IUPHAR-DB:the IUPHAR database of G protein-coupled receptors and ion channels

The IUPHAR database (IUPHAR-DB) integrates peer-reviewed pharmacological, chemical, genetic, functional and anatomical information on the 354 nonsensory G protein-coupled receptors (GPCRs), 71 ligand-gated ion channel subunits and 141 voltage-gated-like ion channel subunits encoded by the human, rat and mouse genomes. These genes represent the targets of approximately one-third of currently approved drugs and are a major focus of drug discovery and development programs in the pharmaceutical industry. IUPHAR-DB provides a comprehensive description of the genes and their functions, with information on protein structure and interactions, ligands, expression patterns, signaling mechanisms, functional assays and biologically important receptor variants (e.g. single nucleotide polymorphisms and splice variants). In addition, the phenotypes resulting from altered gene expression (e.g. in genetically altered animals or in human genetic disorders) are described. The content of the database is peer reviewed by members of the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification (NC-IUPHAR); the data are provided through manual curation of the primary literature by a network of over 60 subcommittees of NC-IUPHAR. Links to other bioinformatics resources, such as NCBI, Uniprot, HGNC and the rat and mouse genome databases are provided. IUPHAR-DB is freely available at http://www.iuphar-db.org. © 2008 The Author(s).

Effects of two intervention strategies on the behavior of nurses and nurse students related to advance directives

Advance directives are one mechanism for preserving the rights of individuals to exercise some control over their health care when serious illness may prevent them from direct participation. Nurses, as the health care providers with the closest and most sustained contact with critically ill and dying patients, are positioned to assist patients to plan for future health care needs. Although a majority of nurses favor the concept of advance directives for their patients and for themselves, they have not played a significant role in facilitating advance health care planning with their patients nor implemented advance health care planning for themselves.^ Research has also shown that differing forms of education and counseling increase the completion rates for advance directives in selected populations, mostly the elderly and seriously ill. Not yet developed are effective educational strategies to assist nurses and nurse students to make optimal contributions in assisting their clients' plans for future health care decision-making. This study sought to determine whether specific learning strategies (a) increased the involvement of nurses and nurse students in facilitating advance care planning with patients and (b) increased the percentage of the nurses' and nurse students' own personal advance care planning activities.^ The study compared two learning interventions and two populations, nurses and nurse students. The participants were randomly assigned to one of the two learning interventions, L1 or L2. Participants in L1 received a lecture, discussion and exploration of the forces impacting on advance directive behavior. Participants in L2 received the same intervention components with the additional component of group practice completing advance directives.^ Analysis of the data by chi-square and logistic regression did not support the hypotheses that the practice component would make a difference in the participants' facilitation of advance care planning with patients or in their own personal advance care planning activities. There were significant differences in post-intervention behavior between the nurse and nurse student groups. The nurses in the study did significantly more facilitation of advance care planning with patients and completed significantly more advance care documents than the nurse students post-intervention. However, the nurse students held more post-intervention family discussions than did the nurses. ^

Fostering the development of identity and intimacy during late adolescence

This dissertation tested the effectiveness of a psychosocial intervention, the Personal Development in the Context of Relationships (PDCR) program. The aim of the PDCR seeks to foster the development (or enhancement) of a sense of identity and intimacy among adolescents who participate in the program. The PDCR is a psychosocial group intervention which utilizes interpersonal relationship issues as a context to foster personal development in identity formation and facilitate the development of an individual's capacity for intimacy. The PDCR uses intervention strategies which include skills and knowledge development, experiential group exercises, and exploration for insight. Participants consisted of 110 late adolescents. A mixed-subjects design (pre-post-follow up) was used to assess the effectiveness, efficacy and utility of the PDCR on the experimental condition relative to a content/social contact control group and a time control condition. Identity exploration and identity commitment were measured by the Ego Identity Process Questionnaire (EIPQ). Total intimacy and identity role satisfaction were measured by the Erikson Psychosocial Stage Inventory (EPSI). Relationship quality and closeness were measured by the Relationship Quality Scale (RQS) and the Relationship Closeness Inventory (RCI) in an effort to assess whether any potential impact on interpersonal relationships occurs. Mixed MANOVAs were used to analyze the data with results yielding significant values for increased total identity exploration from pre to post test and decreases in total identity commitment from pre to post to follow-up test in the experimental group relative to the control conditions on the EIPQ. Further results indicated increases in total intimacy from pre to post to follow-up test in the experimental group relative to the control conditions on the EPSI. No clear trends emerged from pre to post to follow-up test for the Relationship measures. Results are discussed in terms of both practical and theoretical implications. ^

Exploring the role of therapy process and outcome in interventions that target adolescent identity and intimacy

This study examined the feasibility of using a session impact measure with a sample of 24 at risk high school students participating in an intervention targeting identity and intimacy. Three therapists led 3 intervention groups with the same format. The study investigated the impact of therapy process, including Group, Facilitator, Skills, and Exploration impacts as measured by the Session Evaluation Form (SEF). The study also investigated the differential impact of session process on intervention outcome as measured by the CPSS, EPSI, RAVS, EIPQ and Youth Report Form. Analyses were conducted using descriptive statistics, frequencies, one-way analysis of variance (ANOVA), and Chi square tests. The results supported the utility of the SEF and they tentatively supported the impact of the therapist on participants' perceptions of therapeutic processes and on intervention outcome. In particular, Group 1 performed better than Group 3. This study found that the SEF is a useful session impact measure. ^

Integration and querying of heterogeneous, autonomous, distributed database systems

Today, databases have become an integral part of information systems. In the past two decades, we have seen different database systems being developed independently and used in different applications domains. Today's interconnected networks and advanced applications, such as data warehousing, data mining & knowledge discovery and intelligent data access to information on the Web, have created a need for integrated access to such heterogeneous, autonomous, distributed database systems. Heterogeneous/multidatabase research has focused on this issue resulting in many different approaches. However, a single, generally accepted methodology in academia or industry has not emerged providing ubiquitous intelligent data access from heterogeneous, autonomous, distributed information sources. ^ This thesis describes a heterogeneous database system being developed at High-performance Database Research Center (HPDRC). A major impediment to ubiquitous deployment of multidatabase technology is the difficulty in resolving semantic heterogeneity. That is, identifying related information sources for integration and querying purposes. Our approach considers the semantics of the meta-data constructs in resolving this issue. The major contributions of the thesis work include: (i) providing a scalable, easy-to-implement architecture for developing a heterogeneous multidatabase system, utilizing Semantic Binary Object-oriented Data Model (Sem-ODM) and Semantic SQL query language to capture the semantics of the data sources being integrated and to provide an easy-to-use query facility; (ii) a methodology for semantic heterogeneity resolution by investigating into the extents of the meta-data constructs of component schemas. This methodology is shown to be correct, complete and unambiguous; (iii) a semi-automated technique for identifying semantic relations, which is the basis of semantic knowledge for integration and querying, using shared ontologies for context-mediation; (iv) resolutions for schematic conflicts and a language for defining global views from a set of component Sem-ODM schemas; (v) design of a knowledge base for storing and manipulating meta-data and knowledge acquired during the integration process. This knowledge base acts as the interface between integration and query processing modules; (vi) techniques for Semantic SQL query processing and optimization based on semantic knowledge in a heterogeneous database environment; and (vii) a framework for intelligent computing and communication on the Internet applying the concepts of our work. ^

The role of splicing factors and small nuclear RNAs in spliceosomal formation

Protein coding genes are comprised of protein-coding exons and non-protein-coding introns. The process of splicing involves removal of the introns and joining of the exons to form a mature messenger RNA, which subsequently undergoes translation into polypeptide. The spliceosome is a large, RNA/protein assembly of five small nuclear RNAs as well as over 300 proteins, which catalyzes intron removal and exon ligation. The selection of specific exons for inclusion in the mature messenger RNA is spatiotemporally regulated and results in production of an enormous diversity of polypeptides from a single gene locus. This phenomenon, known as alternative splicing, is regulated, in part, by protein splicing factors, which target the spliceosome to exon/intron boundaries. The first part of my dissertation (Chapters II and III) focuses on the discovery and characterization of the 45 kilodalton FK506 binding protein (FKBP45), which I discovered in the silk moth, Bombyx mori, as a U1 small nuclear RNA binding protein. This protein family binds the immunosuppressants FK506 and rapamycin and contains peptidyl-prolyl cis-trans isomerase activity, which converts polypeptides from cis to trans about a proline residue. This is the first time that an FKBP has been identified in the spliceosome. The second section of my dissertation (Chapters IV, V, VI and VII) is an investigation of the potential role of small nuclear RNA sequence variants in the control of splicing. I identified 46 copies of small nuclear RNAs in the 6X whole genome shotgun of the Bombyx mori p50T strain. These variants may play a role in differential binding of specific proteins that mediate alternative splicing. Along these lines, further investigation of U2 snRNA sequence variants in Bombyx mori demonstrated that some U2 snRNAs preferentially assemble into high molecular weight spliceosomal complexes over others. Expression of snRNA variants may represent another mechanism by which the cell is able to fine tune the splicing process.

Extended Coverage for Public Safety and Critical Communications Using Multi-hop and D2D Communications

In this thesis, we proposed the use of device-to-device (D2D) communications for extending the coverage area of active base stations, for public safety communications with partial coverage. A 3GPP standard compliant D2D system level simulator is developed for HetNets and public safety scenarios and used to evaluate the performance of D2D discovery and communications underlying cellular networks. For D2D discovery, the benefits of time-domain inter-cell interference coordi- nation (ICIC) approaches by using almost blank subframes were evaluated. Also, the use of multi-hop is proposed to improve, even further, the performance of the D2D discovery process. Finally, the possibility of using multi-hop D2D communications for extending the coverage area of active base stations was evaluated. Improvements in energy and spectral efficiency, when compared with the case of direct UE-eNB communi- cations, were demonstrated. Moreover, UE power control techniques were applied to reduce the effects of interference from neighboring D2D links.

Exploring therapy process and outcome in interventions that target at risk adolescents

The purpose of this study was to conduct a larger scale replication and extension study on the use of a Session Impact Measure the Session Evaluation Form. Ninety-one public high school students in Miami Florida were obtained through self or counselor referrals and placed in one or two of five counseling groups for one or two school semesters. To investigate differences in therapy processes across counseling groups, participants were administered a Session Evaluation Form at the end of each therapy session. This assessed group members' perception of four therapy process domains, Group, Facilitator, Skills and Exploration Impacts. The pattern significant results for the MANOVAs provided strong evidence for the greater impact of the group on therapy process relative to the impact of facilitator. Further research is needed to identify more specifically, ways, group process differences interact with other treatment variables.

Exploring the role of therapy process and outcome in interventions that target adolescent identity and intimacy

This study examined the feasibility of using a session impact measure with a sample of 24 at risk high school students participating in an intervention targeting identity and intimacy. Three therapists led 3 intervention groups with the same format. The study investigated the impact of therapy process, including Group, Facilitator, Skills, and Exploration impacts as measured by the Session Evaluation Form (SEF). The study also investigated the differential impact of session process on intervention outcome as measured by the CPSS, EPSI, RAVS, EIPQ and Youth Report Form. Analyses were conducted using descriptive statistics, frequencies, one-way analysis of variance (ANOVA), and Chi square tests. The results supported the utility of the SEF and they tentatively supported the impact of the therapist on participants' perceptions of therapeutic processes and on intervention outcome. In particular, Group 1 performed better than Group 3. This study found that the SEF is a useful session impact measure.

The Role of Splicing Factors and Small Nuclear RNAS in Spliceosomal Formation

Protein coding genes are comprised of protein-coding exons and non-protein-coding introns. The process of splicing involves removal of the introns and joining of the exons to form a mature messenger RNA, which subsequently undergoes translation into polypeptide. The spliceosome is a large, RNA/protein assembly of five small nuclear RNAs as well as over 300 proteins, which catalyzes intron removal and exon ligation. The selection of specific exons for inclusion in the mature messenger RNA is spatio-temporally regulated and results in production of an enormous diversity of polypeptides from a single gene locus. This phenomenon, known as alternative splicing, is regulated, in part, by protein splicing factors, which target the spliceosome to exon/intron boundaries. The first part of my dissertation (Chapters II and III) focuses on the discovery and characterization of the 45 kilodalton FK506 binding protein (FKBP45), which I discovered in the silk moth, Bombyx mori, as a U1 small nuclear RNA binding protein. This protein family binds the immunosuppressants FK506 and rapamycin and contains peptidyl-prolyl cis-trans isomerase activity, which converts polypeptides from cis to trans about a proline residue. This is the first time that an FKBP has been identified in the spliceosome. The second section of my dissertation (Chapters IV, V, VI and VII) is an investigation of the potential role of small nuclear RNA sequence variants in the control of splicing. I identified 46 copies of small nuclear RNAs in the 6X whole genome shotgun of the Bombyx mori p50T strain. These variants may play a role in differential binding of specific proteins that mediate alternative splicing. Along these lines, further investigation of U2 snRNA sequence variants in Bombyx mori demonstrated that some U2 snRNAs preferentially assemble into high molecular weight spliceosomal complexes over others. Expression of snRNA variants may represent another mechanism by which the cell is able to fine tune the splicing process.

Integration and querying of heterogeneous, autonomous, distributed database systems

Today, databases have become an integral part of information systems. In the past two decades, we have seen different database systems being developed independently and used in different applications domains. Today's interconnected networks and advanced applications, such as data warehousing, data mining & knowledge discovery and intelligent data access to information on the Web, have created a need for integrated access to such heterogeneous, autonomous, distributed database systems. Heterogeneous/multidatabase research has focused on this issue resulting in many different approaches. However, a single, generally accepted methodology in academia or industry has not emerged providing ubiquitous intelligent data access from heterogeneous, autonomous, distributed information sources. This thesis describes a heterogeneous database system being developed at Highperformance Database Research Center (HPDRC). A major impediment to ubiquitous deployment of multidatabase technology is the difficulty in resolving semantic heterogeneity. That is, identifying related information sources for integration and querying purposes. Our approach considers the semantics of the meta-data constructs in resolving this issue. The major contributions of the thesis work include: (i.) providing a scalable, easy-to-implement architecture for developing a heterogeneous multidatabase system, utilizing Semantic Binary Object-oriented Data Model (Sem-ODM) and Semantic SQL query language to capture the semantics of the data sources being integrated and to provide an easy-to-use query facility; (ii.) a methodology for semantic heterogeneity resolution by investigating into the extents of the meta-data constructs of component schemas. This methodology is shown to be correct, complete and unambiguous; (iii.) a semi-automated technique for identifying semantic relations, which is the basis of semantic knowledge for integration and querying, using shared ontologies for context-mediation; (iv.) resolutions for schematic conflicts and a language for defining global views from a set of component Sem-ODM schemas; (v.) design of a knowledge base for storing and manipulating meta-data and knowledge acquired during the integration process. This knowledge base acts as the interface between integration and query processing modules; (vi.) techniques for Semantic SQL query processing and optimization based on semantic knowledge in a heterogeneous database environment; and (vii.) a framework for intelligent computing and communication on the Internet applying the concepts of our work.

Navigation and meteorological data during campaign TARA_20110826Z of the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present dataset contains navigation and meteorological data measured during one campaign of the Tara Oceans Expedition. Latitude and Longitude were obtained from TSG data.

Navigation and meteorological data during campaign TARA_20110928Z of the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present dataset contains navigation and meteorological data measured during one campaign of the Tara Oceans Expedition. Latitude and Longitude were obtained from TSG data.

Navigation and meteorological data during campaign TARA_20110626Z of the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present dataset contains navigation and meteorological data measured during one campaign of the Tara Oceans Expedition. Latitude and Longitude were obtained from TSG data.