Showing papers by "Andrew Collins published in 2017"

High throughput toxicity screening and intracellular detection of nanomaterials

Abstract: With the growing numbers of nanomaterials (NMs), there is a great demand for rapid and reliable ways of testing NM safety-preferably using in vitro approaches, to avoid the ethical dilemmas associated with animal research. Data are needed for developing intelligent testing strategies for risk assessment of NMs, based on grouping and read-across approaches. The adoption of high throughput screening (HTS) and high content analysis (HCA) for NM toxicity testing allows the testing of numerous materials at different concentrations and on different types of cells, reduces the effect of inter-experimental variation, and makes substantial savings in time and cost. HTS/HCA approaches facilitate the classification of key biological indicators of NM-cell interactions. Validation of in vitro HTS tests is required, taking account of relevance to in vivo results. HTS/HCA approaches are needed to assess dose- and time-dependent toxicity, allowing prediction of in vivo adverse effects. Several HTS/HCA methods are being validated and applied for NM testing in the FP7 project NANoREG, including Label-free cellular screening of NM uptake, HCA, High throughput flow cytometry, Impedance-based monitoring, Multiplex analysis of secreted products, and genotoxicity methods-namely High throughput comet assay, High throughput in vitro micronucleus assay, and γH2AX assay. There are several technical challenges with HTS/HCA for NM testing, as toxicity screening needs to be coupled with characterization of NMs in exposure medium prior to the test; possible interference of NMs with HTS/HCA techniques is another concern. Advantages and challenges of HTS/HCA approaches in NM safety are discussed. WIREs Nanomed Nanobiotechnol 2017, 9:e1413. doi: 10.1002/wnan.1413 For further resources related to this article, please visit the WIREs website.

The next three decades of the comet assay: a report of the 11th International Comet Assay Workshop.

Abstract: The International Comet Assay Workshops are a series of scientific conferences dealing with practical and theoretical aspects of the Comet Assay (single-cell gel electrophoresis)-a simple method for detecting DNA strand breaks. The first paper describing such an assay was published over 30 years ago in 1984 by Swedish researchers O. Ostling and K. J. Johanson. Appropriately, the theme for the 2015 meeting was looking to the future: 'The Next 3 Decades of the Comet Assay'. The programme included 25 oral and 43 poster presentations depicting the latest advances in technical developments as well as applications of the comet assay in genotoxicity testing (in vitro and in vivo) and biomonitoring of both humans and the environment. Open discussion sessions based on questions from the participants allowed exchange of practical details on current comet assay protocols. This report summarises technical issues of high importance which were discussed during the sessions. We provide information on ways to improve the assay performance, by testing for cytotoxicity, by using reference samples to reduce or allow for inter-experimental variation, and by standardising quantification of the damage, including replicates and scoring enough comets to ensure statistical validity. After 30 years of experimentation with the comet assay, we are in a position to control the important experimental parameters and make the comet assay a truly reliable method with a wealth of possible applications.

In vitro genotoxicity testing of four reference metal nanomaterials, titanium dioxide, zinc oxide, cerium oxide and silver: towards reliable hazard assessment.

Abstract: There is serious concern about the potential harmful effects of certain nanomaterials (NMs), on account of their ability to penetrate cell membranes and the increased reactivity that results from their increased surface area compared with bulk chemicals. To assess the safety of NMs, reliable tests are needed. We have investigated the possible genotoxicity of four representative NMs, derived from titanium dioxide, zinc oxide, cerium oxide and silver, in two human cell lines, A549 alveolar epithelial cells and lymphoblastoid TK6 cells. A high-throughput version of the comet assay was used to measure DNA strand beaks (SBs) as well as oxidised purines (converted to breaks with the enzyme formamidopyrimidine DNA glycosylase). In parallel, cytotoxicity was measured with the alamarBlue® assay, and the ability of NM-treated cells to survive was assessed by their colony-forming efficiency. TiO2 and CeO2 NMs were only slightly cytotoxic by the alamarBlue® test, and had no long-term effect on colony-forming efficiency. However, both induced DNA damage at non-cytotoxic concentrations; the damage decreased from 3 to 24-h exposure, except in the case of CeO2-treated A549 cells. ZnO and Ag NMs affected cell survival, and induced high levels of DNA damage at cytotoxic concentrations. At lower concentrations, there was significant damage, which tended to persist over 24 h. The implication is that all four reference metal NMs tested-whether cytotoxic or not-are genotoxic. A full assessment of NM toxicity should include tests on different cell types, different times of incubation and a wide range of (especially non-cytotoxic) concentrations; a test for cell viability should be performed in parallel. Inclusion of Fpg in the comet assay allows detection of indirect genotoxic effects via oxidative stress.

Convection enhanced delivery of panobinostat (LBH589)-loaded pluronic nano-micelles prolongs survival in the F98 rat glioma model

Abstract: BACKGROUND The pan-histone deacetylase inhibitor panobinostat is a potential therapy for malignant glioma, but it is water insoluble and does not cross the blood-brain barrier when administered systemically. In this article, we describe the in vitro and in vivo efficacy of a novel water-soluble nano-micellar formulation of panobinostat designed for administration by convection enhanced delivery (CED). MATERIALS AND METHODS The in vitro efficacy of panobinostat-loaded nano-micelles against rat F98, human U87-MG and M059K glioma cells and against patient-derived glioma stem cells was measured using a cell viability assay. Nano-micelle distribution in rat brain was analyzed following acute CED using rhodamine-labeled nano-micelles, and toxicity was assayed using immunofluorescent microscopy and synaptophysin enzyme-linked immunosorbent assay. We compared the survival of the bioluminescent syngenic F98/Fischer344 rat glioblastoma model treated by acute CED of panobinostat-loaded nano-micelles with that of untreated and vehicle-only-treated controls. RESULTS Nano-micellar panobinostat is cytotoxic to rat and human glioma cells in vitro in a dose-dependent manner following short-time exposure to drug. Fluorescent rhodamine-labelled nano-micelles distribute with a volume of infusion/volume of distribution (Vi/Vd) ratio of four and five respectively after administration by CED. Administration was not associated with any toxicity when compared to controls. CED of panobinostat-loaded nano-micelles was associated with significantly improved survival when compared to controls (n=8 per group; log-rank test, P<0.001). One hundred percent of treated animals survived the 60-day experimental period and had tumour response on post-mortem histological examination. CONCLUSION CED of nano-micellar panobinostat represents a potential novel therapeutic option for malignant glioma and warrants translation into the clinic.

Non-coding NOTCH1 mutations in chronic lymphocytic leukemia; their clinical impact in the UK CLL4 trial.

Abstract: Non-coding NOTCH1 mutations in chronic lymphocytic leukemia; their clinical impact in the UK CLL4 trial

Vitamin D deficiency, oxidative stress and antioxidant status: only weak association seen in the absence of advanced age, obesity or pre-existing disease.

Abstract: Vitamin D deficiency (plasma 25-hydroxycholecalciferol (25(OH)D)70 % of participants were vitamin D deficient. No significant correlations and no biomarker differences across 25(OH)D quartiles or groups were seen except for total antioxidant status. A weak direct association (r 0·252, P<0·05) was observed between 25(OH)D and FRAP, and those in the lowest 25(OH)D quartile and group had significantly lower FRAP values. Results did not reveal a clear link between vitamin D status and oxidative stress biomarkers in the absence of advanced age, obesity and disease, though some evidence of depleted antioxidant status in those with vitamin D deficiency was seen. Poor antioxidant status may pre-date increased oxidative stress. Study of effects of correction of deficiency on antioxidant status and oxidative stress in vitamin D-deficient but otherwise healthy subjects is needed.

Evaluating phenotype-driven approaches for genetic diagnoses from exomes in a clinical setting

Abstract: Next generation sequencing is transforming clinical medicine and genome research, providing a powerful route to establishing molecular diagnoses for genetic conditions; however, challenges remain given the volume and complexity of genetic variation. A number of methods integrate patient phenotype and genotypic data to prioritise variants as potentially causal. Some methods have a clinical focus while others are more research-oriented. With clinical applications in mind we compare results from alternative methods using 21 exomes for which the disease causal variant has been previously established through traditional clinical evaluation. In this case series we find that the PhenIX program is the most effective, ranking the true causal variant at between 1 and 10 in 85% of these cases. This is a significantly higher proportion than the combined results from five alternative methods tested (p = 0.003). The next best method is Exomiser (hiPHIVE), in which the causal variant is ranked 1–10 in 25% of cases. The widely different targets of these methods (more clinical focus, considering known Mendelian genes, in PhenIX, versus gene discovery in Exomiser) is perhaps not fully appreciated but may impact strongly on their utility for molecular diagnosis using clinical exome data.

Germline variation in ADAMTSL1 is associated with prognosis following breast cancer treatment in young women

Abstract: To identify genetic variants associated with breast cancer prognosis we conduct a meta-analysis of overall survival (OS) and disease-free survival (DFS) in 6042 patients from four cohorts. In young women, breast cancer is characterized by a higher incidence of adverse pathological features, unique gene expression profiles and worse survival, which may relate to germline variation. To explore this hypothesis, we also perform survival analysis in 2315 patients aged ≤ 40 years at diagnosis. Here, we identify two SNPs associated with early-onset DFS, rs715212 (P meta = 3.54 × 10−5) and rs10963755 (P meta = 3.91 × 10−4) in ADAMTSL1. The effect of these SNPs is independent of classical prognostic factors and there is no heterogeneity between cohorts. Most importantly, the association with rs715212 is noteworthy (FPRP <0.2) and approaches genome-wide significance in multivariable analysis (P multivariable = 5.37 × 10−8). Expression quantitative trait analysis provides tentative evidence that rs715212 may influence AREG expression (P eQTL = 0.035), although further functional studies are needed to confirm this association and determine a mechanism. Genetic variance can influence breast cancer prognosis. Here, the authors conduct a meta-analysis to explore genetic variance linked to breast cancer in young women, identifying a prognostic association with germline variation of ADAMTSL1.

A Method for Key Performance Indicator Assessment in Manufacturing Organizations

Abstract: Key Performance Indicators (KPIs) are an essential element of an organization’s ability to monitor its strategic health, helping to ensure the strategic goals of the organization are achieved. However, KPI assessment and improvement is often an ad hoc and consultant-driven process rather than one undertaken using scientific principles. This paper outlines the development and subsequent deployment of a method for KPI assessment founded in scholarly literature and balancing practitioner concerns for ease of use. The proposed method draws heavily on organizational stakeholder involvement at varying levels throughout the KPI assessment process, improving current methods by introducing a mathematical foundation based on value-focused thinking. The proposed method allows stakeholders to evaluate the organization’s KPIs in an effort to determine organizational performance against predetermined KPI thresholds. The method is demonstrated on a case study and suggestions for future research are offered. Keyword — Key performance indicators, assessment, performance management, performance measurement, decision analysis

Functionalized Triblock Copolymer Vectors for the Treatment of Acute Lymphoblastic Leukemia

Abstract: The chemotherapeutic Parthenolide is an exciting new candidate for the treatment of acute lymphoblastic leukemia, but like many other small-molecule drugs, it has low aqueous solubility. As a consequence, Parthenolide can only be administered clinically in the presence of harmful cosolvents. Accordingly, we describe the synthesis, characterization, and testing of a range of biocompatible triblock copolymer micelles as particle-based delivery vectors for the hydrophobic drug Parthenolide. The drug-loaded particles are produced via an emulsion-to-micelle transition method, and the effects of introducing anionic and cationic surface charges on stability, drug sequestration, biocompatibility, and efficacy are investigated. Significantly, we demonstrate high levels of efficacy in the organic solvent-free systems against human mesenchymal stem cells and primary T-acute lymphoblastic leukemia patient cells, highlighting the effectiveness of the delivery vectors for the treatment of acute lymphoblastic leukemia.

Modeling the impact of traffic incidents during hurricane evacuations using a large scale microsimulation

Abstract: Traffic incidents occurring during large-scale evacuations have been suspected of causing potentially severe delays. Previous work using mesoscopic simulations suggested that while incidents may substantially extend evacuation times for those immediately impacted, overall evacuation times for all evacuees were not significantly increased. Using highly detailed, dynamic transportation micro-simulation with greater realism and accuracy, this study assessed the impact of traffic incidents on two hypothetical hurricane evacuations from a coastal city in the United States. Six evacuation scenarios were tested with up to 143,000 evacuees and 800,000 background vehicles simulated over a 24-hour period. Scenarios included from 35 to 48 traffic incidents with locations, rates, severities, and durations based on both historical values for peak period traffic and estimates based on total vehicle miles traveled per road segment. The impacts of simulated traffic incidents, assigned to match one of three severity levels, were modeled by temporary reductions in affected lane segment capacities and reductions in vehicle speeds for other lanes in the segment. Work supports findings that while traffic incidents significantly extend the travel time of those involved, the total time required for all evacuees to clear the evacuating area is only marginally impacted. The findings also show that the time incidents occur relative to current and immediately following traffic may significantly impact evacuation clearance times for comparatively short periods.

Development of a traffic incident model involving multiple municipalities for inclusion in large microscopic evacuation simulations

Abstract: Evacuating citizens might have to cross multiple regions to reach safety and, as such, evacuation models may need to include geographical areas that cross municipal boundaries. If the modeler is fortunate, the data required for the model can be obtained from a single source (i.e., a government agency). However, it is likely that several sources will be required to meet the fidelity required. This can lead to interoperability and integrity issues for the modeler due to the different format and content of the data. This paper presents a case study of determining the traffic incident features (type, duration, location, and effect), for a large-scale microscopic regional evacuation simulation, which required data from three different operating authorities (two cities in the United States and one state department of transportation). Through this case study example, many issues relating to data integration are discussed. This study contributes by extending our knowledge of traffic incidents that occur across municipal boundaries and how to represent them in simulations of evacuations. Though existing sources (e.g., Highway Capacity Manual or simulation software) provide guidelines for macroscopic incident modeling, they do not provide guidelines for large-scale microscopic incident modeling. The authors hope that this case study provides an example that will help other evacuation modelers faced with similar challenges and suggest that the modelers consider the use of estimates instead, e.g., traffic incidents increase the evacuation time by five to ten percent.

TLR9 stimulation of B-cells induces transcription of p53 and prevents spontaneous and irradiation-induced cell death independent of DNA damage responses. Implications for Common variable immunodeficiency.

Abstract: In the present study, we address the important issue of whether B-cells protected from irradiation-induced cell death, may survive with elevated levels of DNA damage. If so, such cells would be at higher risk of gaining mutations and undergoing malignant transformation. We show that stimulation of B-cells with the TLR9 ligands CpG-oligodeoxynucleotides (CpG-ODN) prevents spontaneous and irradiation-induced death of normal peripheral blood B-cells, and of B-cells from patients diagnosed with Common variable immunodeficiency (CVID). The TLR9-mediated survival is enhanced by the vitamin A metabolite retinoic acid (RA). Importantly, neither stimulation of B-cells via TLR9 alone or with RA increases irradiation-induced DNA strand breaks and DNA damage responses such as activation of ATM and DNA-PKcs. We prove that elevated levels of γH2AX imposed by irradiation of stimulated B-cells is not due to induction of DNA double strand breaks, but merely reflects increased levels of total H2AX upon stimulation. Interestingly however, we unexpectedly find that TLR9 stimulation of B-cells induces low amounts of inactive p53, explained by transcriptional induction of TP53. Taken together, we show that enhanced survival of irradiated B-cells is not accompanied by elevated levels of DNA damage. Our results imply that TLR9-mediated activation of B-cells not only promotes cell survival, but may via p53 provide cells with a barrier against harmful consequences of enhanced activation and proliferation. As CVID-derived B-cells are more radiosensitive and prone to undergo apoptosis than normal B-cells, our data support treatment of CVID patients with CpG-ODN and RA.

Agent-based model of criminal gang formation

Abstract: Criminal gangs are of major concern at both the local and international levels. Understanding how gangs form and how they impact society is of interest to criminology. This paper presents an Agent-based Model (ABM) to help in developing a theory on how gangs impact society as a whole. The agents live in a social space and are able climb the social hierarchy and gain resources through service. Criminals steal resources from the weak. The results produced two extreme outputs; either all became alternating criminals or all formed a utopia of non-criminals. The extreme results are also seen in the distribution of agents which were either completely spread or all centralized. In either case, all agents prospered at the same rate which we believe is a consequence of any agent to join the criminal gang in the model.

Twelve-Gel Comet Assay Format for Quick Examination of DNA Damage and Repair.

Abstract: The comet assay (single cell gel electrophoresis) is a sensitive, versatile method for detecting DNA damage in eukaryotic cells. The traditional comet assay format has 1 or 2 gels on a microscope slide, 1 sample per slide, and there is a limit of 40 gels per experiment given the size of a typical electrophoresis tank. To increase throughput, we have designed and tested a system with 12 minigels on one slide, allowing analysis of up to 12 times more samples in one electrophoresis run. The novel comet assay format compares well with the traditional technology. The various steps are suitable for further automation, and the formats can be adapted to fully automated scoring. The new procedures save time at all stages as fewer slides are handled, and the amounts of reagents needed are reduced significantly. This format is particularly useful for testing of numerous genotoxic agents and nanomaterials at different concentrations and on different types of cells; simultaneous analysis of different lesions using a range of enzymes; and analysis of cell extracts for DNA repair activity.

The Effect of Neighborhood Density and GIS Layout on the Foreclosure Contagion Effect

Abstract: Agent-based modeling and simulation has been used to examine the effects of foreclosures on property values and the overall health of the property market. Past agent-based simulations simplistically use an equally-spaced grid structure for the layout of the properties. This simple spacing does not reflect the actual size and dispersion of properties. Instead, we use GIS models of actual neighborhoods to study the impact of size and spacing within a real estate agent-based simulation to investigate the foreclosure contagion effect. The topologies of five neighborhoods in Virginia Beach, Virginia were uploaded into an agent-based simulation using publicly accessible GIS data. The results indicate that non-linear pricing changes occur within the neighborhoods. Moreover, the density of a neighborhood is a significant determining factor in explaining differential results.

Strategically Forming Groups in the El Farol Bar Problem

Abstract: The El Farol bar problem sprung from one patron's wish to avoid the bar's busy nights in the 1990s. The problem became of interest to economists because of its potential application to other consumer choice behavior problems, e.g., route selection on a congested roadway. The El Farol bar problem involves multiple decision-making agents trying to outwit each other and only attend the bar when it is not overcrowded. Each agent makes their decision based on historical data and draws their attendance strategy from a limited pool. We adapt the model of the problem developed, by Rand and Wilensky, to include group decision-making behavior and strategic group formation. In our version, agents can use the best strategy from the whole group, not just their own set. However, the larger the group, the more it adds to the overcrowding issue. Thus, an agent must balance access to a large attendance strategy pool with group size. We had hypothesized that including strategic group formation will increase overall social welfare, but our analysis shows that allowing agent groups results in a undesirable scenario for all agents; this is due to the limited rationality of the agents.

Proposed unified discrete event simulation content roadmap for M&S curricula

Abstract: This paper presents a new educational roadmap for teaching discrete event system (DES) simulation software design. This roadmap represents the hierarchical structure and inter-relationships characterizing the worldviews of DES simulation, namely, event scheduling and process interaction. The roadmap was developed from the authors' experience while teaching DES simulation to both undergraduate and graduate students, spanning several years. The roadmap's development was motivated by the need to strive for greater completeness as well as fewer inconsistencies in the material curriculum. The commonality between the worldviews is highlighted in striving for a uniform approach. The intent of this paper is to provide other educators a foundation for their own DES simulation course development. A simple example is used to illustrate the worldviews within the roadmap.

Dynamics of knowledge-seeking interactions in organizational networks

Abstract: Organizational communication structures (OCS) enable and constrain information flow and are, therefore, influential in the organization's efficiency and productivity. Companies have often reorganized their structure to improve efficiency. However, OCS is a function of the informal network as well as the formal hierarchical structure within the organization. Any analysis of OCS must include informal networks to be valid. Individual interactions are what define the OCS and aids knowledge transfer. Using Agent-based Modeling, we create OCS with agents that have the same knowledge-seeking goals but different knowledge environments. Agents develop an informal communication network through which they obtain knowledge elements to complete tasks. Their network expands through references provided by peers when the knowledge sought cannot be found within their group. We compare the networks to determine if the knowledge-seeking theory alone is sufficient to determine the OCS. Network differences indicate that theory alone is insufficient to explain the formation of informal OCS.

Individual strategic behavior in a team formation agent-based simulation

Abstract: The modern knowledge worker is faced with managing their time across multiple projects. To ensure the successful completion of one project, the worker might be inclined to put more time into that project than was originally intended, at the expense of other projects with which they are involved. This paper looks at the impact of this type of strategic behavior on the output of research teams. Our model was an adaption of Bakshy and Wilensky's team assembly model which looked at the formation of academic teams to complete some collaborative research task. The agents, who represent researchers, make strategic decision to increase their prestige through the selection of the teams they work with. The results indicate that the average size of the disjoint components, sets on connected agents, decreases when prestige is introduced. This implies a smaller, more cliquey, "invisible" college is formed within a given field of study.

Corrigendum: Reference cells and ploidy in the comet assay.

Abstract: [This corrects the article on p. 61 in vol. 6, PMID: 25774164.].