bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypohidrotic Ectodermal Dysplasia in Two Siblings with Missing Teeth: A Dental Perspective
Authors: Khurana Pankaj , Singhal Kamal Kumar 
Published: January 2014

ABSTRACT
Hereditary ectodermal dysplasia (ED) is a rare inherited disorder involving skin, hair, nails, sweat glands and teeth. Different combination of defects may give rise to variable phenotypes. ED is divided into two common types depending whether sweat glands are involved: hypohidrotic form and hidrotic form.
Hypohidrotic ED in two brothers aged 12 and 9 years is being reported. The importance of early prosthetic management in restoring function, esthetics and facilitating social interaction has been discussed.

How to cite this article
Khurana P, Talwar M, Singhal KK. Hypohidrotic Ectodermal Dysplasia in Two Siblings with Missing Teeth: A Dental Perspective. Int J Experiment Dent Sci 2013; 2(2):130-133.
Designing and Evaluation of Skin Extract Agar for Isolation of Microflora from Raw Buffalo Hide
Authors: Polkade Ashish , Shede Prafulla , Kanekar Pradhnya , Dhakephalkar Prashant , Sarnaik Seema 
Published: January 2014

Abstract Present study was aimed to design nutrient medium most suitable for isolation and enumeration of microbial flora associated with raw buffalo hide. Skin extract agar (SEA) was designed and standardized on the basis of its chemical analysis. SEA and nutrient medium supplemented with skin extract was inoculated with buffalo hide wash. Total viable count as well as diversity of microbial colonies were enumerated on SEA as well as on nutrient agar and standard plate count agar both supplemented with skin extract (1% v/v). Bacterial strains forming diverse types of colonies on the media tested were identified on the basis of their 16S rRNA gene sequences. The SEA was found to yield higher number of bacteria and to support growth of Acinetobacter, Exiguobacterium and Stenotrophomonas which otherwise difficult to selectively isolate from buffalo hide using nutrient agar and standard plate count agar. Diversity of microbial colonies formed on SEA was significantly higher than that observed on nutrient agar or standard plate count agar. Feasibility of utilizing SEA as a microbiological medium for isolation and identification of microflora from raw buffalo hide was successfully demonstrated. Use of skin extract medium can maximize recovery of taxonomically distinct bacteria from raw buffalo hide. This basic study, with proper manipulations could lead to development of product for enumeration and isolation of bacteria from buffalo hides especially cattle pathogens related to skin diseases.
Mechanical Aesthetics:
Authors: Mackintosh Will B. 
Published: January 2014

Abstract
In the 1830s, Pennsylvania's Main Line of Public Works was at the cutting edge of the transportation revolution. Travelers embraced the speed and convenience of the line, but struggled to articulate the aesthetic experience of new forms of travel. This article uses the narratives of John Alonzo Clark, a Philadelphia minister, to explore the ways in which Pennsylvania travelers applied existing categories of the beautiful, the sublime, and the picturesque to innovative technological experiences. Clark and travelers like him found that mechanized transportation on the Main Line of Public Works heightened their experience of the landscape and distilled the older categories to their essence. Far from perceiving a tension between modern technology and landscape appreciation, these travelers found that together the two created novel and pleasurable aesthetic experiences.
Avaliação da eficácia de uma atividade educativopreventiva com pré-escolares: estudo piloto de um ensaio clínico randomizado
Authors: Barreto Débora Magalhães , Paiva Saul Martins , Jorge Maria Letícia Ramos- , Ferreira Meire Coelho 
Published: January 2014

Objetivo: Avaliar a eficácia de uma atividade educativo-preventiva em saúde bucal com pré-escolares. Materiais e Métodos: Trinta e oito crianças, entre 3 e 5 anos, foram, aleatoriamente, designadas para um dos dois grupos: experimental (E) e controle (C). Índice de placa visível inicial (IPV inicial), de sangramento gengival inicial (ISG inicial), e ceo-d foram determinados, e um questionário foi preenchido pelos pais. As crianças do grupo E participaram de atividade educativo-preventiva (AEP) e as do grupo C não participaramde AEP. A AEP contemplou educação em saúde bucal e escovação supervisionada. Os desfechos índice de placa visível final (IPV final) e índice de sangramento gengival final (ISG final) foram medidos após a 4ªsemana do estudo. Estatística descritiva e inferencial foi realizada, considerando o nível de significância de 5%. A magnitude de efeito foi calculada para comparação de grupos e de momentos distintos. Resultados:Houve uma diferença significativa entre os grupos C e E para placa visível e sangramento gengival final (p = 0,005; 0,004, respectivamente), o que foi confirmado por uma magnitude de efeito elevada para placa visívelfinal. Diminuição significativa para placa visível foi observada ao final do estudo para o grupo E (p = 0,001), confirmado por uma magnitude de efeito elevada. Para o grupo C houve um aumento significativo de placavisível e sangramento gengival ao final do estudo (p < 0,001; p = 0,043, respectivamente). Conclusão: A atividade educativo-preventiva na escola mostrou ser eficaz na redução da placa visível e do sangramentogengival. No entanto, reforços motivacionais em base regular devem ser realizados objetivando a manutenção da saúde bucal obtida. A participação dos pais, além de reforçar o trabalho realizado junto às crianças, permitiráque todo o núcleo familiar seja favorecido com as ações.Descritores: Assitência odontológica para crianças. Índice de placa dentária. Índice periodontal.
Hábitos relacionados à saúde bucal em crianças nascidas prematuras: uma preocupação para equipes multiprofissionais de saúde
Authors: Viana Karolline Alves , Euzébio Ludmilla Ferreira , Cortines Andréa Araujo de Oliveira , Costa Luciane Rezende 
Published: January 2014

Objetivo: Identificar hábitos alimentares, de sucção não nutritiva e de higiene bucal nos primeiros três anos de vida de crianças nascidas prematuras. Materiais e Métodos: Estudo descritivo retrospectivo baseado em dados secundários obtidos de prontuários odontológicos das 109 crianças com história de nascimento prematuro, acompanhadas no Ambulatório Odontológico de Prematuridade do Hospital das Clínicas daUniversidade Federal de Goiás, de fevereiro de 2011 a julho de 2012. Consideraram-se informações da primeira consulta odontológica: idade atual, sexo, idade gestacional, hábitos alimentares (tipo de aleitamento,ingestão de açúcar extrínseco), hábitos bucais não nutritivos (sucção de chupeta e sucção digital) e hábitos de higiene bucal. Os dados foram analisados por estatística descritiva com auxílio do software IBM SPSS versão20.0. Resultados: No primeiro exame odontológico, as crianças nascidas prematuras tinham de 1 a 33 meses de idade (média de 8,6±7,2), sendo 49 (45,0%) meninas e 60 (55,0%) meninos. A ocorrência de aleitamentonatural em menores de 6 meses foi de 22,8%, com predominância de aleitamento artificial (45,6%). Do total de nascidos prematuros, 79,8% utilizavam mamadeira e 58,7% realizavam sucção de chupeta. Em relação à higiene bucal, 73,4% da amostra realizava higiene bucal e 44,4% utilizava a fralda como instrumento. Conclusão: Os percentuais de aleitamento materno exclusivo foram baixos. A maioria das crianças apresentou algum hábitode sucção não nutritiva. A prática de higiene bucal mostrou-se insatisfatória. Assim, o estabelecimento de programas educativo-preventivos é essencial no apoio às famílias para os cuidados bucais a essas crianças,visando à promoção de saúde e prevenção de alterações no sistema estomatognático.Descritores: Nascimento prematuro. Saúde bucal. Hábitos.
Using Item Response Theory to Model Multiple Phenotypes and Their Joint Heritability in Family Data
Authors: Fragoso Tiago M. , Giolo Suely R. , Pereira Alexandre C. , de Andrade Mariza , Soler Julia M. P. 
Published: January 2014

ABSTRACTMany important complex diseases are composed of a series of phenotypes, which makes the disease diagnosis and its genetic dissection difficult. The standard procedures to determine heritability in such complex diseases are either applied for single phenotype analyses or to compare findings across phenotypes or multidimensional reduction procedures, such as principal components analysis using all phenotypes. However each method has its own problems and the challenges are even more complex for extended family data and categorical phenotypes. In this paper, we propose a methodology to determine a scale for complex outcomes involving multiple categorical phenotypes in extended pedigrees using item response theory (IRT) models that take all categorical phenotypes into account, allowing informative comparison among individuals. An advantage of the IRT framework is that a straightforward joint heritability parameter can be estimated for categorical phenotypes. Furthermore, our methodology allows many possible extensions such as the inclusion of covariates and multiple variance components. We use Markov Chain Monte Carlo algorithm for the parameter estimation and validate our method through simulated data. As an application we consider the metabolic syndrome as the multiple phenotype disease using data from the Baependi Heart Study consisting of 1,696 individuals in 95 families. We adjust IRT models without covariates and include age and age squared as covariates. The results showed that adjusting for covariates yields a higher joint heritability () than without co variates () indicating that the covariates absorbed some of the error variance.
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis
Authors: Sreedharan Vipin T. , Schultheiss Sebastian J. , Jean Géraldine , Kahles André , Bohnert Regina , Drewe Philipp , Mudrakarta Pramod , Görnitz Nico , Zeller Georg , Rätsch Gunnar 
Published: January 2014

Abstract
We present Oqtans, an open-source workbench for quantitative transcriptome analysis, that is integrated in Galaxy. Its distinguishing features include customizable computational workflows and a modular pipeline architecture that facilitates comparative assessment of tool and data quality. Oqtans integrates an assortment of machine learning-powered tools into Galaxy, which show superior or equal performance to state-of-the-art tools. Implemented tools comprise a complete transcriptome analysis workflow: short-read alignment, transcript identification/quantification and differential expression analysis. Oqtans and Galaxy facilitate persistent storage, data exchange and documentation of intermediate results and analysis workflows. We illustrate how Oqtans aids the interpretation of data from different experiments in easy to understand use cases. Users can easily create their own workflows and extend Oqtans by integrating specific tools. Oqtans is available as (i) a cloud machine image with a demo instance at cloud.oqtans.org, (ii) a public Galaxy instance at galaxy.cbio.mskcc.org, (iii) a git repository containing all installed software (oqtans.org/git); most of which is also available from (iv) the Galaxy Toolshed and (v) a share string to use along with Galaxy CloudMan.
Contact: vipin@cbio.mskcc.org, ratschg@mskcc.org
Supplementary information: Supplementary data are available at Bioinformatics online.
PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data
Authors: Bakir-Gungor Burcu , Egemen Ece , Sezerman Osman Ugur 
Published: January 2014

Abstract
Summary: Genome-wide association studies (GWAS) have revolutionized the search for the variants underlying human complex diseases. However, in a typical GWAS, only a minority of the single-nucleotide polymorphisms (SNPs) with the strongest evidence of association is explained. One possible reason of complex diseases is the alterations in the activity of several biological pathways. Here we present a web server called Pathway and Network-Oriented GWAS Analysis to devise functionally important pathways through the identification of SNP-targeted genes within these pathways. The strength of our methodology stems from its multidimensional perspective, where we combine evidence from the following five resources: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein–protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways.
Availability: PANOGA web server is freely available at: http://panoga.sabanciuniv.edu/. The source code is available to academic users ‘as is’ on request.
Contact: burcub@gatech.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Evolutionary footprint of coevolving positions in genes
Authors: Dib Linda , Silvestro Daniele , Salamin Nicolas 
Published: January 2014

Abstract
Motivation: The analysis of molecular coevolution provides information on the potential functional and structural implication of positions along DNA sequences, and several methods are available to identify coevolving positions using probabilistic or combinatorial approaches. The specific nucleotide or amino acid profile associated with the coevolution process is, however, not estimated, but only known profiles, such as the Watson–Crick constraint, are usually considered a priori in current measures of coevolution.
Results: Here, we propose a new probabilistic model, Coev, to identify coevolving positions and their associated profile in DNA sequences while incorporating the underlying phylogenetic relationships. The process of coevolution is modeled by a 16 × 16 instantaneous rate matrix that includes rates of transition as well as a profile of coevolution. We used simulated, empirical and illustrative data to evaluate our model and to compare it with a model of ‘independent’ evolution using Akaike Information Criterion. We showed that the Coev model is able to discriminate between coevolving and non-coevolving positions and provides better specificity and specificity than other available approaches. We further demonstrate that the identification of the profile of coevolution can shed new light on the process of dependent substitution during lineage evolution.
Availability: http://www2.unil.ch/phylo/bioinformatics/coev
Contact: nicolas.salamin@unil.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata
Authors: Gatto Laurent , Breckels Lisa M. , Wieczorek Samuel , Burger Thomas , Lilley Kathryn S. 
Published: January 2014

Abstract
Motivation: Experimental spatial proteomics, i.e. the high-throughput assignment of proteins to sub-cellular compartments based on quantitative proteomics data, promises to shed new light on many biological processes given adequate computational tools.
Results: Here we present pRoloc, a complete infrastructure to support and guide the sound analysis of quantitative mass-spectrometry-based spatial proteomics data. It provides functionality for unsupervised and supervised machine learning for data exploration and protein classification and novelty detection to identify new putative sub-cellular clusters. The software builds upon existing infrastructure for data management and data processing.
Availability: pRoloc is implemented in the R language and available under an open-source license from the Bioconductor project (http://www.bioconductor.org/). A vignette with a complete tutorial describing data import/export and analysis is included in the package. Test data is available in the companion package pRolocdata.
Contact: lg390@cam.ac.uk
MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation
Authors: Stecher Glen , Liu Li , Sanderford Maxwell , Peterson Daniel , Tamura Koichiro , Kumar Sudhir 
Published: January 2014

Abstract
Summary: Computational diagnosis of amino acid variants in the human exome is the first step in assessing the disruptive impacts of non-synonymous single nucleotide variants (nsSNVs) on human health and disease. The Molecular Evolutionary Genetics Analysis software with mutational diagnosis (MEGA-MD) is a suite of tools developed to forecast the deleteriousness of nsSNVs using multiple methods and to explore nsSNVs in the context of the variability permitted in the long-term evolution of the affected position. In its graphical interface for use on desktops, it enables interactive computational diagnosis and evolutionary exploration of nsSNVs. As a web service, MEGA-MD is suitable for diagnosing variants on an exome scale. The MEGA-MD suite intends to serve the needs for conducting low- and high-throughput analysis of nsSNVs in diverse applications.
Availability: www.megasoftware.net/mega-md and www.mypeg.info
Contact: s.kumar@asu.edu
Environmental and fishery-driven dynamics of the common octopus (Octopus vulgaris) based on time-series analyses from leeward Algarve, southern Portugal
Authors: Sonderblohm Carlos P. , Pereira João , Erzini Karim 
Published: January 2014

Abstract
Dynamic factor analysis was used to explore monthly landings per unit effort (LPUE) series of Octopus vulgaris and environmental variables recorded in the southwest Iberian Peninsula, south Portugal. Despite the large fluctuations in the octopus abundance series, results showed a strong aggregation pattern for the last 3 months of the year, possibly related to the input of new recruits to the fishery. The calculated common trend for the 12 months time-series presented significant correlations with autumn rainfall of the previous year (lag − 1), particularly for the October, November, and December series. Other important correlations were found for the Western Mediterranean Oscillation index (lag − 1), Ekman transport, summer river run-off (lag − 1), horizontal and vertical component of windstress, among others. The main trend describes a moderate steady increase in LPUE during the last 10 years, suggesting that octopus abundance has increased from 1990 to 2010. The strong correlations of the monthly octopus LPUE series, together with the annual life cycle, suggest that after environmentally controlled recruitment, population dynamics is largely fishery driven, resulting in strong seasonality in the landings.
A framework for mapping small-scale coastal fisheries using fishers' knowledge
Authors: Léopold Marc , Guillemot Nicolas , Rocklin Delphine , Chen Cheryl 
Published: January 2014

Abstract
Collecting spatial information on fisheries catch and effort is essential to understanding the spatial processes of exploited population dynamics and to manage heterogeneously distributed resources and uses. The use of fishers' knowledge through geographical information systems (GISs) is increasingly considered as a promising source of local information on small-scale coastal fisheries. In this paper we describe the first framework for mapping entire small-scale coastal fisheries using fishers' knowledge on catch size and fishing effort. Four mangrove and coral reef fisheries targeting invertebrates or finfish in New Caledonia (southwest Pacific) were mapped following a five-step framework: (i) stratified random sampling of regular fishers; (ii) collection of fishers' knowledge of fishing areas, fishing effort, and catch size through map-based interviews; (iii) data integration into a spatial geodatabase; (iv) statistical extrapolation of fisher data to the fishery scale; and (v) mapping of catch, effort, and catch per unit effort (CPUE) for each fishery using a GIS overlay procedure. We found evidence that fishers' knowledge supplied precise and accurate quantitative and spatial information on catch size, fishing effort and CPUE for entire fisheries. Fisheries maps captured the fine-scale spatial distribution of fishing activities in a variety of ways according to target taxa, gear type, and home ports. Applications include area-based marine conservation planning and fishery monitoring, management, and governance. This integrated framework can be generalized to a large range of data-poor coastal and inland small-scale fisheries.
Transcriptional repressor NIR interacts with the p53-inhibiting ubiquitin ligase MDM2
Authors: Heyne Kristina , Förster Juliane , Schüle Roland , Roemer Klaus 
Published: January 2014

Abstract
NIR (novel INHAT repressor) can bind to p53 at promoters and inhibit p53-mediated gene transactivation by blocking histone acetylation carried out by p300/CBP. Like NIR, the E3 ubiquitin ligase MDM2 can also bind and inhibit p53 at promoters. Here, we present data indicating that NIR, which shuttles between the nucleolus and nucleoplasm, not only binds to p53 but also directly to MDM2, in part via the central acidic and zinc finger domain of MDM2 that is also contacted by several other nucleolus-based MDM2/p53-regulating proteins. Like some of these, NIR was able to inhibit the ubiquitination of MDM2 and stabilize MDM2; however, unlike these nucleolus-based MDM2 regulators, NIR did not inhibit MDM2 to activate p53. Rather, NIR cooperated with MDM2 to repress p53-induced transactivation. This cooperative repression may at least in part involve p300/CBP. We show that NIR can block the acetylation of p53 and MDM2. Non-acetylated p53 has been documented previously to more readily associate with inhibitory MDM2. NIR may thus help to sustain the inhibitory p53:MDM2 complex, and we present evidence suggesting that all three proteins can indeed form a ternary complex. In sum, our findings suggest that NIR can support MDM2 to suppress p53 as a transcriptional activator.
An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments
Authors: Duitama Jorge , Quintero Juan Camilo , Cruz Daniel Felipe , Quintero Constanza , Hubmann Georg , Foulquié-Moreno Maria R. , Verstrepen Kevin J. , Thevelein Johan M. , Tohme Joe 
Published: January 2014

Abstract
Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species.
On the Existence of Solutions for the Critical Fractional Laplacian Equation inℝN
Authors: Shen Zifei , Gao Fashun 
Published: January 2014

We study existence of solutions for the fractional Laplacian equation-Δsu+Vxu=u2*s-2u+fx, uinℝN,u∈Hs(RN), with critical exponent2*s=2N/(N-2s),N>2s,s∈0, 1, whereVx≥0has a potential well andf:ℝN×ℝ→ℝis a lower order perturbation of the critical poweru2*s-2u. By employing the variational method, we prove the existence of nontrivial solutions for the equation.