A Comparative Study of the Warrior Support Tool and the Agile Munitions Support Tool

The purpose of this research is to ascertain if the United States Air Force (USAF) is duplicating effort with the development of the two IT applications, the Warrior Support Tool (WST) and the Agile Munitions Support Tool (AMST), or if one will effectively meet requirements. Specifically, this thesis sought to answer four research questions addressing customer needs for a munitions IT application, identifying the capabilities of the two research IT applications, determining how well each application met the needs of the customer, and determining how supportable each application was in terms of information needs versus existing munitions systems. A mixed qualitative and quantitative paradigm was used to conduct a gap analysis and verification occurred through the use of surveys. Sixty-five munitions users participated in a surveying session to identify differences between the two systems as well as the relative merits of each. Overall, munitions users chose WST as the more favorable application. All but two construct measures supported the overall rating of the application. Munitions personnel liked the screen layout of AMST better than that of WST even though WST seemed to be the application that better used terminology familiar to munitions personnel. WST was also the easier of the two applications to manipulate although the AMST help features were identified as the better of the two. The Warrior Support Tool provided information in a timelier manner than did the Agile Munitions Support Tool

Screening and development of new inhibitors of FtsZ from <i>M. Tuberculosis</i>

A variety of commercial analogs and a newer series of Sulindac derivatives were screened for inhibition of M. tuberculosis (Mtb) in vitro and specifically as inhibitors of the essential mycobacterial tubulin homolog, FtsZ. Due to the ease of preparing diverse analogs and a favorable in vivo pharmacokinetic and toxicity profile of a representative analog, the Sulindac scaffold may be useful for further development against Mtb with respect to in vitro bacterial growth inhibition and selective activity for Mtb FtsZ versus mammalian tubulin. Further discovery efforts will require separating reported mammalian cell activity from both antibacterial activity and inhibition of Mtb FtsZ. Modeling studies suggest that these analogs bind in a specific region of the Mtb FtsZ polymer that differs from human tubulin and, in combination with a pharmacophore model presented herein, future hybrid analogs of the reported active molecules that more efficiently bind in this pocket may improve antibacterial activity while improving other drug characteristics

Sensitive detection of colorectal cancer in peripheral blood by septin 9 DNA methylation assay

BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer deaths despite the fact that detection of this cancer in early stages results in over 90% survival rate. Currently less than 45% of at-risk individuals in the US are screened regularly, exposing a need for better screening tests. We performed two case-control studies to validate a blood-based test that identifies methylated DNA in plasma from all stages of CRC. METHODOLOGY/PRINCIPAL FINDINGS: Using a PCR assay for analysis of Septin 9 (SEPT9) hypermethylation in DNA extracted from plasma, clinical performance was optimized on 354 samples (252 CRC, 102 controls) and validated in a blinded, independent study of 309 samples (126 CRC, 183 controls). 168 polyps and 411 additional disease controls were also evaluated. Based on the training study SEPT9-based classification detected 120/252 CRCs (48%) and 7/102 controls (7%). In the test study 73/126 CRCs (58%) and 18/183 control samples (10%) were positive for SEPT9 validating the training set results. Inclusion of an additional measurement replicate increased the sensitivity of the assay in the testing set to 72% (90/125 CRCs detected) while maintaining 90% specificity (19/183 for controls). Positive rates for plasmas from the other cancers (11/96) and non-cancerous conditions (41/315) were low. The rate of polyp detection (>1 cm) was approximately 20%. CONCLUSIONS/SIGNIFICANCE: Analysis of SEPT9 DNA methylation in plasma represents a straightforward, minimally invasive method to detect all stages of CRC with potential to satisfy unmet needs for increased compliance in the screening population. Further clinical testing is warranted

A combined HM-PCR/SNuPE method for high sensitive detection of rare DNA methylation

<p>Abstract</p> <p>Background</p> <p>DNA methylation changes are widely used as early molecular markers in cancer detection. Sensitive detection and classification of rare methylation changes in DNA extracted from circulating body fluids or complex tissue samples is crucial for the understanding of tumor etiology, clinical diagnosis and treatment. In this paper, we describe a combined method to monitor the presence of methylated tumor DNA in an excess of unmethylated background DNA of non-tumorous cells. The method combines heavy methyl-PCR, which favors preferential amplification of methylated marker sequence from bisulfite-treated DNA with a methylation-specific single nucleotide primer extension monitored by ion-pair, reversed-phase, high-performance liquid chromatography separation.</p> <p>Results</p> <p>This combined method allows detection of 14 pg (that is, four to five genomic copies) of methylated chromosomal DNA in a 2000-fold excess (that is, 50 ng) of unmethylated chromosomal background, with an analytical sensitivity of > 90%. We outline a detailed protocol for the combined assay on two examples of known cancer markers (SEPT9 and TMEFF2) and discuss general aspects of assay design and data interpretation. Finally, we provide an application example for rapid testing on tumor methylation in plasma DNA derived from a small cohort of patients with colorectal cancer.</p> <p>Conclusion</p> <p>The method allows unambiguous detection of rare DNA methylation, for example in body fluid or DNA isolates from cells or tissues, with very high sensitivity and accuracy. The application combines standard technologies and can easily be adapted to any target region of interest. It does not require costly reagents and can be used for routine screening of many samples.</p

Using near-term forecasts and uncertainty partitioning to improve predictions of low-frequency cyanobacterial events

Near-term ecological forecasts provide resource managers advance notice of changes in ecosystem services, such as fisheries stocks, timber yields, or water and air quality. Importantly, ecological forecasts can identify where uncertainty enters the forecasting system, which is necessary to refine and improve forecast skill and guide interpretation of forecast results. Uncertainty partitioning identifies the relative contributions to total forecast variance (uncertainty) introduced by different sources, including specification of the model structure, errors in driver data, and estimation of initial state conditions. Uncertainty partitioning could be particularly useful in improving forecasts of high-density cyanobacterial events, which are difficult to predict and present a persistent challenge for lake managers. Cyanobacteria can produce toxic or unsightly surface scums and advance warning of these events could help managers mitigate water quality issues. Here, we calibrate fourteen Bayesian state-space models to evaluate different hypotheses about cyanobacterial growth using data from eight summers of weekly cyanobacteria density samples in an oligotrophic (low nutrient) lake that experiences sporadic surface scums of the toxin-producing cyanobacterium, Gloeotrichia echinulata. We identify dominant sources of uncertainty for near-term (one-week to four-week) forecasts of G. echinulata densities over two years. Water temperature was an important predictor in calibration and at the four-week forecast horizon. However, no environmental covariates improved over a simple autoregressive (AR) model at the one-week horizon. Even the best fit models exhibited large variance in forecasted cyanobacterial densities and often did not capture rare peak density occurrences, indicating that significant explanatory variables in calibration are not always effective for near-term forecasting of low-frequency events. Uncertainty partitioning revealed that model process specification and initial conditions uncertainty dominated forecasts at both time horizons. These findings suggest that observed densities result from both growth and movement of G. echinulata, and that imperfect observations as well as spatial misalignment of environmental data and cyanobacteria observations affect forecast skill. Future research efforts should prioritize long-term studies to refine process understanding and increased sampling frequency and replication to better define initial conditions. Our results emphasize the importance of ecological forecasting principles and uncertainty partitioning to refine and understand predictive capacity across ecosystems.Accepted manuscrip

Long-range epigenetic silencing at 2q14.2 affects most human colorectal cancers and may have application as a non-invasive biomarker of disease

Large chromosomal regions can be suppressed in cancer cells as denoted by hypermethylation of neighbouring CpG islands and downregulation of most genes within the region. We have analysed the extent and prevalence of long-range epigenetic silencing at 2q14.2 (the first and best characterised example of coordinated epigenetic remodelling) and investigated its possible applicability as a non-invasive diagnostic marker of human colorectal cancer using different approaches and biological samples. Hypermethylation of at least one of the CpG islands analysed (EN1, SCTR, INHBB) occurred in most carcinomas (90%), with EN1 methylated in 73 and 40% of carcinomas and adenomas, respectively. Gene suppression was a common phenomenon in all the tumours analysed and affected both methylated and unmethylated genes. Detection of methylated EN1 using bisulfite treatment and melting curve (MC) analysis from stool DNA in patients and controls resulted in a predictive capacity of, 44% sensitivity in positive patients (27% of overall sensitivity) and 97% specificity. We conclude that epigenetic suppression along 2q14.2 is common to most colorectal cancers and the presence of a methylated EN1 CpG island in stool DNA might be used as biomarker of neoplastic disease

Mode imaging and selection in strongly coupled nanoantennas

The number of eigenmodes in plasmonic nanostructures increases with complexity due to mode hybridization, raising the need for efficient mode characterization and selection. Here we experimentally demonstrate direct imaging and selective excitation of the bonding and antibonding plasmon mode in symmetric dipole nanoantennas using confocal two-photon photoluminescence mapping. Excitation of a high-quality-factor antibonding resonance manifests itself as a two-lobed pattern instead of the single spot observed for the broad bonding resonance, in accordance with numerical simulations. The two-lobed pattern is observed due to the fact that excitation of the antibonding mode is forbidden for symmetric excitation at the feedgap, while concomitantly the mode energy splitting is large enough to suppress excitation of the bonding mode. The controlled excitation of modes in strongly coupled plasmonic nanostructures is mandatory for efficient sensors, in coherent control as well as for implementing well-defined functionalities in complex plasmonic devices.Comment: 11 pages, 5 figures, 1 supplementary informatio

The context and potential of epigenetics in oncology

Cancer has long been known to be a disease caused by alterations in the genetic blueprint of cells. In the past decade it has become evident that epigenetic processes have a function, at least equally important, in neoplasia. Epigenetics describes the mechanisms that result in heritable alterations in gene expression profiles without an accompanying change in DNA sequence. Genetics and epigenetics intricately interact in the pathogenesis of cancer (Esteller, 2007). In this review, we paint a broad picture of current understanding of epigenetic changes in cancer cells and reflect on the immense clinical potential of emerging knowledge of epigenetics in the diagnosis, prognostic assessment, treatment, and screening of cancer

Detection of methylated septin 9 in tissue and plasma of colorectal patients with neoplasia and the relationship to the amount of circulating cell-free DNA

BACKGROUND: Determination of methylated Septin 9 (mSEPT9) in plasma has been shown to be a sensitive and specific biomarker for colorectal cancer (CRC). However, the relationship between methylated DNA in plasma and colon tissue of the same subjects has not been reported. METHODS: Plasma and matching biopsy samples were collected from 24 patients with no evidence of disease (NED), 26 patients with adenoma and 34 patients with CRC. Following bisulfite conversion of DNA a commercial RT-PCR assay was used to determine the total amount of DNA in each sample and the fraction of mSEPT9 DNA. The Septin-9 protein was assessed using immunohistochemistry. RESULTS: The percent of methylated reference (PMR) values for SEPT9 above a PMR threshold of 1% were detected in 4.2% (1/24) of NED, 100% (26/26) of adenoma and 97.1% (33/34) of CRC tissues. PMR differences between NED vs. adenoma and NED vs. CRC comparisons were significant (p<0.001). In matching plasma samples using a PMR cut-off level of 0.01%, SEPT9 methylation was 8.3% (2/24) of NED, 30.8% (8/26) of adenoma and 88.2% (30/34) of CRC. Significant PMR differences were observed between NED vs. CRC (p<0.01) and adenoma vs. CRC (p<0.01). Significant differences (p<0.01) were found in the amount of cfDNA (circulating cell-free DNA) between NED and CRC, and a modest correlation was observed between mSEPT9 concentration and cfDNA of cancer (R2 = 0.48). The level of Septin-9 protein in tissues was inversely correlated to mSEPT9 levels with abundant expression in normals, and diminished expression in adenomas and tumors. CONCLUSIONS: Methylated SEPT9 was detected in all tissue samples. In plasma samples, elevated mSEPT9 values were detected in CRC, but not in adenomas. Tissue levels of mSEPT9 alone are not sufficient to predict mSEPT9 levels in plasma. Additional parameters including the amount of cfDNA in plasma appear to also play a role