63 research outputs found
Design and implementation of a visual interface for conflicts-of-interest management in peer review venues
No full textPeer Review Conference venues are being hosted for both computer scientists and engineers to perform peer reviews on each other's works. To uphold the integrity of this process, it is crucial to minimize Conflict of Interest (COI) between an author and a peer-reviewer pair. To address this, Sourav S. Bhowmick, an associate professor at Nanyang Technological University (NTU), developed a novel data-driven system called CLOSET (COI Finder) to detect unreported COI violations for a given conference venue. This project aims to leverage the output generated by COI Finder, providing users with the tools to visualize, analyze, and manage any potential COI between authors and reviewers for a given conference venue.Bachelor's degre
Systematic Review of Escalated Imatinib Doses Compared with Sunitinib or Best Supportive Care, for the Treatment of People with Unresectable/Metastatic Gastrointestinal Stromal Tumours Whose Disease has Progressed on the Standard Imatinib Dose
No full textPMID: 21971958 [PubMed - indexed for MEDLINE] PMCID: PMC3348468 Free PMC Article This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are creditedPeer reviewe
Effect of Morphology and Size of Halloysite Nanotubes on Functional Pectin Bionanocomposites for Food Packaging Applications
No full textPectin bionanocomposite films filled with various concentrations of two different types of halloysite nanotubes were prepared and characterized in this study as potential films for food packaging applications. The two types of halloysite nanotubes were long and thin (patch) (200-30 000 nm length) and short and stubby (Matauri Bay) (50-3000 nm length) with different morphological, physical, and dispersibility properties. Both matrix (pectin) and reinforcer (halloysite nanotubes) used in this study are considered as biocompatible, natural, and low-cost materials. Various characterization tests including Fourier transform infrared spectroscopy, field emission scanning electron microscopy, release kinetics, contact angle, and dynamic mechanical analysis were performed to evaluate the performance of the pectin films. Exceptional thermal, tensile, and contact angle properties have been achieved for films reinforced by patch halloysite nanotubes due to the patchy and lengthy nature of these tubes, which form a bird nest structure in the pectin matrix. Matauri Bay halloysite nanotubes were dispersed uniformly and individually in the matrix in low and even high halloysite nanotube concentrations. Furthermore, salicylic acid as a biocidal agent was encapsulated in the halloysite nanotubes lumen to control its release kinetics. On this basis, halloysite nanotubes/salicylic acid hybrids were dispersed into the pectin matrix to develop functional biofilms with antimicrobial properties that can be extended over time. Results revealed that shorter nanotubes (Matauri Bay) had better ability for the encapsulation of salicylic acid into their lumen, while patchy structure and longer tubes of patch halloysite nanotubes made the encapsulation process more difficult, as they might need more time and energy to be fully loaded by salicylic acid. Moreover, antimicrobial activity of the films against four different strains of Gram-positive and Gram-negative bacteria indicated the effective antimicrobial properties of pectin/halloysite functionalized films and their potential to be used for food packaging applications. © 2017 American Chemical Society
Costs of testing for ocular Chlamydia trachomatis infection compared to mass drug administration for trachoma in the Gambia: application of results from the PRET study.
No full textBACKGROUND: Mass drug administration (MDA) treatment of active trachoma with antibiotic is recommended to be initiated in any district where the prevalence of trachoma inflammation, follicular (TF) is ≥ 10% in children aged 1-9 years, and then to continue for at least three annual rounds before resurvey. In The Gambia the PRET study found that discontinuing MDA based on testing a sample of children for ocular Chlamydia trachomatis(Ct) infection after one MDA round had similar effects to continuing MDA for three rounds. Moreover, one round of MDA reduced disease below the 5% TF threshold. We compared the costs of examining a sample of children for TF, and of testing them for Ct, with those of MDA rounds. METHODS: The implementation unit in PRET The Gambia was a census enumeration area (EA) of 600-800 people. Personnel, fuel, equipment, consumables, data entry and supervision costs were collected for census and treatment of a sample of EAs and for the examination, sampling and testing for Ct infection of 100 individuals within them. Programme costs and resource savings from testing and treatment strategies were inferred for the 102 EAs in the study area, and compared. RESULTS: Census costs were 108.79. MDA with donated azithromycin cost 796.90 per EA, with Ct testing kits costing 1.38 per result. However stopping or deciding not to initiate treatment in the study area based on testing a sample of EAs for Ct infection (or examining children in a sample of EAs) creates savings relative to further unnecessary treatments. CONCLUSION: Resources may be saved by using tests for chlamydial infection or clinical examination to determine that initial or subsequent rounds of MDA for trachoma are unnecessary
Burkholderia paludis sp. nov., an antibiotic-siderophore producing novel Burkholderia cepacia complex species, isolated from malaysian tropical peat swamp soil
No full textA novel Gram negative rod-shaped bacterium, designated strain MSh1T, was isolated from Southeast Pahang tropical peat swamp forest soil in Malaysia and characterized using a polyphasic taxonomy approach. The predominant cellular fatty acids (> 10.0%) were C16:0 (31.7%), C17:0 cyclo (26.6%), and C19:0 cyclo ω8c (16.1%). The polar lipids detected were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant ubiquinone was Q-8. This revealed that strain MSh1T belongs to the genus Burkholderia. The type strain MSh1T can be differentiated from other Burkholderia cepacia complex (Bcc) species by phylogenetic analysis of 16S rRNA gene sequence, multilocus sequence analysis (MLSA), average nucleotide identity (ANI) and biochemical tests. DNA-DNA relatedness values between strain MSh1T and closely related type strains were below the 70% threshold value. Based on this polyphasic study of MSh1T, it can be concluded that this strain represents a novel species within the Bcc, for which the name Burkholderia paludis sp. nov. is proposed. The type strain is MSh1T (= DSM 100703T = MCCC 1K01245T). The dichloromethane extract of MSh1T exhibited antimicrobial activity against four Gram positive bacteria (Enterococcus faecalis ATCC 29212, E. faecalis ATCC 700802, Staphylococcus aureus ATCC 29213, S. aureus ATCC 700699) and a Gram negative bacteria (Escherichia coli ATCC 25922). Further purification work has led to the isolation of Compound 1, pyochelin. Pyochelin demonstrated antimicrobial activity against four S. aureus strains and three E. faecalis strains with MIC-values of 3.13 μg/ml and 6.26 μg/ml, respectively. SEM analysis showed that the cellular morphology of E. faecalis ATCC 700802 was not affected by pyochelin; suggesting that it might target the intracellular components. Pyochelin, a siderophore with antimicrobial activity might be useful in treating bacterial infections caused by S. aureus and E. faecalis, however further work has to be done. © 2016 Ong, Aw, Lee, Yule, Cheow and Lee
Newly Isolated Paenibacillus tyrfis sp. nov., from Malaysian Tropical Peat Swamp Soil with Broad Spectrum Antimicrobial Activity
No full textEmergence of antimicrobial resistance coupled with the slowdown in discovery of new antimicrobial compounds points to serious consequences for human health. Therefore, scientists are looking for new antimicrobial compounds from unique and understudied ecosystems such as tropical peat swamp forests. Over the course of isolating antimicrobial producing bacteria from North Selangor tropical peat swamp forest, Malaysia, a Gram variable, rod shaped, endospore forming, facultative anaerobic novel strain MSt1T that exerts potent and broad spectrum antimicrobial activity was isolated. Phylogenetic analysis using 16S rRNA gene sequences showed that strain MSt1T belonged to the genus Paenibacillus with the highest similarity to Paenibacillus elgii SD17T (99.5%). Whole genome comparison between strain MSt1T with its closely related species using average nucleotide identity (ANI) revealed that similarity between strain MSt1T with P. elgii B69 (93.45%) and Paenibacillus ehimensis A2 (90.42%) was below the recommended threshold of 95%. Further analysis using in silico pairwise DDH also showed that similarity between strain MSt1T with P. elgii B69 (55.4%) and P. ehimensis A2 (43.7%) was below the recommended threshold of 70%. Strain MSt1T contained meso-diaminopilemic acid in the cell wall and MK-7 as the major menaquinone. The major fatty acids of strain MSt1T were anteiso-C15:0 (48.2%) and C16:0 (29.0%) whereas the polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unknown lipid, two unknown glycolipids, and one unknown phospholipid. Total DNA G+C content of strain MSt1T was 51.5 mol%. The extract from strain MSt1T exerted strong antimicrobial activity against Escherichia coli ATCC 25922 (MIC = 1.5 μg/mL), MRSA ATCC 700699 (MIC = 25 μg/mL) and Candida albicans IMR (MIC = 12.5 μg/mL). Partially purified active fraction exerted a strong effect against E. coli ATCC 25922 resulting in cell rupture when viewed with SEM. Based on distinctive taxonomic differences between strain MSt1T when compared to its closely related type species, we propose that strain MSt1T represents a novel species within the genus of Paenibacillus, for which the name Paenibacillus tyrfis sp. nov. (= DSM 100708T = MCCC 1K01247T) is proposed. © 2016 Aw, Ong, Lee, Cheow, Yule and Lee
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The human myeloproliferative disorders: molecular pathogenesis and clonal heterogeneity
No full textThe classical myeloproliferative disorders (MPD), comprising essential thrombocythaemia (ET), polycythaemia vera (PV) and idiopathic myelofibrosis (IMF), are clonal premalignant haematopoietic neoplasms associated with activating mutations in signalling pathway molecules and a variable tendency to develop acute myeloid leukaemia (AML). This thesis examined genotype-phenotype associations of JAK2 and MPL mutations, the presence of clonal diversity in the MPD and the genetic events associated with progressive disease.
Mutations in MPL were identified in 4% of ET and 7% of IMF but not in PV. Three different acquired MPL mutations were identified, one of which had been reported as an inherited allele. Although MPL mutations did not delineate a distinct clinical or histopathological subtype of ET, molecular testing provides an important new tool in the diagnostic armamentarium. Clones homozygous for the JAK2 V617F mutation were identified in female but not male patients with ET, suggesting that gender differences may be important in the determination of disease phenotype. In patients with two acquired genetic alterations, a signalling pathway mutation and a cytogenetic abnormality were usually present within the same clone. By contrast, coexistence of two signalling pathway mutations indicated the presence of biclonal disease that in two patients had arisen independently and not from a shared founder clone.
RAS mutations were identified as potential cooperating events in patients with JAK2 or MPL mutant IMF. In patients developing AML following a JAK2 V617F-positive MPD, those with V617F-positive leukaemia had progressed via an accelerated phase of disease and harboured acquired alterations of RUNX1 or EVI1. V617F-negative leukaemias tended to follow directly from ET or PV, and loss of the JAK2 mutation by reversion to wild-type due to mitotic recombination, gene deletion or gene conversion was excluded. The thesis concludes with a discussion of how clonal heterogeneity can be integrated into current models of MPD disease pathogenesis
The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing
No full textPeer reviewe
Microbiological quality and safety of pizza held out of temperature control in university dining halls
No full textPizza has become a very popular food and USDA estimates that about 13% of the US population will consume pizza on any particular day. While any food may occasionally be out of temperature control, the fraction of the time that this is true for pizza at Rutgers University is greater than for other foods. Hot food temperatures obtained from 19,754 non pizza samples and 1,336 pizza temperatures taken from dining facilities operated by Rutgers University between and 2001 and 2020. A more focused project was designed to further study the microbiology, pH and water activity of pizza, and a total of 57 pizza samples were collected for this phase of the project. Pizza was tested for total aerobic plate count, Staphylococcus aureus, Bacillus cereus, Lactic acid bacteria, coliforms and E. coli. Pizza water activity was measured using a digital aw meter Surface pH of each individual pizza component (topping, cheese, bread) was measured by using a bench-top pH meter. Predictions for the growth of four relevant pathogens, both with and without lag phase were made for select pH and water activity values identified at 20, 25 and 30 °C using ComBase. Rutgers University dining hall data show that most (approximately 90%) of foods that are not pizza are held at the appropriate temperature. It’s also true that only about 60% of all foods that are pizza are held at the appropriate temperature. At least 70% or more of all pizza sample tested contain some detectable level of microorganisms. When pizza contained detectable microorganisms, the average total aerobic plate count ranged from 2.72 log CFU/g for cheese pizza to 3.34 log CFU/g for pizza topped with vegetables. Only two pizza samples (one pepperoni, one cheese) collected contained detectable S. aureus and contained ~50 CFU/g. Two other samples contained hemolytic Gram-positive rods (B. cereus) with ~50 and 100 CFY/g and these were found on pizza with mushrooms and pizza with red onions, and bell peppers. Five pizza samples (2 cheese, 2 vegetable and 1 meat) contained coliforms with a range from 4 to 9 MPN/g and no E. coli were detected. While samples picked up at higher temperatures, tended to have a slightly lower concentration of bacteria, the correlation coefficients (R2 values) are quite low (Cheese 0.0544, Vegetarian 0.0097, Meat 0.026). Based on the pH and water activity measurements most (but not all) of the pizza samples would be considered to potentially require time temperature control for safety. When high counts occur on pizza, this is generally due to the presence of lactic acid bacteria most likely from the cheese. The modeling analysis shows that the organism most likely to pose a risk would be S. aureus, and the largest magnitude increase predicted is 0.89 log CFU at 30 °C, pH 5.52 and water activity 0.963. The overall conclusion from this analysis is that while pizza represents a theoretical risk, the actual risk would likely only manifest for pizza samples that are held out of temperature control for time periods in excess of eight hours.M.S.Includes bibliographical reference
Abstract P4-09-14: Analysis of breast cancer recurrence using gene set enrichment analysis
No full textAbstract
Background: Even after successful treatment of primary breast tumors, there is a continued risk of recurrence. The risk varies between subtypes and there are ongoing efforts that aim to improve prediction of such risks for individual patients. Detection of subclinical metastases might be achieved by biomarkers in blood. In this study, we profiled protein expression in blood plasma from patients with known clinical outcome (recurrence vs no recurrence) to identify prognostic markers of breast cancer recurrence.
Methods: The subjects and specimens were made available through the Clinical Breast Care Project using IRB-approved protocols. We analyzed blood plasma samples taken at the time of diagnosis from consented patients who subsequently relapsed (33 cases) as well as those with no disease recurrence (31 controls). Based on hormone receptor and lymph node status the samples were grouped as: ER-/HER2- (17 cases/15 controls), ER+/LN+ (10/10) and ER+/LN- (6/6). We used aptamer-based SOMAscan assay platform to study the expression of 1252 proteins. We analyzed the protein expression data by using their coding genes in order to apply the Gene Set Enrichment Analysis method (GSEA v.2, Broad Institute). Pathway databases of KEGG, REACTOME, BIOCARTA and C4 collection were used. Significant gene sets were called at 5% FDR, and overlaps and low coverage gene sets (Tags <70%) were removed. Statistical analysis and clustering were done using R.
Results: Unsupervised clustering showed some difference in signal in the ER+/LN- group. Even though there was a lack of significantly differentiated proteins between the cases and controls of this group, many significant gene sets were identified. After applying the cutoff filters and removing the overlaps, there were 5 gene sets enriched with the pathway collection, involved in B-cell receptor signaling, mRNA metabolism, tight junction and SCF-KIT signaling. Similarly, 9 gene sets from the MORF compendium were differentially expressed with the C4 collection and included neighborhood genes of NME2, ACTG1, EIF3S2, AP2M1, DAP3, UBE2I, NPM1, AATF and NPM1. In contrast, neither differentially expressed proteins nor gene sets were identified from the ER+/LN+ and ER-/HER2- groups. Since the sample size of the ER+/LN- group was small, we conducted a similar analysis by randomly choosing 6 case and control samples in the other two groups respectively. There were still no differentially expressed proteins or gene sets identified above the specified cutoff parameters.
Conclusion: Using plasma protein expression data we identified underlying gene sets differentially expressed between ER+/LN- patients who had cancer recurrence and no recurrence. Many genes in these sets were already known biomarkers (e.g. PTEN, AKT1, STAT3, SET etc.). These results can be used for understanding patterns of recurrence in different cancer subtypes. Further research is needed to estimate the clinical significance of these gene products.
The views expressed in this article are those of the author and do not reflect the official policy of the Department of Army/Navy/Air Force, the Department of Defense, or U.S. Government.
Citation Format: Praveen Kumar A, Kovatich AJ, Biancotto A, Cheung F, Davidson-Moncada JK, Kvecher L, Liu J, Ru Y, Kovatich AW, Deyarmin B, Fantacone-Campbell JL, Hooke JA, Raj Kumar PK, Rui H, Hu H, Shriver CD. Analysis of breast cancer recurrence using gene set enrichment analysis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-09-14.</jats:p
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