Life Sciences Community Research Articles

A Minimal Information Model for Potential Drug-Drug Interactions.

Despite the significant health impacts of adverse events associated with drug-drug interactions, no standard models exist for managing and sharing evidence describing potential interactions between medications. Minimal information models have been used in other communities to establish community consensus around simple models capable of communicating useful information. This paper reports on a new minimal information model for describing potential drug-drug interactions. A task force of the Semantic Web in Health Care and Life Sciences Community Group of the World-Wide Web consortium engaged informaticians and drug-drug interaction experts in in-depth examination of recent literature and specific potential interactions. A consensus set of information items was identified, along with example descriptions of selected potential drug-drug interactions (PDDIs). User profiles and use cases were developed to demonstrate the applicability of the model. Ten core information items were identified: drugs involved, clinical consequences, seriousness, operational classification statement, recommended action, mechanism of interaction, contextual information/modifying factors, evidence about a suspected drug-drug interaction, frequency of exposure, and frequency of harm to exposed persons. Eight best practice recommendations suggest how PDDI knowledge artifact creators can best use the 10 information items when synthesizing drug interaction evidence into artifacts intended to aid clinicians. This model has been included in a proposed implementation guide developed by the HL7 Clinical Decision Support Workgroup and in PDDIs published in the CDS Connect repository. The complete description of the model can be found at https://w3id.org/hclscg/pddi.

Improvement in Laboratory Eating Behavior at the Microstructural Level of Bites by Young Women with Overweight and Obesity

Abstract Objectives Effective weight management interventions that target within-meal eating behaviors, such as biting, chewing, swallowing, and pausing, are limited. The Eating Pace Instructional Classes (EPIC) intervention successfully coached healthy young-adult females with overweight and obesity to eat slower by modifying their within-meal eating behaviors. It was hypothesized that the experimental group who received the 5-week EPIC intervention would reduce bite frequency, bite size, and bite number more than the non-treatment control group. Methods This was a secondary data analysis of mixed-macronutrient ad libitum meals eaten over a universal eating monitor (UEM) in the laboratory, before (PRE) and after (POST) the intervention. A total of 82 meals was analyzed: PRE and POST meals for each experimental participant (E: n = 21, mean age 20.2 ± 3.1 years, mean BMI 30.9 ± 2.1 kg/m2) and each control participant (C: n = 20, mean age 21.4 ± 4.7 years, mean BMI 31.7 ± 2.8 kg/m2). A manual approach was created from pilot work and calculated bite outcomes from UEM data during scale stability, using the range of 1–31 grams for a bite of food and other specific criteria. From this manual method, we developed bite analysis software in MatLab that calculated bite frequency, bite size, and bite number for each meal. Results Repeated-measures analysis of variance indicated a significant time-by-group effect for mean bite frequency (E: −0.75 ± 0.39, C: +0.18 ± 0.42 bites/minute; P = 0.025, ηp2 = 0.123), but changes in mean bite size (E: −0.50 ± 0.04, C: +0.68 ± 1.06 grams; P = 0.254, ηp2 = 0.033) and mean bite number (E: +2.57 ± 6.66, C: +2.45 ± 2.94 bites; P = 0.974, ηp2 = 0.000) did not reach significance. Conclusions The EPIC intervention that reduced the overall eating rate of women who were overweight and obese effectively decreased bite frequency. There was a trend towards smaller bite size, and bite number did not change significantly. These promising results support the incorporation of the EPIC approach and our microstructural methodology into the design and assessment of weight management interventions that modify within-meal eating behaviors. Funding Sources The randomized controlled EPIC Study, the basis for this secondary data analysis, was funded by a University of Rhode Island College of the Environment and Life Sciences (CELS) Community Access to Research and Extension Services (CARES) grant.

Alginate-based Microcapsules Facilitate Targeted Release of Lactobacillus plantarum LAB12 in vivo

Event Abstract Back to Event Alginate-based microcapsules facilitate targeted release of Lactobacillus plantarum LAB12 in vivo Muhamad Fareez Ismail1, 2, 3, Siong Meng Lim1, 2 and Kalavathy Ramasamy1, 2* 1 Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Malaysia 2 Collaborative Drug Discovery Research (CDDR) Group, Universiti Teknologi MARA (UiTM), Pharmaceutical and Life Sciences Community of Research, Malaysia 3 Faculty of Dentistry, Mahsa University, Malaysia Background Microencapsulation can essentially provide probiotic lactic acid bacteria (LAB) a protective barrier against harsh gastrointestinal conditions. Although cell liberation in the intestines is deemed a mandatory prerequisite for effective application, in vivo validation of the delivery of LAB to the target site and subsequent digestibility of encapsulating matrix remains limited. Methods This study validated the release and fate of orally administered L. plantarum LAB12 encapsulated in a unique blend of alginate (Alg) and pea protein isolate (PPi) in Sprague Dawley rats (male; 4-6 weeks). Fate of the ingested microencapsulated LAB12 was examined at 1 and 4 hours post-ingestion in the stomach and the large intestines, respectively, by means of confocal imaging. The release of microencapsulated LAB12 were quantitatively assessed in terms of the proportion and relative abundance of theL. plantarum in various gut sections by qPCR. Results The microcapsules started to disintegrate in the large intestines 4 hours post-ingestion as evident by the presence of rod-shaped LAB12 and small pieces of polymeric matrix. qPCR confirmed that ingesta harvested from the stomach exhibited very minimal traces (<1 log CFU g-1) of L. plantarum which was unlikely associated with cell burst release from Alg-PPi microcapsules. Relative abundance of L. plantarum indicated an almost complete release of LAB12 from capsules after 16 hours post ingestion at target sites which included the ileum, caecum and colon. Conclusion Alg-PPi could serve as an ideal wall matrix that protects LAB12 from harsh gastric conditions and facilitate their release in the target site within the intestinal tract. Keywords: Lactobacillus plantarum LAB12, microencapsulation, Alginate, Pea protein isolate, Targeted release Conference: International Conference on Drug Discovery and Translational Medicine 2018 (ICDDTM '18) “Seizing Opportunities and Addressing Challenges of Precision Medicine”, Putrajaya, Malaysia, 3 Dec - 5 Feb, 2019. Presentation Type: Poster Presentation Topic: Inflammatory diseases Citation: Ismail M, Lim S and Ramasamy K (2019). Alginate-based microcapsules facilitate targeted release of Lactobacillus plantarum LAB12 in vivo. Front. Pharmacol. Conference Abstract: International Conference on Drug Discovery and Translational Medicine 2018 (ICDDTM '18) “Seizing Opportunities and Addressing Challenges of Precision Medicine”. doi: 10.3389/conf.fphar.2019.63.00032 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 22 Oct 2018; Published Online: 17 Jan 2019. * Correspondence: Dr. Kalavathy Ramasamy, Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Bandar Puncak Alam, Malaysia, kalav922@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Muhamad Fareez Ismail Siong Meng Lim Kalavathy Ramasamy Google Muhamad Fareez Ismail Siong Meng Lim Kalavathy Ramasamy Google Scholar Muhamad Fareez Ismail Siong Meng Lim Kalavathy Ramasamy PubMed Muhamad Fareez Ismail Siong Meng Lim Kalavathy Ramasamy Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Lactobacillus plantarum LAB12 Enhances Cognitive Function via Modulation of Neurotransmitters and Neuropeptides in Antibiotic- and LPS-challenged Rats

Event Abstract Back to Event Lactobacillus plantarum LAB12 enhances cognitive function via modulation of neurotransmitters and neuropeptides in antibiotic- and LPS-challenged rats Muhammad Syukri Noor Azman1, 2, Siong Meng Lim1, 2, Fei Tieng Lim2 and Kalavathy Ramasamy1, 2* 1 Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Malaysia 2 Collaborative Drug Discovery Research (CDDR) Group, Universiti Teknologi MARA (UiTM), Pharmaceutical and Life Sciences Community of Research, Malaysia Background Based on the notion that probiotic lactic acid bacteria (LAB) could potentially correct dysbiosis of microbiota and ameliorate neuroinflammation via the Gut-Brain Axis, this study assessed the effects of LAB12 on memory, expression of major neurotransmitters and neuropeptides. Methods Sprague Dawley rats (male, 3 months old) were being administered with an antibiotic cocktail (imipenem, vancomycin, ampicillin, ciprofloxacin and metronidazole) before being challenged with 0.25mg/kg LPS. The rodents were divided into four groups (n=6/group): wild-type, LPS control, antibiotics (ABX) +LPS and ABX+LAB12+LPS. The rats were subjected to the Morris Water Maze Test. Rat hippocampi were harvested and subjected to biochemical analyses and metabolic assays. Results LAB12 improved spatial learning and memory in antibiotic- and LPS-challenged rats. ABX+LAB12+LPS group was presented with reduced escape latency and escape distance when compared to the ABX+LPS counterpart. In terms of neurotransmitters in the hippocampus, increased serotonin (5HT) and gamma-aminobutyric acid (GABA) was observed in ABX+LAB12+LPS when compared to ABX+LPS. There were also increased neurotensin (NT) and neuropeptide Y (NPY) levels in the hippocampus of ABX+LAB12+LPS when compared to ABX+LPS, indicating enhanced cognitive processing. Whilst mitochondrial complex enzymes (II, III and IV) were impaired in the hippocampus of ABX+LPS rats, supplementation of LAB12 ameliorated this effect. Conclusion The present findings implied that L. plantarum LAB12 could potentially improve memory impairment via modulation of neurotransmitters and neuropeptides in the CNS. Keywords: Lactobacillus plantarum LAB12, Memory enhancing, neurotransmitters, Neuropeptides, antibiotics Conference: International Conference on Drug Discovery and Translational Medicine 2018 (ICDDTM '18) “Seizing Opportunities and Addressing Challenges of Precision Medicine”, Putrajaya, Malaysia, 3 Dec - 5 Feb, 2019. Presentation Type: Poster Presentation Topic: Mental health Citation: Noor Azman M, Lim S, Lim F and Ramasamy K (2019). Lactobacillus plantarum LAB12 enhances cognitive function via modulation of neurotransmitters and neuropeptides in antibiotic- and LPS-challenged rats. Front. Pharmacol. Conference Abstract: International Conference on Drug Discovery and Translational Medicine 2018 (ICDDTM '18) “Seizing Opportunities and Addressing Challenges of Precision Medicine”. doi: 10.3389/conf.fphar.2018.63.00074 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 27 Nov 2018; Published Online: 17 Jan 2019. * Correspondence: PhD. Kalavathy Ramasamy, Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia, kalav922@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Muhammad Syukri Noor Azman Siong Meng Lim Fei Tieng Lim Kalavathy Ramasamy Google Muhammad Syukri Noor Azman Siong Meng Lim Fei Tieng Lim Kalavathy Ramasamy Google Scholar Muhammad Syukri Noor Azman Siong Meng Lim Fei Tieng Lim Kalavathy Ramasamy PubMed Muhammad Syukri Noor Azman Siong Meng Lim Fei Tieng Lim Kalavathy Ramasamy Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Hepatoprotection by probiotics in vivo: a systematic review and meta-analysis

Event Abstract Back to Event Hepatoprotection by probiotics in vivo: a systematic review and meta-analysis Faezah Sabirin1, 2, 3, Siong Meng Lim1, 2, Chin Fen Neoh1, 2 and Kalavathy Ramasamy1, 2* 1 Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Malaysia 2 Collaborative Drug Discovery Research (CDDR) Group, Universiti Teknologi MARA (UiTM), Pharmaceutical and Life Sciences Community of Research, Malaysia 3 Faculty of Dentistry, Universiti Teknologi MARA, Malaysia Background The severity of nonalcoholic fatty liver disease (NAFLD) has been found to be associated with gut dysbiosis. Probiotics, which are beneficial in maintaining a healthy gut, may be useful in delaying development of NAFLD. This study was undertaken to systematically review and analyse the impact of evidence pertaining to probiotic supplementation in NAFLD in vivo. Methods Literature search was conducted between October 2017 - May 2018 using Cochrane, PubMed/ MEDLINE, Embase, Springer and Web of Science. Article identification and data extraction were performed by four reviewers based on inclusion and exclusion criteria. Risk of bias was assessed using SYRCLE tool. Meta-analysis was performed using RevMan 5.3. The primary outcomes included severity of liver histopathology [i.e. total NAFLD activity score (NAS)] and serum alanine aminotransferase (ALT). The secondary outcomes included hepatic lipid and triglyceride, as well as serum triglyceride, HDL and LDL cholesterol. Mean differences (MD) or standard MD (SMD) between groups were analysed using Random-Effect Model. Statistical heterogeneity was assessed using I2 test. Results Twenty-eight studies were included in the systematic review whilst only 9 were selected for subsequent meta-analysis. The shortlisted literature was predominantly presented with low or unclear risk of bias. When compared to control, the total NAS was significantly lower in probiotic group (MD=-1.81; 95% CI=-2.37, -1.24, p<0.00001). The heterogeneity was moderate but insignificant (I2=55%, p=0.05). Significant reduction in ALT was noted in probiotic group (MD=-0.99; 95% CI=-1.55, -0.43, p=0.0005). The heterogeneity was, however, substantial (I2=70%, p<0.0001) when compared to control. The significant reduction in total NAS was accompanied by significantly lower hepatic lipid (p<0.00001) and triglyceride (p<0.0001). Nevertheless, no significant changes were noted in other serum parameters. Conclusion Probiotic supplementation was associated with significant reduction in total NAS and ALT. The present findings strongly implied the hepatoprotective potential of proboitics. Keywords: Dysbiosis, Hepatic lipid, ALT, NAFLD (non alcoholic fatty liver disease), Probiotics, total NAFLD activity score, hepatic triglyceride Conference: International Conference on Drug Discovery and Translational Medicine 2018 (ICDDTM '18) “Seizing Opportunities and Addressing Challenges of Precision Medicine”, Putrajaya, Malaysia, 3 Dec - 5 Feb, 2019. Presentation Type: Oral Presentation Topic: Metabolic diseases Citation: Sabirin F, Lim S, Neoh C and Ramasamy K (2019). Hepatoprotection by probiotics in vivo: a systematic review and meta-analysis. Front. Pharmacol. Conference Abstract: International Conference on Drug Discovery and Translational Medicine 2018 (ICDDTM '18) “Seizing Opportunities and Addressing Challenges of Precision Medicine”. doi: 10.3389/conf.fphar.2018.63.00140 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 22 Oct 2018; Published Online: 17 Jan 2019. * Correspondence: Dr. Kalavathy Ramasamy, Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia, kalav922@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Faezah Sabirin Siong Meng Lim Chin Fen Neoh Kalavathy Ramasamy Google Faezah Sabirin Siong Meng Lim Chin Fen Neoh Kalavathy Ramasamy Google Scholar Faezah Sabirin Siong Meng Lim Chin Fen Neoh Kalavathy Ramasamy PubMed Faezah Sabirin Siong Meng Lim Chin Fen Neoh Kalavathy Ramasamy Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Identifying ELIXIR Core Data Resources.

The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR's sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure.

Information Literacy Instruction Programs: Supporting the College of Agriculture and Life Sciences Community at Virginia Tech

When developing instructional programs related to information literacy at a university, a logical audience to focus on is undergraduates. However, information literacy spans far beyond the traditional ability to find, access, evaluate, use, and properly cite information. It also encompasses the ability to evaluate the impact of scholarship, determine appropriate data-management practices, understand author rights, promote ethical use of scholarship, and maintain an awareness of changes in scholarly communication. Between 2010 and 2016 librarians at Virginia Tech have focused on developing programs to strengthen several of these information literacy skills across the continuum of students, faculty, and extension agents in the College of Agriculture and Life Sciences (CALS). Starting with undergraduates, traditional information literacy skills were incorporated into the two CALS First-Year Experience programs. A scientific writing workshop and online information literacy course were designed for CALS graduate students. Extension agents and faculty were introduced to both traditional and more advanced applications to explore how changes in the information landscape impacts their work. This paper will discuss how these librarians have partnered to create and promote these information literacy initiatives.

Identifying ELIXIR Core Data Resources.

The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR's sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure.

Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications.

The HUPO Human Proteome Project (HPP) has two overall goals: (1) stepwise completion of the protein parts list-the draft human proteome including confidently identifying and characterizing at least one protein product from each protein-coding gene, with increasing emphasis on sequence variants, post-translational modifications (PTMs), and splice isoforms of those proteins; and (2) making proteomics an integrated counterpart to genomics throughout the biomedical and life sciences community. PeptideAtlas and GPMDB reanalyze all major human mass spectrometry data sets available through ProteomeXchange with standardized protocols and stringent quality filters; neXtProt curates and integrates mass spectrometry and other findings to present the most up to date authorative compendium of the human proteome. The HPP Guidelines for Mass Spectrometry Data Interpretation version 2.1 were applied to manuscripts submitted for this 2016 C-HPP-led special issue [ www.thehpp.org/guidelines ]. The Human Proteome presented as neXtProt version 2016-02 has 16,518 confident protein identifications (Protein Existence [PE] Level 1), up from 13,664 at 2012-12, 15,646 at 2013-09, and 16,491 at 2014-10. There are 485 proteins that would have been PE1 under the Guidelines v1.0 from 2012 but now have insufficient evidence due to the agreed-upon more stringent Guidelines v2.0 to reduce false positives. neXtProt and PeptideAtlas now both require two non-nested, uniquely mapping (proteotypic) peptides of at least 9 aa in length. There are 2,949 missing proteins (PE2+3+4) as the baseline for submissions for this fourth annual C-HPP special issue of Journal of Proteome Research. PeptideAtlas has 14,629 canonical (plus 1187 uncertain and 1755 redundant) entries. GPMDB has 16,190 EC4 entries, and the Human Protein Atlas has 10,475 entries with supportive evidence. neXtProt, PeptideAtlas, and GPMDB are rich resources of information about post-translational modifications (PTMs), single amino acid variants (SAAVSs), and splice isoforms. Meanwhile, the Biology- and Disease-driven (B/D)-HPP has created comprehensive SRM resources, generated popular protein lists to guide targeted proteomics assays for specific diseases, and launched an Early Career Researchers initiative.

Effect of an Exercise and Dietary Intervention on Cognitive Function in Obese Older Women

BACKGROUND: Cognitive decline in older adults is a public health problem and prior research shows that higher levels of physical activity and dietary factors are associated with higher cognitive function. However, it is unclear how an exercise and diet intervention affects cognitive function in obese older women. PURPOSE: To examine the effect of a combined Tai Chi (TC), resistance training (RT), and diet intervention on cognitive function and to evaluate the relationship between cognitive function and physical function in older obese women. METHODS: This was a non-randomized study where 31 obese (BMI= 37.6 ± 4.5 kg/m2) older (age= 65.1 ± 8.4 years) women (61% African-American) were recruited to a 12-week intervention (EXD) group or to a control (CON) group. Cognitive function was measured via the Repeatable Battery for the Assessment of Neurological Status (RBANS) test. Other outcomes were grip strength, 4 m walk, leg strength, chair stands, and timed up and go. Baseline measures were assessed under standardized conditions prior to the start and at the end of the study by trained staff supervised by a licensed speech-language pathologist. The EXD group (n=17; 5 dropouts) engaged in three 45 min TC sessions and two 45 min RT sessions per week. A registered dietitian conducted the behaviorally based diet sessions once a week. The CON group (n=8; 1 missing data) was asked to maintain a normal lifestyle. Pearson correlations were done for baseline physical function and RBANS score and analysis of covariance was used to compare RBANS score change between groups adjusted for baseline. RESULTS: RBANS score was positively correlated with grip strength (r = 0.51) and negatively correlated with timed up and go, (r = -0.40), chair stand (r = -0.28) and gait speed (r = -0.37) times (all p<0.05). Baseline RBANS score (87.5 ± 19.5) and baseline age were not correlated and RBANS scores were not different between groups (p= 0.80). There were no differences in RBANS score change in the EXD vs. CON groups (3.1 ± 2.0 vs. 2.5 ± 2.9; p=0.86). CONCLUSIONS: An exercise and diet intervention does not change cognitive function in older obese women, but baseline cognitive function is moderately correlated with physical function. A longer intervention needs to be tested in a larger sample to verify these results. Supported by the College of Environment and Life Sciences Community Access to Research and Extension Services (CELS CARES) grant, USDA, at the University of Rhode Island.

Semantic enrichment of longitudinal clinical study data using the CDISC standards and the semantic statistics vocabularies

BackgroundThere is an increasing recognition of the need for the data capture phase of clinical studies to be improved and for more effective sharing of clinical data. The Health Care and Life Sciences community has embraced semantic technologies to facilitate the integration of health data from electronic health records, clinical studies and pharmaceutical research. This paper explores the integration of clinical study data exchange standards and semantic statistic vocabularies to deliver clinical data as linked data in a format that is easier to enrich with links to complementary data sources and consume by a broad user base.MethodsWe propose a Linked Clinical Data Cube (LCDC), which combines the strength of the RDF Data Cube and DDI-RDF vocabulary to enrich clinical data based on the CDISC standards. The CDISC standards provide the mechanisms for the data to be standardised, made more accessible and accountable whereas the RDF Data Cube and DDI-RDF vocabularies provide novel approaches to managing large volumes of heterogeneous linked data resources.ResultsWe validate our approach using a large-scale longitudinal clinical study into neurodegenerative diseases. This dataset, comprising more than 1600 variables clustered in 25 different sub-domains, has been fully converted into RDF forming one main data cube and one specialised cube for each sub-domain. One sub-domain, the Medications specialised cube, has been linked to relevant external vocabularies, such as the Australian Medicines Terminology and the ATC DDD taxonomy and DrugBank terminology. This provides new dimensions on which to query the data that promote the exploration of drug-drug and drug-disease interactions.ConclusionsThis implementation highlights the effectiveness of the association of the semantic statistics vocabularies for the publication of large heterogeneous data sets as linked data and the integration of the semantic statistics vocabularies with the CDISC standards. In particular, it demonstrates the potential of the two vocabularies in overcoming the monolithic nature of the underlying model and improving the navigation and querying of the data from multiple angles to support richer data analysis of clinical study data. The forecasted benefits are more efficient use of clinicians’ time and the potential to facilitate cross-study analysis.

Education

The SIAM Review Education section has many objectives. One of them is to bring contemporary applications to mathematics courses that would otherwise be outside of the mainstream curriculum. Another is to present topics in applied mathematics in new ways that provide a pedagogical advantage. In this issue, we feature an article that does both. In “Population Interactions in Ecology: A Rule-Based Approach to Modeling Ecosystems in a Mass-Conserving Framework,” authors Cropp and Norbury take a comprehensive and modern look at population modeling. In many differential equations and dynamics textbooks, population dynamics begins and ends with the famous Lotka--Volterra model with perhaps some mild variations as exercises. Presented as an application of the analysis of systems of differential equations, this approach leaves the student and instructor with the sense that the deep questions of ecology can be answered with attractors and limit cycles. Unfortunately, those in the life sciences community do not accept the model as relevant. Indeed, if this is the only exposure mathematics students have to population models, it may leave students with an overly simplistic perspective on ecology. On the other side of the disciplinary divide, courses for nonmathematics majors tend to present population ecology in a “just in time” fashion where solutions to the Verhulst equation are presented as formulae without much explanation. These students will be left without the necessary modeling and analytical skills to quantitatively study ecological systems. This Education section feature takes on the problem directly through what they call the “conservative normal” (CN) framework. While the approach is a theoretical basis for understanding ecological systems, it has considerable merit as a way for students to construct and understand models of populations in a food web. The CN framework is a system of rules that maps ecological principles to mathematical structures and formulae. For instance, the first rule is that one should measure a population by the limiting nutrient it contains (e.g., do not model the number of plankton cells, model the mass of nitrogen in the living population). It is both a modeling approach and a unified way for students to think about many interacting species. Other rules include mechanisms for change in populations, resource constraints, and other essential processes that govern ecological systems. The authors then apply CN to a variety of small but interesting problems. These include ecological systems of autotrophs where multiple species compete for a single resource, and systems of mixotrophs such as phytoplankton that can switch between growing inefficiently via photosynthesis and grazing on other phytoplankton. Given that phytoplankton consume a significant fraction of the carbon dioxide produced from burning fossil fuels, one could argue that it may be more relevant for nonmathematicians to learn about these mixotrophic systems before dwelling on cycles in the Canadian Lynx and the Snowshoe Hare populations. The CN framework puts whole categories of ecological systems on equal footing for students to explore. In summary, this article is a notable contribution that spans a disciplinary divide between the mathematics and life sciences communities. As such, the CN framework may be a valuable resource in classes for mathematicians as well as classes for nonmathematicians. On one hand, it presents classic applications of differential equations in an exciting new way, and on the other, it links biological principles to mathematical structures in a way that will appeal to nonmathematicians. While the examples in this article are aimed at the undergraduate curriculum, the CN framework is useful in many broad contexts, including systems with spatial dependence that would likely end up in a graduate curriculum or more specialized course. Most importantly, for the relatively low cost of introducing the framework, this approach gives students a broader perspective on ecological systems and the modeling process in general than what is typically provided in differential equations and dynamical systems texts.

MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data.

Multi-omics data-driven scientific discovery crucially rests on high-throughput technologies and data sharing. Currently, data are scattered across single omics repositories, stored in varying raw and processed formats, and are often accompanied by limited or no metadata. The Multi-Omics Profiling Expression Database (MOPED, http://moped.proteinspire.org ) version 2.5 is a freely accessible multi-omics expression database. Continual improvement and expansion of MOPED is driven by feedback from the Life Sciences Community. In order to meet the emergent need for an integrated multi-omics data resource, MOPED 2.5 now includes gene relative expression data in addition to protein absolute and relative expression data from over 250 large-scale experiments. To facilitate accurate integration of experiments and increase reproducibility, MOPED provides extensive metadata through the Data-Enabled Life Sciences Alliance (DELSA Global, http://delsaglobal.org ) metadata checklist. MOPED 2.5 has greatly increased the number of proteomics absolute and relative expression records to over 500,000, in addition to adding more than four million transcriptomics relative expression records. MOPED has an intuitive user interface with tabs for querying different types of omics expression data and new tools for data visualization. Summary information including expression data, pathway mappings, and direct connection between proteins and genes can be viewed on Protein and Gene Details pages. These connections in MOPED provide a context for multi-omics expression data exploration. Researchers are encouraged to submit omics data which will be consistently processed into expression summaries. MOPED as a multi-omics data resource is a pivotal public database, interdisciplinary knowledge resource, and platform for multi-omics understanding.

Diet quality in community dwelling obese women following a behavioral‐based diet, tai chi, and resistance training intervention (1026.7)

Up to 48% of older adults may be at increased nutrition risk. This is a concern as the number of older adults is projected to double by 2030 and obesity is suspected to rise to over 20% in the same population. The purpose of this analysis is to examine the impact of a diet and exercise intervention on diet quality in obese women in an urban setting. There were 26 women with mean age of 65.3 ± 8.1 years and BMI of 38.0 ±4.6 kg/m2 who completed a community based diet and exercise intervention. Seventeen women, 65% African‐American, were assigned to the intervention group (EXD) and participated in 12 weeks of Tai Chi (TC), resistance training (RT), and behavioral based diet intervention. Nine women were assigned to the control group (CON). The Dietary Screening Tool (DST) was used to assess diet quality; higher scores indicate better quality. Using an independent t‐test the EXD group had a significantly higher diet quality compared to the CON group (66.5 ± 10.2 vs. 53.5 ± 13.8; p=0.025) at post ‐intervention. Results from this analysis indicate that a behaviorally‐based diet, TC, and RT intervention may result in improved diet quality, however further research is needed.Grant Funding Source: College of Environment and Life Sciences Community Access to Research and Extension Services, USDA

The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community

The biology and disease oriented branch of the Human Proteome Project (B/D-HPP) was established by the Human Proteome Organization (HUPO) with the main goal of supporting the broad application of state-of the-art measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human disease. This will be accomplished through the generation of research and informational resources that will support the routine and definitive measurement of the process or disease relevant proteins. The B/D-HPP is highly complementary to the C-HPP and will provide datasets and biological characterization useful to the C-HPP teams. In this manuscript we describe the goals, the plans, and the current status of the of the B/D-HPP.

Life Support For Montreal R&amp;D

As drug companies move their R&D operations out of Quebec in rapid succession, Canadian authorities are trying to sustain the region’s life sciences community. In the latest effort, the government, along with AstraZeneca and Pfizer, is committing $100 million over five years to establish the NeoMed Institute, a nonprofit research center in Montreal. NeoMed aspires to bridge the gap between basic research and early clinical studies for drug candidates by offering universities and biotech start-ups funding and services. The hope is to eventually restore some of the hundreds of R&D jobs the region has lost in the past two years. AstraZeneca and Pfizer, along with any other big pharma partners that join NeoMed, will have an option to license molecules developed there. AstraZeneca is kicking in its former neuroscience research facility, which was focused on developing small molecules, along with $5 million and intellectual property for three potential pain drugs. ...

Integration and analysis of multi-type high-throughput data for biomolecular knowledge discovery

Erik Bongcam-Rudloff received his doctorate in medical sciences from Uppsala University, Sweden. He is now the Director of the SLU Global Bioinformatics Centre (SGBC) at the Swedish University of Agricultural Sciences. Erik was the chairman of EMBnet (2003-2010), a science-based group of worldwide collaborating bioinformatics nodes. He also coordinated the "Test Cases" work package 4 in the FP6 EMBRACE project (2005-2010). The goal of WP4 was to collect test cases from the scientific community to identify real research problems and to provide solutions for content and tool integration. Bongcam-Rudloff is today Chair of SeqAhead, a Biomedical European COST Action: "Next Generation Sequencing Data Analysis Network" and Coordinator of ALLBIO, a FP7 project: "Broadening the Bioinformatics Infrastructure to unicellular, animal, and plant science". He is also the founder of eBioinformatics.org the creators of eBiotools, eBioKit, eBioX and eBioKit. His main research deals with development of bioinformatics solutions for the Life Sciences community. In this talk he will discuss the new techniques that are now driving the generation of knowledge (especially in biomedicine and molecular life sciences) to new dimensions eg. NGS. He will also discuss the new opportunities in human and non-human research that these techniques create but also the new challenges in the design of ontologies for data and methods, and choosing common interoperability standards.

The Need for Professional Society Advocacy for a Laboratory-acquired Illness/Incident Reporting and Analysis System

Biosafety professionals have long recognized the value of information derived from the reporting and analysis of laboratory-acquired illnesses (LAIs). Analysis of events surrounding an exposure event which resulted in an LAI has been used to identify equipment and facility design issues and flaws in operational procedures, as well as the hazardous characteristics of biological agents that are being studied or manipulated. Information obtained from the investigation and analysis of LAIs is a valuable resource for assessing risks posed by proposed work with pathogens, designing and selecting protective equipment and facilities, and developing agent-specific occupational health and surveillance programs. Lessons learned from analyzing LAIs also can provide a basis for developing educational tools in the form of case studies and utilized for training laboratory workers, principal investigators, and biosafety professionals. Some institutions such as the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) have a good track record of reporting and publishing exposure events that have resulted in LAIs and continue to look for new ways to present this information to the life-sciences community and their stakeholders (CDC, 2000; Mabeus, 2012; Rusnak, 2004). Unfortunately, institutions that routinely report and share lessons learned from LAIs remain the exception rather than the rule. All institutions that have experienced LAIs should be encouraged to share with the larger life-science community, via publication in scientific journals or reporting in another accessible resource LAIrelated information and analysis of the event. Sharing the nature of the incident, the probable cause, and lessons learned with relevant stakeholders would allow many individuals and facilities to benefit from an unfortunate event (Kozlovac, 2011). One hallmark of an organization that incorporates safety as an institutional value within its organizational culture is encouraging employee participation in reporting accidents, near misses, and unsafe conditions. Another hallmark is that the organization’s leadership has established a mechanism to investigate reported issues and ensure corrective actions are identified, documented, and communicated to relevant staff in a timely manner. Although most organizations have developed internal reporting mechanisms, perhaps one of the disincentives for an organization to report and share information on LAIs and incidents with the broader community is the absence of an easy, voluntary mechanism for sharing LAI information. Indeed, a central theme common to published LAI research within the scientific literature—beginning with the first surveys conducted by Kisskalt (1915), continuing with the collective work of Sulkin and Pike (1951, 1979), and the more recent reviews by Sewell (1995), Harding and Byers (2000), and Weinstein and Singh (2009)—is that LAI risk determination is hampered by the lack of a systematic reporting mechanism at the regional, national, or international level. Indeed, biosafety professionals have intermittently discussed the need and recommended the establishment of such a system for many years. Unfortunately, establishing such a system has been beset with many challenges and obstacles, including a lack of sustained advocacy from professional biosafety organizations.

Opportunities and Challenges for the Life Sciences Community

Twenty-first century life sciences have transformed into data-enabled (also called data-intensive, data-driven, or big data) sciences. They principally depend on data-, computation-, and instrumentation-intensive approaches to seek comprehensive understanding of complex biological processes and systems (e.g., ecosystems, complex diseases, environmental, and health challenges). Federal agencies including the National Science Foundation (NSF) have played and continue to play an exceptional leadership role by innovatively addressing the challenges of data-enabled life sciences. Yet even more is required not only to keep up with the current developments, but also to pro-actively enable future research needs. Straightforward access to data, computing, and analysis resources will enable true democratization of research competitions; thus investigators will compete based on the merits and broader impact of their ideas and approaches rather than on the scale of their institutional resources. This is the Final Report for Data-Intensive Science Workshops DISW1 and DISW2. The first NSF-funded Data Intensive Science Workshop (DISW1, Seattle, WA, September 19-20, 2010) overviewed the status of the data-enabled life sciences and identified their challenges and opportunities. This served as a baseline for the second NSF-funded DIS workshop (DISW2, Washington, DC, May 16-17, 2011). Based on the findings of DISW2 the following overarching recommendation to the NSF was proposed: establish a community alliance to be the voice and framework of the data-enabled life sciences. After this Final Report was finished, Data-Enabled Life Sciences Alliance (DELSA, www.delsall.org ) was formed to become a Digital Commons for the life sciences community.

A Vision for 21st Century U.S. Policy to Support Sustainable Advancement of Scientific Discovery and Technological Innovation

OMICS: A Journal of Integrative BiologyVol. 14, No. 4 OpinionA Vision for 21st Century U.S. Policy to Support Sustainable Advancement of Scientific Discovery and Technological InnovationEugene KolkerEugene KolkerBioinformatics & High-throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington.High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington.Predictive Analytics, Seattle Children's Hospital, Seattle, Washington.Division of Biomedical & Health Informatics, Department of Medical Education & Biomedical Informatics, School of Medicine, University of Washington, Seattle, Washington.Search for more papers by this authorPublished Online:20 Aug 2010https://doi.org/10.1089/omi.2010.0068AboutSectionsView articleView Full TextPDF/EPUB ToolsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View articleFiguresReferencesRelatedDetailsCited ByA General Theory for “Post” Systems Biology: Iatromics and the Environtome Nezih Hekim and Vural Özdemir1 July 2017 | OMICS: A Journal of Integrative Biology, Vol. 21, No. 7Progress and Challenges in Developing Metabolic Footprints from Diet in Human Gut Microbial Cometabolism1 April 2015 | The Journal of Nutrition, Vol. 145, No. 5Unraveling the Complexities of Life Sciences Data Roger Higdon, Winston Haynes, Larissa Stanberry, Elizabeth Stewart, Gregory Yandl, Chris Howard, William Broomall, Natali Kolker, and Eugene Kolker13 February 2013 | Big Data, Vol. 1, No. 1Clarifying Omics Concepts, Challenges, and Opportunities for Prunus Breeding in the Postgenomic Era Pedro Martínez-Gómez, Raquel Sánchez-Pérez, and Manuel Rubio3 May 2012 | OMICS: A Journal of Integrative Biology, Vol. 16, No. 5Opportunities and Challenges for the Life Sciences Community Eugene Kolker, Elizabeth Stewart, and Vural Ozdemir8 March 2012 | OMICS: A Journal of Integrative Biology, Vol. 16, No. 3Integrated Cellular Pathology—Systems Biology of Human Diseases Anthoula Gaigneaux, Sébastien Chateauvieux, and Marc Diederich9 February 2012 | OMICS: A Journal of Integrative Biology, Vol. 16, No. 1-2Designing the Next Generation of Vaccines for Global Public Health Fabio Bagnoli, Barbara Baudner, Ravi P.N. Mishra, Erika Bartolini, Luigi Fiaschi, Paolo Mariotti, Vincenzo Nardi-Dei, Phil Boucher, and Rino Rappuoli1 September 2011 | OMICS: A Journal of Integrative Biology, Vol. 15, No. 9The Human Gutome: Nutrigenomics of the Host–Microbiome Interactions Dimiter V. Dimitrov2 August 2011 | OMICS: A Journal of Integrative Biology, Vol. 15, No. 7-8 Volume 14Issue 4Aug 2010 InformationCopyright 2010, Mary Ann Liebert, Inc.To cite this article:Eugene Kolker.A Vision for 21st Century U.S. Policy to Support Sustainable Advancement of Scientific Discovery and Technological Innovation.OMICS: A Journal of Integrative Biology.Aug 2010.333-335.http://doi.org/10.1089/omi.2010.0068Published in Volume: 14 Issue 4: August 20, 2010Online Ahead of Print:July 30, 2010PDF download