2,373 research outputs found

    Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

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    <p>Abstract</p> <p>Background</p> <p>The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortunately, efforts to annotate, classify, and analyze these chemical entities have largely remained in the hands of human curators using manual or semi-automated protocols, leaving many novel entities unclassified. Since chemical function is often closely linked to structure, accurate structure-based classification and annotation of chemical entities is imperative to understanding their functionality.</p> <p>Results</p> <p>As part of an exploratory study, we have investigated the utility of semantic web technologies in automated chemical classification and annotation of lipids. Our prototype framework consists of two components: an ontology and a set of federated web services that operate upon it. The formal lipid ontology we use here extends a part of the LiPrO ontology and draws on the lipid hierarchy in the LIPID MAPS database, as well as literature-derived knowledge. The federated semantic web services that operate upon this ontology are deployed within the Semantic Annotation, Discovery, and Integration (SADI) framework. Structure-based lipid classification is enacted by two core services. Firstly, a structural annotation service detects and enumerates relevant functional groups for a specified chemical structure. A second service reasons over lipid ontology class descriptions using the attributes obtained from the annotation service and identifies the appropriate lipid classification. We extend the utility of these core services by combining them with additional SADI services that retrieve associations between lipids and proteins and identify publications related to specified lipid types. We analyze the performance of SADI-enabled eicosanoid classification relative to the LIPID MAPS classification and reflect on the contribution of our integrative methodology in the context of high-throughput lipidomics.</p> <p>Conclusions</p> <p>Our prototype framework is capable of accurate automated classification of lipids and facile integration of lipid class information with additional data obtained with SADI web services. The potential of programming-free integration of external web services through the SADI framework offers an opportunity for development of powerful novel applications in lipidomics. We conclude that semantic web technologies can provide an accurate and versatile means of classification and annotation of lipids.</p

    Indicators Measuring the Performance of Malaria Programs Supported by the Global Fund in Asia, Progress and the Way Forward

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    INTRODUCTION: In 2010, the Global Fund provided more than 75% of external international financing for malaria control. The Global Fund uses performance based funding in the grants it finances. This paper analyses the indicators used to measure the performance of Global Fund supported malaria grants in Asia. METHODS: Indicators used in the performance frameworks for all Global Fund supported malaria grants in Asia were retrieved from grant database and grouped into impact, outcome, output and input categories and categorized by service delivery areas. Indicators of each group were compared over rounds. Indicators used in performance frameworks were compared with internationally adopted indicators included in the Monitoring and Evaluation Toolkit developed by the Global Fund and international technical agencies. RESULTS: Between 2002 and 2010, 1,434 indicators were included in the performance frameworks of the 48 malaria grants awarded in Asia, including 229 impact and 227 outcome indicators, 437 output and 541 input indicators, with an average of 29.9 indicators per grant. The proportion of impact and outcome indicators increased over rounds, with that of input indicators declining from 44.1% in Round 1 to 22.7% in Round 9. CONCLUSIONS: Input indicators, which have predominated the performance frameworks of the Global Fund supported malaria programs in Asia have declined between Rounds 1 and 9. However, increased alignment with internationally adopted indicators included in the Monitoring and Evaluation Toolkit is needed to improve the validity of reported results

    In situ phase transformation synthesis of unique Janus Ag2O/Ag2CO3 heterojunction photocatalyst with improved photocatalytic properties

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    Herein, Ag2O/Ag2CO3 nanocomposite with unique Janus morphology was synthesized by a facile ion-exchange followed by an in situ phase transformation method with precise control of its nucleation and growth processes. Contrary to conventional synthetic procedures of Janus architectures, the present Janus system was constructed without the need for surfactants or toxic chemicals. Most importantly, the visible-light-absorbing Janus Ag2O/Ag2CO3 nanocomposite exhibits a remarkable performance toward the degradation of Rhodamine B and 4-chlorophenol, far superior to that observed for bare Ag2CO3. The obvious enhancement of the photocatalytic performance of this nanocomposite is mainly attributed to the intimate Ag2O/Ag2CO3 interface created by its exceptional Janus architecture, which in turn allows for rapid charge transfer processes. Additionally, the Janus system exhibited a high photostability during recycling experiments with no significant change in the degradation activity

    A prospective study of differences in duodenum compared to remaining small bowel motion between radiation treatments: Implications for radiation dose escalation in carcinoma of the pancreas

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    PURPOSE: As a foundation for a dose escalation trial, we sought to characterize duodenal and non-duodenal small bowel organ motion between fractions of pancreatic radiation therapy. PATIENTS AND METHODS: Nine patients (4 women, 5 men) undergoing radiation therapy were enrolled in this prospective study. The patients had up to four weekly CT scans performed during their course of radiation therapy. Pancreas, duodenum and non-duodenal small bowel were then contoured for each CT scan. On the initial scan, a four-field plan was generated to fully cover the pancreas. This plan was registered to each subsequent CT scan. Dose-volume histogram (DVH) analyses were performed for the duodenum, non-duodenal small bowel, large bowel, and pancreas. RESULTS: With significant individual variation, the volume of duodenum receiving at least 80% of the prescribed dose was consistently greater than the remaining small bowel. In the patient with the largest inter-fraction variation, the fractional volume of non-duodenal small bowel irradiated to at least the 80% isodose line ranged from 1% to 20%. In the patient with the largest inter-fraction variation, the fractional volume of duodenum irradiated to at least the 80% isodose line ranged from 30% to 100%. CONCLUSION: The volume of small bowel irradiated during four-field pancreatic radiation therapy changes substantially between fractions. This suggests dose escalation may be possible. However, dose limits to the duodenum should be stricter than for other segments of small bowel

    Thermal and mechanical properties of hemp fabric-reinforced nanoclay-cement nano-composites

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    The influence of nanoclay on thermal and mechanical properties of hemp fabric-reinforced cement composite is presented in this paper. Results indicate that these properties are improved as a result of nanoclay addition. An optimum replacement of ordinary Portland cement with 1 wt% nanoclay is observed through improved thermal stability, reduced porosity and water absorption as well as increased density, flexural strength, fracture toughness and impact strength of hemp fabric-reinforced nanocomposite. The microstructural analyses indicate that the nanoclay behaves not only as a filler to improve the microstructure but also as an activator to promote the pozzolanic reaction and thus improve the adhesion between hemp fabric and nanomatrix

    Localized delivery of CRISPR/dCas9 via layer-by-layer self-assembling peptide coating on nanofibers for neural tissue engineering

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    The clustered regularly interspaced short palindromic repeat (CRISPR) systems have a wide variety of applications besides precise genome editing. In particular, the CRISPR/dCas9 system can be used to control specific gene expression by CRISPR activation (CRISPRa) or interference (CRISPRi). However, the safety concerns associated with viral vectors and the possible off-target issues of systemic administration remain huge concerns to be safe delivery methods for CRISPR/Cas9 systems. In this study, a layer-by-layer (LbL) self-assembling peptide (SAP) coating on nanofibers is developed to mediate localized delivery of CRISPR/dCas9 systems. Specifically, an amphiphilic negatively charged SAP− is first coated onto PCL nanofibers through strong hydrophobic interactions, and the pDNA complexes and positively charged SAP+-RGD are then absorbed via electrostatic interactions. The SAP-coated scaffolds facilitate efficient loading and sustained release of the pDNA complexes, while enhancing cell adhesion and proliferation. As a proof of concept, the scaffolds are used to activate GDNF expression in mammalian cells, and the secreted GDNF subsequently promotes neurite outgrowth of rat neurons. These promising results suggest that the LbL self-assembling peptide coated nanofibers can be a new route to establish a bioactive interface, which provides a simple and efficient platform for the delivery of CRISPR/dCas9 systems for regenerative medicine.Agency for Science, Technology and Research (A*STAR)Ministry of Education (MOE)Accepted versio
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