903 resultados para Scoring
Resumo:
Transcriptional regulation has been studied intensively in recent decades. One important aspect of this regulation is the interaction between regulatory proteins, such as transcription factors (TF) and nucleosomes, and the genome. Different high-throughput techniques have been invented to map these interactions genome-wide, including ChIP-based methods (ChIP-chip, ChIP-seq, etc.), nuclease digestion methods (DNase-seq, MNase-seq, etc.), and others. However, a single experimental technique often only provides partial and noisy information about the whole picture of protein-DNA interactions. Therefore, the overarching goal of this dissertation is to provide computational developments for jointly modeling different experimental datasets to achieve a holistic inference on the protein-DNA interaction landscape.
We first present a computational framework that can incorporate the protein binding information in MNase-seq data into a thermodynamic model of protein-DNA interaction. We use a correlation-based objective function to model the MNase-seq data and a Markov chain Monte Carlo method to maximize the function. Our results show that the inferred protein-DNA interaction landscape is concordant with the MNase-seq data and provides a mechanistic explanation for the experimentally collected MNase-seq fragments. Our framework is flexible and can easily incorporate other data sources. To demonstrate this flexibility, we use prior distributions to integrate experimentally measured protein concentrations.
We also study the ability of DNase-seq data to position nucleosomes. Traditionally, DNase-seq has only been widely used to identify DNase hypersensitive sites, which tend to be open chromatin regulatory regions devoid of nucleosomes. We reveal for the first time that DNase-seq datasets also contain substantial information about nucleosome translational positioning, and that existing DNase-seq data can be used to infer nucleosome positions with high accuracy. We develop a Bayes-factor-based nucleosome scoring method to position nucleosomes using DNase-seq data. Our approach utilizes several effective strategies to extract nucleosome positioning signals from the noisy DNase-seq data, including jointly modeling data points across the nucleosome body and explicitly modeling the quadratic and oscillatory DNase I digestion pattern on nucleosomes. We show that our DNase-seq-based nucleosome map is highly consistent with previous high-resolution maps. We also show that the oscillatory DNase I digestion pattern is useful in revealing the nucleosome rotational context around TF binding sites.
Finally, we present a state-space model (SSM) for jointly modeling different kinds of genomic data to provide an accurate view of the protein-DNA interaction landscape. We also provide an efficient expectation-maximization algorithm to learn model parameters from data. We first show in simulation studies that the SSM can effectively recover underlying true protein binding configurations. We then apply the SSM to model real genomic data (both DNase-seq and MNase-seq data). Through incrementally increasing the types of genomic data in the SSM, we show that different data types can contribute complementary information for the inference of protein binding landscape and that the most accurate inference comes from modeling all available datasets.
This dissertation provides a foundation for future research by taking a step toward the genome-wide inference of protein-DNA interaction landscape through data integration.
Resumo:
The degree of development and operability of the indicators for the Marine Strategy Framework Directive (MSFD) using Descriptor 1 (D1) Biological Diversity was assessed. To this end, an overview of the relevance and degree of operability of the underlying parameters across 20 European countries was compiled by analysing national directives, legislation, regulations, and publicly available reports. Marked differences were found between countries in the degree of ecological relevance as well as in the degree of implementation and operability of the parameters chosen to indicate biological diversity. The best scoring EU countries were France, Germany, Greece and Spain, while the worst scoring countries were Italy and Slovenia. No country achieved maximum scores for the implementation of MSFD D1. The non-EU countries Norway and Turkey score as highly as the top-scoring EU countries. On the positive side, the chosen parameters for D1 indicators were generally identified as being an ecologically relevant reflection of Biological Diversity. On the negative side however, less than half of the chosen parameters are currently operational. It appears that at a pan-European level, no consistent and harmonized approach currently exists for the description and assessment of marine biological diversity. The implementation of the MSFD Descriptor 1 for Europe as a whole can therefore at best be marked as moderately successful.
Resumo:
Aquaculture is currently the fastest expanding global animal food production sector and is a key future contributor to food security. An increase in food security will be dependent upon the development and improvement of sustainable practices. A prioritization exercise was undertaken, focusing on the future knowledge needs to underpin UK sustainable aquaculture (both domestic and imported products) using a ‘task force’ group of 36 ‘practitioners’ and 12 ‘research scientists’ who have an active interest in sustainable aquaculture. A long list of 264 knowledge needs related to sustainable aquaculture was developed in conjunction with the task force. The long list was further refined through a three stage process of voting and scoring, including discussions of each knowledge need. The top 25 knowledge needs are presented, as scored separately by ‘practitioners’ or ‘research scientists’. There was similar agreement in priorities identified by these two groups. The priority knowledge needs will provide guidance to structure ongoing work to make science accessible to practitioners and help to prioritize future science policy needs and funding. The process of knowledge exchange, and the mechanisms by which this can be achieved, effectively emerged as the top priority for sustainable aquaculture. Viable alternatives to wild fish-based aquaculture feeds, resource constraints that will potentially limit expansion of aquaculture, sustainable offshore aquaculture and the treatment of sea lice also emerged as strong priorities. Although the exercise was focused on UK needs for sustainable aquaculture, many of the emergent issues are considered to have global application.
Resumo:
Antecedentes. Pes Adulto planus (pie plano) es un problema común encontrado por muchos profesionales de la salud. A pesar de la percepción de que el pie plano puede causar dolor y deteriorar su función, la disponibilidad y el uso generalizado de diversos tratamientos, no hay consenso sobre la estrategia óptima de tratamiento. Objetivo. Evaluar la efectividad de las intervenciones conservadoras (no quirúrgicos) para pie plano en los adultos. Método. Se realizó una búsqueda sistemática de la literatura. Esto incluye: el Registro Cochrane Central de Ensayos Controlados; los Juicios CMSG Especializados Registro; una búsqueda electrónica se realizó utilizando MEDLINE (1960 a junio de 2012), EMBASE (1980 a junio de 2012), y CINAHL (1982 - junio de 2012). Revistas especializadas, listas de referencias de ensayos y artículos de revisión se realizaron búsquedas manuales. Criterios de selección: Ensayos aleatorios o cuasialeatorios de intervenciones de tratamiento para el pie plano en los adultos. Se excluyeron los ensayos que incluyeron patologías específicas como el dolor plantar del talón, las fracturas por sobrecarga de los metatarsianos, disfunción del tendón tibial posterior-, fracturas de tobillo, patologías del pie reumatoide, enfermedades neuromusculares y las complicaciones del pie diabético. Recopilación y análisis de datos: Dos autores seleccionaron de forma independiente los resultados de la búsqueda para identificar a aquellos que satisfacen los criterios de inclusión y evaluaron la calidad de los incluidos mediante una lista de control basado en la Evaluación de la Colaboración Cochrane de Riesgo. Esta herramienta se centró en el riesgo de la selección, el rendimiento, la detección, la heterogeneidad y el sesgo de notificación. Resultados. Cuatro ensayos, con 140 sujetos, cumplieron los criterios de inclusión para la revisión. Los cuatro fueron juzgados como de alto riesgo de sesgo en al menos un área, y también estaban en riesgo de sesgo incierto en al menos otra zona. Todos anotaron altamente en relación al sesgo de deserción, debido al corto seguimiento tiempos y diseños experimentales utilizados. Los datos no se agruparon debido al alto nivel de heterogeneidad identificada en las intervenciones evaluadas, los participantes seleccionados y medir los resultados. Los resultados de un estudio sugieren que después de cuatro semanas de uso ortesis puede resultar en una mejora significativa en vaivén lateral medio, y pueden resultar en una mejor, aunque no significativa, en general relacionados con la calidad de vida de los pies (Roma 2004). Un estudio (Redmond 2009) sugiere que su efecto sobre la distribución de la presión plantar en el pie puede no depender de si son personalizados o dispositivos prefabricados. Aunque este estudio se identificaron cambios significativos en algunas variables de presión plantar tanto con la costumbre y dispositivos prefabricados, otro (Esterman 2005) no encontró ningún efecto significativo de longitud ¾ ortesis prefabricadas sobre el dolor, la incidencia de lesiones, salud pie o de calidad de vida en un grupo de reclutas de la fuerza aérea. El cuarto estudio (Jung 2009) sugiere que el ejercicio de los músculos intrínsecos del pie puede mejorar el efecto de las ortesis. A pesar de estos resultados, ya que cada estudio incurrió riesgo de sesgo en al menos un área no se pueden sacar conclusiones
Resumo:
An innovative bioadhesive patch intended primarily as a vulval drug delivery system and, specifically, as a means to deliver photosensitisers, or their prodrugs, for photodynamic purposes is described. The patch was formulated with a copolymer of methyl vinyl ether and maleic anhydride (PMVE/MA) as a bioadhesive matrix and poly(vinyl chloride) as a drug-impervious backing layer. Adhesive strength to neonate porcine skin, as a model substrate, was evaluated using peel and tensile testing measurements. Acceptabilities of non-drug loaded patches were appraised using human volunteers and visual-analogue scoring devices. An optimal formulation, with water uptake and peel strengths appropriate for vulval drug delivery, was cast from a 20% (w/w) PMVE/MA solution and adhered with a strength of approximately 1.7 N cm-2. Patient evaluation demonstrated comfort and firm attachment for up to 4 h in mobile patients. Aminolevulinic acid, a commonly used photosensitiser, was formulated into the candidate formulation and applied to vulval intraepithelial neoplastic lesions. Fluorescence under ultraviolet illumination revealed protoporphyrin synthesis. The patch achieves the extended application times obligatory in topical photodynamic therapy of vulval lesions, thereby contributing to potential methods for the eradication of neoplastic lesions in the lower female reproductive tract.
Resumo:
We present a new way of extracting policy positions from political texts that treats texts not as discourses to be understood and interpreted but rather, as data in the form of words. We compare this approach to previous methods of text analysis and use it to replicate published estimates of the policy positions of political parties in Britain and Ireland, on both economic and social policy dimensions. We “export” the method to a non-English-language environment, analyzing the policy positions of German parties, including the PDS as it entered the former West German party system. Finally, we extend its application beyond the analysis of party manifestos, to the estimation of political positions from legislative speeches. Our “language-blind” word scoring technique successfully replicates published policy estimates without the substantial costs of time and labor that these require. Furthermore, unlike in any previous method for extracting policy positions from political texts, we provide uncertainty measures for our estimates, allowing analysts to make informed judgments of the extent to which differences between two estimated policy positions can be viewed as significant or merely as products of measurement error.
Resumo:
The histological grading of cervical intraepithelial neoplasia (CIN) remains subjective, resulting in inter- and intra-observer variation and poor reproducibility in the grading of cervical lesions. This study has attempted to develop an objective grading system using automated machine vision. The architectural features of cervical squamous epithelium are quantitatively analysed using a combination of computerized digital image processing and Delaunay triangulation analysis; 230 images digitally captured from cases previously classified by a gynaecological pathologist included normal cervical squamous epithelium (n = 30), koilocytosis (n = 46), CIN 1 (n = 52), CIN 2 (n = 56), and CIN 3 (n=46). Intra- and inter-observer variation had kappa values of 0.502 and 0.415, respectively. A machine vision system was developed in KS400 macro programming language to segment and mark the centres of all nuclei within the epithelium. By object-oriented analysis of image components, the positional information of nuclei was used to construct a Delaunay triangulation mesh. Each mesh was analysed to compute triangle dimensions including the mean triangle area, the mean triangle edge length, and the number of triangles per unit area, giving an individual quantitative profile of measurements for each case. Discriminant analysis of the geometric data revealed the significant discriminatory variables from which a classification score was derived. The scoring system distinguished between normal and CIN 3 in 98.7% of cases and between koilocytosis and CIN 1 in 76.5% of cases, but only 62.3% of the CIN cases were classified into the correct group, with the CIN 2 group showing the highest rate of misclassification. Graphical plots of triangulation data demonstrated the continuum of morphological change from normal squamous epithelium to the highest grade of CIN, with overlapping of the groups originally defined by the pathologists. This study shows that automated location of nuclei in cervical biopsies using computerized image analysis is possible. Analysis of positional information enables quantitative evaluation of architectural features in CIN using Delaunay triangulation meshes, which is effective in the objective classification of CIN. This demonstrates the future potential of automated machine vision systems in diagnostic histopathology. Copyright (C) 2000 John Wiley and Sons, Ltd.
Resumo:
The impetus towards basing practice and policy decisions more explicitly on sound research requires tools to facilitate the systematic appraisal of the quality of research encompassing a diverse range of methods and designs. Five exemplar tools were developed and assessed in terms of their usefulness in selecting studies for inclusion in a systematic review. The widely used ‘hierarchy of evidence’ was adapted and used to appraise internal validity. Four tools were then developed to appraise the external validity dimensions of generalizability (two scales) and methods of data collection (two scales). Methods of combining the scores generated by each tool were explored. Qualitative and quantitative studies were appraised, not separated into two spheres but by using complementary tools developed to appraise different aspects of rigour. There was a high level of agreement between researchers in applying the tools to twenty-two studies on decision making by professionals about the longterm care of older people. The scales for internal validity and generalizability discriminated between the qualities of studies appropriately. The two tools to appraise data collection gave diverse results. Excluding studies that scored in the lowest category on any scale appeared to be the scoring system that was most justifiable. This approach is presented to stimulate debate about the practical application of the evidence-based initiative to social work and social care. This study may assist in developing clearer definitions and common language about appraising rigour that should further the process of selecting robust research for synthesis to inform practice and policy decisions.
Resumo:
PURPOSE. To examine internal consistency, refine the response scale, and obtain a linear scoring system for the visual function instrument, the Daily Living Tasks Dependent on Vision (DLTV). METHODS. Data were available from 186 participants with a clinical diagnosis of AMD who completed the 22-item DLTV (DLTV-22) according to four-point ordinal response scale. An independent group of 386 participants with AMD were administered a reduced version of the DLTV with 11 items (DLTV-11), according to a five-point response scale. Rasch analysis was performed on both datasets and used to generate item statistics for measure order, response odds ratios per item and per person, and infit and outfit mean square statistics. The Rasch output from the DLTV-22 was examined to identify redundant items and for factorial validity and person item measure separation reliabilities. RESULTS. The average rating for the DLTV-22 changed monotonically with the magnitude of the latent person trait. The expected versus observed average measures were extremely close, with step calibrations evenly separated for the four-point ordinal scale. In the case of the DLTV-11, step calibrations were not as evenly separated, suggesting that the five-point scale should be reduced to either a four- or three-point scale. Five items in the DLTV-22 were removed, and all 17 remaining items had good infit and outfit mean squares. PCA with residuals from Rasch analysis identified two domains containing 7 and 10 items each. The domains had high person separation reliabilities (0.86 and 0.77 for domains 1 and 2, respectively) and item measure reliabilities (0.99 and 0.98 for domains 1 and 2, respectively). CONCLUSIONS. With the improved internal consistency, establishment of the accuracy and precision of the rating scale for the DLTV and the establishment of a valid domain structure we believe that it constitutes a useful instrument for assessing visual function in older adults with age-related macular degeneration.
Resumo:
Background
Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties by gene expression profile. Lamb et al first proposed the Connectivity Map [Lamb et al (2006), Science 313, 1929–1935] to make successful connections among small molecules, genes, and diseases using genomic signatures.
Results
Here we have built on the principles of the Connectivity Map to present a simpler and more robust method for the construction of reference gene-expression profiles and for the connection scoring scheme, which importantly allows the valuation of statistical significance of all the connections observed. We tested the new method with two randomly generated gene signatures and three experimentally derived gene signatures (for HDAC inhibitors, estrogens, and immunosuppressive drugs, respectively). Our testing with this method indicates that it achieves a higher level of specificity and sensitivity and so advances the original method.
Conclusion
The method presented here not only offers more principled statistical procedures for testing connections, but more importantly it provides effective safeguard against false connections at the same time achieving increased sensitivity. With its robust performance, the method has potential use in the drug development pipeline for the early recognition of pharmacological and toxicological properties in chemicals and new drug candidates, and also more broadly in other 'omics sciences.
Resumo:
The role of rhodopsin as a structural prototype for the study of the whole superfamily of G protein-coupled receptors (GPCRs) is reviewed in an historical perspective. Discovered at the end of the nineteenth century, fully sequenced since the early 1980s, and with direct three-dimensional information available since the 1990s, rhodopsin has served as a platform to gather indirect information on the structure of the other superfamily members. Recent breakthroughs have elicited the solution of the structures of additional receptors, namely the beta 1- and beta 2-adrenergic receptors and the A(2A) adenosine receptor, now providing an opportunity to gauge the accuracy of homology modeling and molecular docking techniques and to perfect the computational protocol. Notably, in coordination with the solution of the structure of the A(2A) adenosine receptor, the first "critical assessment of GPCR structural modeling and docking" has been organized, the results of which highlighted that the construction of accurate models, although challenging, is certainly achievable. The docking of the ligands and the scoring of the poses clearly emerged as the most difficult components. A further goal in the field is certainly to derive the structure of receptors in their signaling state, possibly in complex with agonists. These advances, coupled with the introduction of more sophisticated modeling algorithms and the increase in computer power, raise the expectation for a substantial boost of the robustness and accuracy of computer-aided drug discovery techniques in the coming years.
Resumo:
Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered.
Psychological and social profile of family caregivers upon commencement of palliative care provision
Resumo:
Context
Palliative care services are required to support patients who have advanced, life-threatening, noncurable disease, and their family caregivers. Comprehensive psychological and social support for bereaved family members also is expected. However, recent systematic reviews have demonstrated significant gaps in evidence-based approaches for such support. Furthermore, a comprehensive understanding of the psychological and social response to the family caregiver role is required for support to be optimized.
Objectives
We sought to examine the psychological and social profile of family caregivers on commencement of receiving palliative care services.
Methods
A self-report questionnaire was administered to primary family caregivers of patients within two weeks of admission to three palliative care services in Melbourne, Australia. The questionnaire incorporated six instruments that measured 11 family caregiver-related psychosocial factors; four instruments that measured caregiver psychological distress factors; 14 mental health lifetime risk factors; and a sociodemographic questionnaire.
Results
Three hundred and two family caregivers participated. Nearly half (44%) of the caregivers had a probable anxiety and/or depressive disorder, with 40% scoring more than the cutoff score for probable anxiety and 20% scoring more than the cutoff score for probable depression. Additionally, approximately 15% of caregivers met the criteria for pre-loss grief, and around 10% reported moderate to severe levels of demoralization. Caregivers who had a probable anxiety and/or depressive disorder also reported higher levels of pre-loss grief.
Conclusion
This study provides further evidence of the prevalence of poor psychosocial well-being in this population. The results reinforce the need to develop suitable strategies for psychological and social support for family caregivers.
Resumo:
Twenty-four shed-reared lambs were each infected orally with 250 metacercariae of Fasciola hepatica, using either the triclabendazole (TCBZ)-sensitive Cullompton isolate or the TCBZ-resistant Sligo isolate. Twelve weeks after infection the lambs were treated with TCBZ (10 mg/kg) or with the experimental fasciolicide, Compound Alpha (Cpd alpha), a benzimidazole derivative of TCBZ (15 mg/kg). The lambs were euthanised 48,72 and 96 h after TCBZ treatment, or 24, 48 and 72 h after Cpd a treatment, and flukes were collected from the liver and/or gall bladder of each animal. Untreated animals harbouring 12-week infections were euthanised 24 h after administration of anthelmintic to the treatment groups, and the untreated flukes provided control material. A semi-quantitative assessment of the degree of histological change induced by the two drugs after different times of exposure was achieved by scoring the intensity of three well-defined lesions that developed in the testes and uteri of a representative sample of flukes from each lamb. In general, it was found that in those tissues where active meiosis and/or mitosis occurred (testis, ovary, and vitelline follicles), there was progressive loss of cell content due to apparent failure of cell division to keep pace with expulsion of the mature or effete products. Further, actively dividing cell types tended to become individualised, rounded and condensed, characteristic of apoptotic cell death. Protein synthetic activity was apparently inhibited in the Mehlis' secretory cells. In the uterus, where successful formation of shelled eggs represents the culmination of a complex sequence of cytokinetic, cytological and synthetic activity involving the vitelline follicles, the ovary and the Mehlis' gland, histological evidence indicating failure of ovigenesis was evident from 24 h post-treatment onwards. The development of these lesions may be related to the known antitubulin activity of the benzimidazole class of anthelmintics, to the induction of apoptosis in cells where mitosis or meiosis has aborted due to failure of spindle formation, and to drug-induced inhibition of protein synthesis. The semi-quantitative findings indicated that Cpd a is slightly less efficacious than TCBZ itself in causing histological damage to the reproductive structures of TCBZ-sensitive flukes, and that, like TCBZ, it caused no histological damage in flukes of the TCBZ-resistant isolate. This study illustrates the potential utility of histological techniques for conveniently screening representative samples of flukes in field trials designed to validate instances of drug resistance or to test the efficacy of new products against known drug-resistant and drug-susceptible fluke isolates. It also provides reference criteria for drug-induced histopathological changes in fluke reproductive structures which may aid interpretation of TEM findings. (C) 2009 Elsevier B.V. All rights reserved.
Resumo:
Objectives
To evaluate how involvement in life situations (participation) in children with cerebral palsy varies with type and severity of impairment and to investigate geographical variation in participation.
Design
Cross sectional study. Trained interviewers visited parents of children with cerebral palsy; multilevel multivariable regression related participation to impairments, pain, and sociodemographic characteristics.
Setting
Eight European regions with population registers of children with cerebral palsy; one further region recruited children from multiple sources.
Participants
1174 children aged 8-12 with cerebral palsy randomly selected from the population registers, 743 (63%) joined in the study; the further region recruited 75 children.
Main outcome measure
Children’s participation assessed by the Life-H questionnaire covering 10 main areas of daily life. Scoring ignored adaptations or assistance required for participation.
Results
Children with pain and those with more severely impaired walking, fine motor skills, communication, and intellectual abilities had lower participation across most domains. Type of cerebral palsy and problems with feeding and vision were associated with lower participation for specific domains, but the sociodemographic factors examined were not. Impairment and pain accounted for up to a sixth of the variation in participation. Participation on all domains varied substantially between regions: children in east Denmark had consistently higher participation than children in other regions. For most participation domains, about a third of the unexplained variation could be ascribed to variation between regions and about two thirds to variation between individuals.
Conclusions
Participation in children with cerebral palsy should be assessed in clinical practice to guide intervention and assess its effect. Pain should be carefully assessed. Some European countries facilitate participation better than others, implying some countries could make better provision. Legislation and regulation should be directed to ensuring this happens.