bluuebunny/crossref_metadata_2025_split huggingface dataset:
Duality Theory for Variable Costs in Joint Production
Authors: LaFrance Jeffrey T. , Pope Rulon D. 
Published: March 2010

AbstractDuality methods for incomplete systems of consumer demand equations are adapted to the dual structure of variable cost functions in joint production. This allows identification of necessary and sufficient restrictions on technology and cost so that conditional factor demands can be written as functions of input prices, fixed inputs, and cost. These are observable when variable inputs are chosen and committed to production, hence the identified restrictions allow ex ante conditional demands to be studied using observable data. This class of production technologies is consistent with all von Neumann–Morgenstern utility functions when ex post production and/or output prices are uncertain.
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq
Authors: Johannes Frank , Wardenaar René , Colomé-Tatché Maria , Mousson Florence , de Graaf Petra , Mokry Michal , Guryev Victor , Timmers H.Th. Marc , Cuppen Edwin , Jansen Ritsert C. 
Published: March 2010

AbstractMotivation: ChIP-chip and ChIP-seq technologies provide genome-wide measurements of various types of chromatin marks at an unprecedented resolution. With ChIP samples collected from different tissue types and/or individuals, we can now begin to characterize stochastic or systematic changes in epigenetic patterns during development (intra-individual) or at the population level (inter-individual). This requires statistical methods that permit a simultaneous comparison of multiple ChIP samples on a global as well as locus-specific scale. Current analytical approaches are mainly geared toward single sample investigations, and therefore have limited applicability in this comparative setting. This shortcoming presents a bottleneck in biological interpretations of multiple sample data.Results: To address this limitation, we introduce a parametric classification approach for the simultaneous analysis of two (or more) ChIP samples. We consider several competing models that reflect alternative biological assumptions about the global distribution of the data. Inferences about locus-specific and genome-wide chromatin differences are reached through the estimation of multivariate mixtures. Parameter estimates are obtained using an incremental version of the Expectation–Maximization algorithm (IEM). We demonstrate efficient scalability and application to three very diverse ChIP-chip and ChIP-seq experiments. The proposed approach is evaluated against several published ChIP-chip and ChIP-seq software packages. We recommend its use as a first-pass algorithm to identify candidate regions in the epigenome, possibly followed by some type of second-pass algorithm to fine-tune detected peaks in accordance with biological or technological criteria.Availability: R source code is available at http://gbic.biol.rug.nl/supplementary/2009/ChromatinProfiles/Access to Chip-seq data: GEO repository GSE17937Contact: f.johannes@rug.nlSupplementary information: Supplementary data are available at Bioinformatics online.
Integrative mixture of experts to combine clinical factors and gene markers
Authors: Lê Cao Kim-Anh , Meugnier Emmanuelle , McLachlan Geoffrey J. 
Published: March 2010

AbstractMotivation: Microarrays are being increasingly used in cancer research to better characterize and classify tumors by selecting marker genes. However, as very few of these genes have been validated as predictive biomarkers so far, it is mostly conventional clinical and pathological factors that are being used as prognostic indicators of clinical course. Combining clinical data with gene expression data may add valuable information, but it is a challenging task due to their categorical versus continuous characteristics. We have further developed the mixture of experts (ME) methodology, a promising approach to tackle complex non-linear problems. Several variants are proposed in integrative ME as well as the inclusion of various gene selection methods to select a hybrid signature.Results: We show on three cancer studies that prediction accuracy can be improved when combining both types of variables. Furthermore, the selected genes were found to be of high relevance and can be considered as potential biomarkers for the prognostic selection of cancer therapy.Availability: Integrative ME is implemented in the R package integrativeME (http://cran.r-project.org/).Contact: k.lecao@uq.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
TiSGeD: a database for tissue-specific genes
Authors: Xiao Sheng-Jian , Zhang Chi , Zou Quan , Ji Zhi-Liang 
Published: March 2010

Abstract
Summary: The tissue-specific genes are a group of genes whose function and expression are preferred in one or several tissues/cell types. Identification of these genes helps better understanding of tissue–gene relationship, etiology and discovery of novel tissue-specific drug targets. In this study, a statistical method is introduced to detect tissue-specific genes from more than 123 125 gene expression profiles over 107 human tissues, 67 mouse tissues and 30 rat tissues. As a result, a novel subject-specialized repository, namely the tissue-specific genes database (TiSGeD), is developed to represent the analyzed results. Auxiliary information of tissue-specific genes was also collected from biomedical literatures.
Availability: http://bioinf.xmu.edu.cn/databases/TiSGeD/index.html
Contact: appo@bioinf.xmu.edu.cn; zhiliang.ji@gmail.com
Central venous pressure at emergency room presentation predicts cardiac rehospitalization in patients with decompensated heart failure
Authors: Uthoff Heiko , Thalhammer Christoph , Potocki Mihael , Reichlin Tobias , Noveanu Markus , Aschwanden Markus , Staub Daniel , Arenja Nisha , Socrates Thenral , Twerenbold Raphael , Mutschmann‐Sanchez Sarah , Heinisch Corinna , Jaeger Kurt A. , Mebazaa Alexandre , Mueller Christian 
Published: March 2010

AimsTo investigate the relationship between central venous pressure (CVP) at presentation to the emergency room (ER) and the risk of cardiac rehospitalization and mortality in patients with decompensated heart failure (DHF).Methods and resultsCentral venous pressure was determined non‐invasively using high‐resolution compression sonography at presentation in 100 patients with DHF. Cardiac hospitalizations and cardiac and all‐cause mortality were assessed as a function of continuous CVP levels and predefined CVP categories (low <6 cm H2O, intermediate 6–23 cm H2O, and high >23 cm H2O). Endpoints were adjudicated blinded to CVP. At presentation, mean age was 78 ± 11 years, 60% of patients were male, mean B‐type natriuretic peptide level was 1904 ± 1592 pg/mL, and mean CVP was 13.7 ± 7.0 cm H2O (range 0–33). During follow‐up (median 12 months), 25 cardiac rehospitalizations, 26 cardiac deaths, and 7 non‐cardiac deaths occurred. Univariate and stepwise multivariate Cox regression analysis revealed an independent relationship between CVP and cardiac rehospitalization (HR 1.09, 95% CI 1.01–1.18, P = 0.034). Kaplan–Meier analyses confirmed a stepwise increase in cardiac rehospitalization for low‐to‐high CVP (log‐rank test P = 0.015). No association between CVP and (cardiac) mortality was detectable.ConclusionCentral venous pressure at ER presentation in patients with DHF is an independent predictor of cardiac rehospitalization but not of cardiac and all‐cause mortality.
A tale of CIN—the Cannabis Infringement Notice scheme in Western Australia
Authors: Lenton Simon , Allsop Steve 
Published: March 2010

ABSTRACTAims To describe the development and enactment of the Western Australian (WA) Cannabis Infringement Notice scheme and reflect on the lessons for researchers and policy‐makers interested in the translation of policy research to policy practice.Methods An insiders' description of the background research, knowledge transfer strategies and political and legislative processes leading to the enactment and implementation of the WA Cannabis Control Act 2003. Lenton and Allsop were involved centrally in the process as policy‐researcher and policy‐bureaucrat.Results In March 2004, Western Australia became the fourth Australian jurisdiction to adopt a ‘prohibition with civil penalties’ scheme for possession and cultivation of small amounts of cannabis. We reflect upon: the role of research evidence in the policy process; windows for policy change; disseminating findings when apparently no one is listening; the risks and benefits of the researcher as advocate; the differences between working on the inside and outside of government; and the importance of relationships, trust and track record.Conclusions There was a window of opportunity and change was influenced by research that was communicated by a reliable and trusted source. Those who want to conduct research that informs policy need to understand the policy process more clearly, look for and help create emerging windows that occur in the problem and political spheres, and make partnerships with key stakeholders in the policy arena. The flipside of the process is that, when governments change, policy born in windows of opportunity can be a casualty.
Pharmacodynamic and efficacy studies of the novel proteasome inhibitor NPI‐0052 (marizomib) in a human plasmacytoma xenograft murine model
Authors: Singh Ajita V. , Palladino Michael A. , Lloyd George Kenneth , Potts Barbara C. , Chauhan Dharminder , Anderson Kenneth C. 
Published: March 2010

SummaryOur previous study showed that the novel proteasome inhibitor NPI‐0052 induces apoptosis in multiple myeloma (MM) cells resistant to conventional and bortezomib (Velcade™, Takeda, Boston, MA, USA) therapies. In vivo studies using human MM‐xenografts demonstrated that NPI‐0052 is well tolerated, prolongs survival, and reduces tumour recurrence. These preclinical studies provided the basis for an ongoing phase‐1 clinical trial of NPI‐0052 in relapsed/refractory MM patients. Here we performed pharmacodynamic (PD) studies of NPI‐0052 using human MM xenograft murine model. Our results showed that NPI‐0052: (i) rapidly left the vascular compartment in an active form after intravenous (i.v.) administration, (ii) inhibited 20S proteasome chymotrypsin‐like (CT‐L, β5), trypsin‐like (T‐L, β2), and caspase‐like (C‐L, β1) activities in extra‐vascular tumours, packed whole blood (PWB), lung, liver, spleen, and kidney, but not brain and (iii) triggered a more sustained (>24 h) proteasome inhibition in tumours and PWB than in other organs (<24 h). Tissue distribution analysis of radiolabeled compound (3H‐NPI‐0052) in mice demonstrated that NPI‐0052 left the vascular space and entered organs as the parent compound. Importantly, treatment of MM.1S‐bearing mice with NPI‐0052 showed reduced tumour growth without significant toxicity, which was associated with prolonged inhibition of proteasome activity in tumours and PWB but not normal tissues.
The psychosocial effect of Tai Chi on nursing home residents
Authors: Lee Linda YK , Lee Diana TF , Woo Jean 
Published: March 2010

Aim. To determine the psychosocial effect of Tai Chi on nursing home residents.Background. Moving into a nursing home usually imposes a certain degree of psychosocial challenge to older people. However, there is limited evidence suggesting a promising intervention that can promote the psychosocial health for this group. Although previous studies suggest that Tai Chi has the potential to enhance psychosocial well‐being, existing evidence is deemed scarce and thus imposes a limitation on drawing out conclusions on this matter.Design. Non‐equivalent pretest–posttest control group design.Methods. A convenience sample of 139 residents from six nursing homes in Hong Kong was recruited for this study. The experimental group (n = 66) participated in a 26‐week Tai Chi programme, while the control group (n = 73) continued its normal daily activities. The outcome measures included state self‐esteem, the physical and mental component of health‐related quality of life, social support network and social support satisfaction. Resident satisfaction was identified as a covariate because it demonstrated significant correlation with the outcome variables and, likewise, showed significant difference between the two study groups at baseline. Doubly multivariate analysis of covariance was performed to examine the effect of the intervention.Results. Results indicate significant Group × Time interactions, with the experimental group experiencing significant improvement in the composite outcome of state self‐esteem, the physical component of health‐related quality of life and the mental component of health‐related quality of life across the 26‐week study period [F(6, 131) = 2·61,p = 0·02)]. No significant changes were detected regarding the effect of the Tai Chi programme on social support.Conclusion. Tai Chi practice is beneficial for nursing home residents.Relevance to clinical practice. Tai Chi has unique characteristics that are particularly suitable in the practice of health exercise for nursing home residents. The inclusion of Tai Chi in residential care practice for older people is recommended.
The effects of music on physiological responses and sedation scores in sedated, mechanically ventilated patients
Authors: Dijkstra Boukje M , Gamel Claudia , Van Der Bijl Jaap J , Bots Michiel L , Kesecioglu Jozef 
Published: March 2010

Aims and objectives.  A pilot study designed as future randomised controlled trial was carried out to determine the effects of music on physiological responses and sedation scores in sedated, mechanically ventilated patients.Background.  Mechanically ventilated ICU patients, even when receiving intravenous sedatives, may experience stress and anxiety. One possible intervention to reduce stress and anxiety is listening to music.Design.  A randomised controlled trial design with repeated measures was used.Methods.  Data were collected over a six‐month period in 2006. Twenty subjects were randomly assigned to either the experimental or control group. Subjects in the experimental group listened to music three times for 30 minutes over two days; subjects in the control group undertook three 30 minute rest periods. Physiological effects of music on systolic, diastolic and mean arterial blood pressure and heart and respiratory rate were assessed. Sedation scores were also measured.Results.  Physiological parameters did not show a significant difference between the groups. Patients in the experimental group showed significantly higher Ramsay (sedation) scores than patients in the control group after the first session. The higher scores indicate that patients were less responsive to external stimuli.Conclusion.  Our results suggest that listening to music leads to higher sedation scores in sedated, mechanically ventilated ICU patients. No significant decreases in physiological parameters were observed. Listening to music showed no negative changes in the condition of these patients. Future research should focus on the use of other measures, such as stress hormones, to assess stress in sedated, mechanically ventilated ICU patients.Relevance to clinical practice.  For the sedated, mechanically ventilated ICU patient, the benefit of music may lie in the associated (deeper) level of sedation that is achieved, which in turn may make the patient less susceptible to stress and anxiety.
Effects of music therapy on labour pain and anxiety in Taiwanese first‐time mothers
Authors: Liu Yu‐Hsiang , Chang Mei‐Yueh , Chen Chung‐Hey 
Published: March 2010

Aims.  The purpose of the study was to investigate the effects of music on pain reaction and anxiety during labour.Background.  Music therapy has been used on clinical medicine. Only few scientific studies validate the value on labour women.Design.  Randomised controlled trial.Methods.  Sixty primiparas expected to have a normal spontaneous delivery were randomly assigned to either the experimental group (n = 30) or the control group (n = 30). The experimental group received routine care and music therapy, whereas the control group received routine care only. A self‐report visual analogue scale for pain and a nurse‐rated present behavioural intensity were used to measure labour pain. Anxiety was measured with a visual analogue scale for anxiety and finger temperature. Pain and anxiety between groups were compared during the latent phase (2–4 cm cervical dilation) and active phase (5–7 cm) separately.Results.  Our results revealed that compared with the control group, the experimental group had significantly lower pain, anxiety and a higher finger temperature during the latent phase of labour. However, no significant differences were found between the two groups on all outcome measures during the active phase.Conclusions.  This study provides evidence for the use of music as an empirically based intervention of women for labour pain and anxiety during the latent phase of labour.Relevance to clinical practice.  The findings support that music listening is an acceptable and non‐medical coping strategy for labouring women. Especially, apply in reducing the pain and anxiety for women who are at the early phase of labour.
Interactions of multiple disturbances in shaping boreal forest dynamics: a spatially explicit analysis using multi‐temporal lidar data and high‐resolution imagery
Authors: Vepakomma Udayalakshmi , Kneeshaw Daniel , St‐Onge Benoit 
Published: March 2010

Summary1. Mixed‐wood boreal forests are often considered to undergo directional succession from shade‐intolerant to shade‐tolerant species. It is thus expected that overstorey gaps should lead to the recruitment of shade‐tolerant conifers into the canopy in all stand development stages and that the recruitment of shade‐intolerant hardwoods would be minimal except in the largest gaps.2. We analysed short‐term gap dynamics over a large 6‐km2spatial area of mixed‐wood boreal forest across a gradient of stands in different developmental stages with different times of origin since fire (expressed as stand ‘age’) that were affected differentially by the last spruce budworm (SBW) outbreak. Structural measurements of the canopy from lidar data were combined with spectral classification of broad species groups to characterize the gap disturbance regime and to evaluate the effect of gap openings on forest dynamics.3. Estimated annual gap opening rates increased from 0.16% for 84‐year‐old stands to 0.88% for 248‐year‐old stands. Trees on gap peripheries in all stands were more vulnerable to mortality than interior canopy trees.4. Due to recovery from the last SBW outbreak 16 years previously, gap closure rates were higher than opening rates, ranging from 0.44% to 2.05% annually, but did not show any relationship with stand age. There was, however, a continuing legacy of the last SBW outbreak in old‐conifer stands in terms of a continued high mortality of conifers. In all stands, the majority of the openings were filled from below, although a smaller but significant proportion filled from lateral growth of gap edge trees.5. Synthesis. The forest response to moderate‐ to small‐scale disturbances in old‐growth boreal forest counters the earlier assumption that the transition from one forest state to the next is slow and directional with time since the last fire. Overall, a small 6% increase in hardwoods was observed over 5 years, largely due to regeneration in‐filling of hardwoods in gaps instead of successional transition to more shade‐tolerant conifers. Gaps are vital for hardwood maintenance while transition to softwoods can occur without perceived gap‐formation as overstorey trees die, releasing understorey trees.
Diversity of mitochondrial large subunit rDNA haplotypes of Glomus intraradices in two agricultural field experiments and two semi‐natural grasslands
Authors: BÖRSTLER BORIS , THIÉRY ODILE , SÝKOROVÁ ZUZANA , BERNER ALFRED , REDECKER DIRK 
Published: March 2010

Abstract Glomus intraradices, an arbuscular mycorrhizal fungus (AMF), is frequently found in a surprisingly wide range of ecosystems all over the world. It is used as model organism for AMF and its genome is being sequenced. Despite the ecological importance of AMF, little has been known about their population structure, because no adequate molecular markers have been available. In the present study we analyse for the first time the intraspecific genetic structure of an AMF directly from colonized roots in the field. A recently developed PCR‐RFLP approach for the mitochondrial rRNA large subunit gene (mtLSU) of these obligate symbionts was used and complemented by sequencing and primers specific for a particularly frequent mtLSU haplotype. We analysed root samples from two agricultural field experiments in Switzerland and two semi‐natural grasslands in France and Switzerland. RFLP type composition of G. intraradices (phylogroup GLOM A‐1) differed strongly between agricultural and semi‐natural sites and the G. intraradices populations of the two agricultural sites were significantly differentiated. RFLP type richness was higher in the agricultural sites compared with the grasslands. Detailed sequence analyses which resolved multiple sequence haplotypes within some RFLP types even revealed that there was no overlap of haplotypes among any of the study sites except between the two grasslands. Our results demonstrate a surprisingly high differentiation among semi‐natural and agricultural field sites for G. intraradices. These findings will have major implications on our views of processes of adaptation and specialization in these plant/fungus associations.
Indirect genetic effects in a sex‐limited trait: the case of breeding time in red‐billed gulls
Authors: TEPLITSKY C. , MILLS J. A. , YARRALL J. W. , MERILÄ J. 
Published: March 2010

AbstractFemale reproductive performance can be strongly affected by male care, so that breeding time, a trait expressed only by females, can be seen as one trait determined by both male and female genotypes. Animal model analyses of a 46‐year study of red‐billed gulls (Larus novaehollandiae scopulinus) revealed that laying date was not heritable in females (h2 = 0.001 ± 0.030), but significantly so in males (h2 = 0.134 ± 0.029). Heritability of breeding time in males probably reflects genetic variability in some other trait such as courtship feeding ability. In line with predictions of evolutionary models incorporating indirect genetic effects, the strong and consistent directional selection for advanced breeding time has not resulted in detectable selection response in males. Our results demonstrate that a female trait is largely determined by genetic characteristics of its mate, and hence, any evolutionary change in red‐billed gull breeding time depends critically on genetic variation in males.