Standard Genetic Nomenglature of the Pig, with Glossaries

Genetics includes the study of genotypes, phenotypes and the mechanisms of genetic control between them. Genetic terms describe the processes, genes and traits with which genetic phenomena are described and examined. The genetic process terminologies are thoroughly discussed in the previous chapters. Therefore, in this chapter, we will only list the terms for genetic processes and concepts in Appendix I (a general genetic glossary), and concentrate the discussion on pig gene and trait terminologies (Appendix 10; a glossary for pig diseases and defects is also included (Appendix III)

Developmental progress and current status of the Animal QTLdb

The Animal QTL Database (QTLdb; http://www.animalgenome.org/QTLdb) has undergone dramatic growth in recent years in terms of new data curated, data downloads and new functions and tools. We have focused our development efforts to cope with challenges arising from rapid growth of newly published data and end users’ data demands, and to optimize data retrieval and analysis to facilitate users’ research. Evidenced by the 27 releases in the past 11 years, the growth of the QTLdb has been phenomenal. Here we report our recent progress which is highlighted by addition of one new species, four new data types, four new user tools, a new API tool set, numerous new functions and capabilities added to the curator tool set, expansion of our data alliance partners and more than 20 other improvements. In this paper we present a summary of our progress to date and an outlook regarding future directions

Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB

Successful development of biological databases requires accommodation of the burgeoning amounts of data from high-throughput genomics pipelines. As the volume of curated data in Animal QTLdb (https://www.animalgenome.org/QTLdb) increases exponentially, the resulting challenges must be met with rapid infrastructure development to effectively accommodate abundant data curation and make metadata analysis more powerful. The development of Animal QTLdb and CorrDB for the past 15 years has provided valuable tools for researchers to utilize a wealth of phenotype/genotype data to study the genetic architecture of livestock traits. We have focused our efforts on data curation, improved data quality maintenance, new tool developments, and database co-developments, in order to provide convenient platforms for users to query and analyze data. The database currently has 158 499 QTL/associations, 10 482 correlations and 1977 heritability data as a result of an average 32% data increase per year. In addition, we have made \u3e14 functional improvements or new tool implementations since our last report. Our ultimate goals of database development are to provide infrastructure for data collection, curation, and annotation, and more importantly, to support innovated data structure for new types of data mining, data reanalysis, and networked genetic analysis that lead to the generation of new knowledge

Standard Genetic Nomenclature

Genetics includes the study of genotypes and phenotypes, the mechanisms of genetic control between them, and information transfer between generations. Genetic terms describe processes, genes and traits with which genetic phenomena are examined and described. While the genetic terminologies are extensively discussed in this book and elsewhere, the standardization of their names has been an ongoing process. Therefore, this chapter will only concentrate on discussions about the issues involved in the standardization of gene and trait terminologies

In vivo detection of cortical optical changes associated with seizure activity with optical coherence tomography.

The most common technology for seizure detection is with electroencephalography (EEG), which has low spatial resolution and minimal depth discrimination. Optical techniques using near-infrared (NIR) light have been used to improve upon EEG technology and previous research has suggested that optical changes, specifically changes in near-infrared optical scattering, may precede EEG seizure onset in in vivo models. Optical coherence tomography (OCT) is a high resolution, minimally invasive imaging technique, which can produce depth resolved cross-sectional images. In this study, OCT was used to detect changes in optical properties of cortical tissue in vivo in mice before and during the induction of generalized seizure activity. We demonstrated that a significant decrease (P < 0.001) in backscattered intensity during seizure progression can be detected before the onset of observable manifestations of generalized (stage-5) seizures. These results indicate the feasibility of minimally-invasive optical detection of seizures with OCT

Development of quality metrics for ambulatory pediatric cardiology: Transposition of the great arteries after arterial switch operation

ObjectiveTo develop quality metrics (QMs) for the ambulatory care of patients with transposition of the great arteries following arterial switch operation (TGA/ASO).DesignUnder the auspices of the American College of Cardiology Adult Congenital and Pediatric Cardiology (ACPC) Steering committee, the TGA/ASO team generated candidate QMs related to TGA/ASO ambulatory care. Candidate QMs were submitted to the ACPC Steering Committee and were reviewed for validity and feasibility using individual expert panel member scoring according to the RANDâ UCLA methodology. QMs were then made available for review by the entire ACC ACPC during an â open comment period.â Final approval of each QM was provided by a vote of the ACC ACPC Council.PatientsPatients with TGA who had undergone an ASO were included. Patients with complex transposition were excluded.ResultsTwelve candidate QMs were generated. Seven metrics passed the RANDâ UCLA process. Four passed the â open comment periodâ and were ultimately approved by the Council. These included: (1) at least 1 echocardiogram performed during the first year of life reporting on the function, aortic dimension, degree of neoaortic valve insufficiency, the patency of the systemic and pulmonary outflows, the patency of the branch pulmonary arteries and coronary arteries, (2) neurodevelopmental (ND) assessment after ASO; (3) lipid profile by age 11 years; and (4) documentation of a transition of care plan to an adult congenital heart disease (CHD) provider by 18 years of age.ConclusionsApplication of the RANDâ UCLA methodology and linkage of this methodology to the ACPC approval process led to successful generation of 4 QMs relevant to the care of TGA/ASO pediatric patients in the ambulatory setting. These metrics have now been incorporated into the ACPC Quality Network providing guidance for the care of TGA/ASO patients across 30 CHD centers.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142334/1/chd12540_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142334/2/chd12540.pd

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices

Animal QTLdb:an improved database tool for livestock animal QTL/association data dissemination in the post-genome era

The Animal QTL database (QTLdb; http://www.animalgenome.org/QTLdb) is designed to house all publicly available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. An earlier version was published in the Nucleic Acids Research Database issue in 2007. Since then, we have continued our efforts to develop new and improved database tools to allow more data types, parameters and functions. Our efforts have transformed the Animal QTLdb into a tool that actively serves the research community as a quality data repository and more importantly, a provider of easily accessible tools and functions to disseminate QTL and gene association information. The QTLdb has been heavily used by the livestock genomics community since its first public release in 2004. To date, there are 5920 cattle, 3442 chicken, 7451 pigs, 753 sheep and 88 rainbow trout data points in the database, and at least 290 publications that cite use of the database. The rapid advancement in genomic studies of cattle, chicken, pigs, sheep and other livestock animals has presented us with challenges, as well as opportunities for the QTLdb to meet the evolving needs of the research community. Here, we report our progress over the recent years and highlight new functions and services available to the general public

Susceptibility of Canada Geese (Branta canadensis) to Highly Pathogenic Avian Influenza Virus (H5N1)

Prior exposure of Canada geese to a North American low pathogenic virus (H5N2) decreases their susceptibility to Eurasian highly pathogenic avian influenza virus (H5N1)