Evolution of the Sequence Ontology terms and relationships

The Sequence Ontology is undergoing reform to meet the standards of the OBO Foundry. Here we report some of the incremental changes and improvements made to SO. We also propose new relationships to better define the mereological, spatial and temporal aspects of biological sequence

δ13C tracing of dissolved inorganic carbon sources in major world rivers

δ13C tracing of dissolved inorganic carbon sources in major world river

Evolution and gene regulation of the genomic imprinting mechanism

Genomic imprinting describes an epigenetic mechanism by which genes are active or silent depending on their parental origin. Imprinting exists in plants and mammals, but how this monoallelic expression mechanism has evolved is not understood at the molecular level. Here I describe the mapping, sequencing and analysis of vertebrate orthologous imprinted regions spanning 11.5 Mb of genomic sequence from species with and without genomic imprinting. In eutherian (placental) mammals, imprinting can be regulated by differential DNA methylation, non-coding RNAs, enhancers and insulator elements. The systematic sequence comparison of the IGF2-H19 imprinting cluster, in eutherians and marsupials (tammar wallaby and opossum), has revealed the presence of the enigmatic non-coding RNA H19 in marsupials. Furthermore, we have characterised the marsupial H19 expression status and identified key regulatory elements required for the germline imprinting of the neighbouring IGF2 gene. All the major hallmarks of the imprinting mechanism of the IGF2-H19 locus were found to be conserved in therian mammals. In mammals, this imprinting system is therefore the most conserved germline derived epigenetic mechanism discovered so far. The high-quality genomic sequences have provided early glimpses of the genomic landscapes for species such as the monotreme platypus and marsupial tammar wallaby for which little was previously known. Comparative sequence analysis was used to identify candidate regulatory elements in the neighbouring imprinting centre 1 and 2 regions of human chromosome 11p15.5. Nine novel enhancer elements were identified following in vitro gene-reporter assays and correlation of conserved sequences with recent ENCODE data revealed probable functions for a further 24 elements. This project has led to the formation of the Sequence Analysis of Vertebrate Orthologous Imprinted Regions (SAVOIR) consortium and resources developed here are being used by the imprinting community to further our knowledge of the evolution of the genomic imprinting mechanism

Social Supports for Adolescent and Young Adult Polycystic Ovary Syndrome Patients: A Scoping Review

Polycystic ovary syndrome (PCOS) is a chronic disorder with negative health consequences for millions of women. The paucity of research regarding interventions targeting the psychosocial symptoms of PCOS for adolescents and young adults (AYAs), susceptible to low self-esteem and depression, warranted this review. This paper provides an overview of research on the social supports currently available for AYAs and identifies areas where further research is required to elucidate their support needs. A scoping review methodology identified 15 studies that met inclusion criteria. Findings revealed that this is an emerging field of research and most included studies originated in North America. Thematic organization of the findings suggested two broad themes: pre-diagnostic support concerns and post-diagnostic support resources. Within the first theme, three sub-themes arose: (dis)satisfaction with information received about PCOS, delayed diagnoses, and a need for increasing healthcare provider support. A lack of research specific to the support needs of transgender PCOS patients was additionally identified. The results of this study can be used to inform the development of evidence-based support interventions and educational requirements for graduate school curriculums that enable future healthcare providers to adequately provide support when diagnosing, educating, presenting treatment options, and directing PCOS patients to support resources

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true 'machine-actionable interoperability', which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies

Numerical tidal models with unequal grid-spacing

Thesis (M.S.) University of Alaska Fairbanks, 2006A two-dimensional alternating-direction implicit numerical tidal model with unequal grid-spacing is developed and successfully tested. The method is essentially an extension into two dimensions of a one-dimensional implicit method in which tide heights and flow rates are evaluated on the same cross-sections, an approach which permits a river to be schematized into a number of sections of differing lengths. The two-dimensional scheme gives the user considerable control over the density of the computation points in a region by virtue of the fact that heights and depth-mean currents are evaluated midway between points of intersection of a grid constructed from orthogonal lines, the spacing between which may be chosed at will. The method is applied initially to the Irish Sea using a grid of constant spacing. The effects of increasing time step and friction on stability and accuracy are investigated, and the model is proved to be unconditionally stable. The results match those of previous investigators, and some new information on the M₂ currents of the region is obtained. The second application of the model is to a 'rectangular' North Sea, a favorable comparison being obtained when the region is schematized by two grids of equal and unequal spacing. Finally, the model is applied to Cook Inlet, Alaska, a region of complexity sufficient to warrant the use of a scheme possessing the unequal grid-spacing feature. Satisfactory results are obtained after tuning the model by adjustment of the friction coefficient. Movie films were made in order to conceptually clarify the tidal behaviors of the Irish Sea and Cook Inlet. Each film shows as functions of time, perspective views of the sea surface, and current vectors superimposed on a contour map of the sea surface.I. Introduction -- II. Hydraulic calculations using the harmonic method -- III. Hydraulic calculations using the one-dimensional implicit method -- IV. A two-dimensional model with unequal grid-spacing -- V. The finite-difference equations and their solution -- VI. Programming considerations -- VII. Application of the model to the Irish Sea -- VIII. Application of the model to a rectangular North Sea -- IX. Application of the model to Cook Inlet, Alaska -- X. Additional results of interest -- XI. Conclusions -- References -- Appendix I. The harmonic method : calculation of L,M,N, and O -- Appendix II. Example of branch-point solution for the harmonic method -- Appendix III. Analysis of stability and wave-deformation for the one-dimensional implicit method -- Appendix IV. Compact form of the finite-difference equations for the one-dimensional implicit method -- Appendix V. Example of branch-point solution for the one-dimensional implicit method -- Appendix VI. Compact form of the finite-difference equations for the two-dimensional implicit method