Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis?

A significant proportion (up to 62) of oral squamous cell carcinomas (OSCCs) may arise from oral potential malignant lesions (OPMLs), such as leukoplakia. Patient outcomes may thus be improved through detection of lesions at a risk for malignant transformation, by identifying and categorizing genetic changes in sequential, progressive OPMLs. We conducted array comparative genomic hybridization analysis of 25 sequential, progressive OPMLs and same-site OSCCs from five patients. Recurrent DNA copy number gains were identified on 1p in 20/25 cases (80) with minimal, high-level amplification regions on 1p35 and 1p36. Other regions of gains were frequently observed: 11q13.4 (68), 9q34.13 (64), 21q22.3 (60), 6p21 and 6q25 (56) and 10q24, 19q13.2, 22q12, 5q31.2, 7p13, 10q24 and 14q22 (48). DNA losses were observed in 20 of samples and mainly detected on 5q31.2 (35), 16p13.2 (30), 9q33.1 and 9q33.29 (25) and 17q11.2, 3p26.2, 18q21.1, 4q34.1 and 8p23.2 (20). Such copy number alterations (CNAs) were mapped in all grades of dysplasia that progressed, and their corresponding OSCCs, in 70 of patients, indicating that these CNAs may be associated with disease progression. Amplified genes mapping within recurrent CNAs (KHDRBS1, PARP1, RAB1A, HBEGF, PAIP2, BTBD7) were selected for validation, by quantitative real-time PCR, in an independent set of 32 progressive leukoplakia, 32 OSSCs and 21 non-progressive leukoplakia samples. Amplification of BTBD7, KHDRBS1, PARP1 and RAB1A was exclusively detected in progressive leukoplakia and corresponding OSCC. BTBD7, KHDRBS1, PARP1 and RAB1A may be associated with OSCC progression. Proteinprotein interaction networks were created to identify possible pathways associated with OSCC progression.

Chromosomal Mapping of Repetitive DNA and Cytochrome C Oxidase I Sequence Analysis Reveal Differentiation among Sympatric Samples of Astyanax fasciatus (Characiformes, Characidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chromosomal organization and evolutionary history of Mariner transposable elements in Scarabaeinae coleopterans

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Patterns of rDNA and telomeric sequences diversification: contribution to repetitive DNA organization in Phyllostomidae bats

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Multiple-trait genomic evaluation for milk yield and milk quality traits using genomic and phenotypic data in buffalo in Brazil

The use of markers distributed all long the genome may increase the accuracy of the predicted additive genetic value of young animals that are candidates to be selected as reproducers. In commercial herds, due to the cost of genotyping, only some animals are genotyped and procedures, divided in two or three steps, are done in order to include these genomic data in genetic evaluation. However, genomic evaluation may be calculated using one unified step that combines phenotypic data, pedigree and genomics. The aim of the study was to compare a multiple-trait model using only pedigree information with another using pedigree and genomic data. In this study, 9,318 lactations from 3061 buffaloes were used, 384 buffaloes were genotyped using a Illumina bovine chip (Illumina Infinium (R) bovineHD BeadChip). Seven traits were analyzed milk yield (MY), fat yield (FY), protein yield (PY), lactose yield (LY), fat percentage (F%), protein percentage (P%) and somatic cell score (SCSt). Two analyses were done: one using phenotypic and pedigree information (matrix A) and in the other using a matrix based in pedigree and genomic information (one step, matrix H). The (co) variance components were estimated using multiple-trait analysis by Bayesian inference method, applying an animal model, through Gibbs sampling. The model included the fixed effects of contemporary groups (herd-year-calving season), number of milking (2 levels), and age of buffalo at calving as (co) variable (quadratic and linear effect). The additive genetic, permanent environmental, and residual effects were included as random effects in the model. The heritability estimates using matrix A were 0.25, 0.22, 0.26, 0.17, 0.37, 0.42 and 0.26 and using matrix H were 0.25, 0.24, 0.26, 0.18, 0.38, 0.46 and 0.26 for MY, FY, PY, LY, % F, % P and SCCt, respectively. The estimates of the additive genetic effect for the traits were similar in both analyses, but the accuracy were bigger using matrix H (superior to 15% for traits studied). The heritability estimates were moderated indicating genetic gain under selection. The use of genomic information in the analyses increases the accuracy. It permits a better estimation of the additive genetic value of the animals.

The Mitochondrial Genome of the Leaf-Cutter Ant Atta laevigata: A Mitogenome with a Large Number of Intergenic Spacers

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Product-portfolio management: A framework based on Methods, Organization, and Strategy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Análise da presença e articulação teórica da Catalogação de Assunto na literatura científica da International Society for Knowledge Organization ISKO: uma análise de domínio

Subject Cataloging is one of the processes of subject approach to information, beside indexing and subject analysis. In this sense, this research is a part of a broader project which analyses ISKO as an academic space that promotes a dialogical dimension among those theoretical questions. In this sense, it aims to analyze the presence of subject cataloguing in the discussions of knowledge organization as well as how the authors of such subject dialogue each other. Considering the questions, the full collection of ISKO and ISKO-Spain conference proceedings were analyzed in order to verify how present were subject cataloguing matters in those collections. It was possible to identify a group of 36 articles (27 from International ISKO and 9 from ISKO – Spain) whose references were bibliometrically analyzed in terms of documentary forms, average life, language and citation analysis. The results showed that the major ISKO and ISKO-Spain literature on subject cataloguing is based on journal articles, mostly published in English, presenting a relatively young average life (14 years for ISKO and 10 for ISKO-Spain).

Development of twenty-one polymorphic microsatellite markers for the fungus-growing ant, Mycocepurus goeldii (Formicidae: Attini), using Illumina paired-end genomic sequencing

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Prospection of genomic regions divergently selected in racing line of Quarter Horses in relation to cutting line

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genomic screening of testicular germ cell tumors from monozygotic twins

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Challenges and opportunities for knowledge organization at the intersection with information technologies

In this paper we study the intersection of Knowledge Organization with Information Technologies and the challenges and opportunities for Knowledge Organization experts that, in our view, are important to be studied and for them to be aware of. We start by giving some definitions necessary for providing the context for our work. Then we review the history of the Web, beginning with the Internet and continuing with the World Wide Web, the Semantic Web, problems of Artificial Intelligence, Web 2.0, and Linked Data. Finally, we conclude our paper with IT applications for Knowledge Organization in libraries, such as FRBR, BIBFRAME, and several OCLC initiatives, as well as with some of the challenges and opportunities in which Knowledge Organization experts and researchers might play a key role in relation to the Semantic Web.

Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Postmodern archival science and contemporary diplomatics New approaches for archival knowledge organization

New information technologies and new forms of documentary production have led archivists to rethink the role of archival science in the so-called information age. Since the late 1980s, the principles, methods and concepts stated by the well-known manuals of the 19th and the 20th centuries have been reconsidered along with their application to the organic sets of document in the 21st century. In this new scenario of reformulation and reinterpretation regarding the perspectives on archival knowledge organization, two trends with different approaches have emerged in North America and Europe: postmodern archival science and contemporary diplomatics, respectively. The first one was introduced by Terry Cook, who proposed a reformulation of the basic concepts and the functional analysis method focusing on the process and context of document creation. The second approach originated in Italy and incorporated all the theoretical and methodological models of classic diplomatics. The studies following this new trend were disseminated by Luciana Duranti and aimed to ensure the production, access and use of the documentation generated in the present times focusing on document typology, as opposed by the postmodern approach. The purpose of this study is to elucidate the connection points and distinct features between the two trends concerning the organization of archival knowledge.

Aboutness in Fiction: Methodological Perspectives for Knowledge Organization

The subject analysis of narrative texts of fiction is complex; the methodological model of identification of concepts as elaborated for scientific texts is not applicable to fiction. It is proposed here that theoretical and methodological use of the Generative Trajectory of Meaning postulated by Greimas may contribute to the identification of aboutness in narrative texts of fiction.