen scaffold in a diseased bladder model and in healthy bladder resulted in comparable functional and histological outcome, with a good quality of regenerated tissue involving all tissue layers. Improvements may still be needed for larger augmentations or more severely diseased bladders.
T cells from chronic bone infection show reduced proliferation and a high proportion of CD28− CD4 T cells
Authors: Kumar G , Roger P-M , Ticchioni M , Trojani C , Bernard de Dompsur R , Bronsard N , Carles M , Bernard E 
Published: December 2013

SummaryChronic bone infection is associated with bone resorption. From animal studies, CD3/CD28-activated T cells are known to enhance osteoclastogenesis and bone resorption. Because CD28 is expressed constitutively on T cells and its expression is down-regulated by chronic exposure to the inflammatory environment, we characterized co-stimulatory molecule expression on T cells from chronically infected patients. We used cytofluorometric techniques to phenotypically characterize T cells, its co-stimulatory molecules and perforin secretion from infected and non-infected human bones. Chronic bone infection was defined as infection lasting for more than a month. We show a higher T cell activation [human leucocyte antigen D-related (HLA-DR+)] in infected compared to non-infected bones: median being 16 versus 7%, P = 0·009 for CD4 T cells, and 33 versus 15%, P = 0·038 for CD8 T cells, respectively. However, T cell proliferation (Ki67+) was lower for CD8 T cells in infected bones: 26 versus 34%, P = 0·045. In contrast, we detected no difference in apoptosis and regulatory T cells. In infected bone, we found higher CD28-negative CD4+ T cells compared to non-infected bone: 20 versus 8%, respectively (P = 0·005); this T cell subset had higher CD11b expression and perforin secretion. Chronically infected human bones are characterized by an increase of CD28-negative CD4+ T cells, indicating long-term activated cells with cytotoxic ability. Therefore, this alteration of co-stimulatory molecules may modify interactions with osteoclasts and impact bone resorption.
Effects of titanium brush on machined and sand‐blasted/acid‐etched titanium disc using confocal microscopy and contact profilometry
Authors: Park Jun‐Beom , Jeon Yongpyo , Ko Youngkyung 
Published: December 2013

AbstractObjectiveMechanical techniques, including scaling with metal, plastic, or ultrasonic instruments, rubber cup polishing, air‐powder abrasive system and brushing with a conventional or a rotating brush, have been used for the debridement of dental implants. Recently, rotating brushes with titanium bristles (titanium brush) have been introduced for the debridement of implant surface when peri‐implant osseous defects occur. The purpose of this study was to evaluate the effects of a titanium brush on machined (MA) and sand‐blasted and acid‐etched (SA) titanium surfaces using scanning electron microscopy, confocal microscopy and profilometry. Moreover, correlations between the two quantitative evaluation methods (confocal microscopy and contact profilometry) were assessed.Materials and MethodsBothMAandSAdiscs were treated with rotating titanium brush at 300 rpm under irrigation for a total of 40 s. Roughness measurements were taken with confocal microscopy and surface profilometry. Then, theMAandSAsurfaces were evaluated using scanning electron microscopy to determine the changes of the surface properties.ResultsUntreatedMAsurface demonstrated uniform roughness with circumferential machining marks, and scratch lines over the original surfaces were observed after treatment with the titanium brush. Similarly, the titanium brush produced noticeable changes on theSAtitanium surfaces. However, this treatment with titanium brush did not significantly change the roughness parameters, including the arithmetic mean height of the surface (Sa) and the maximum height of the surface (Sz), in bothMAandSAsurfaces. Correlations between two evaluation methods showed a Pearson correlation coefficient of 0.98 with linear regressionR2of 0.96.ConclusionThis study showed that the treatment with the titanium brush did not significantly change the roughness parameters, including Sa and Sz, in bothMAandSAsurfaces. Correlations between confocal microscopy and surface profilometry showed high correlation with a Pearson correlation coefficient of 0.98.