Likelihood and Cost Impact of Engineering Change Requirements for DoD Contracts

Purpose: There appears to be no empirical-based method in the literature for estimating if an engineering change proposal (ECP) will occur or the dollar amount incurred. This paper aims to present an empirically based approach to address this shortfall.Design/Methodology/Approach: Using the cost assessment data enterprise database, 533 contracts were randomly selected via a stratified sampling plan to build two regression models: one to predict the likelihood of a contract experiencing an ECP and the other to determine the expected median per cent increase in baseline contract cost if an ECP was likely. Both models adopted a stepwise approach. A validation set was placed aside prior to any model building.Findings: Not every contract incurs an ECP; approximately 80 per cent of the contracts in the database did not have an ECP. The likelihood of an ECP and the additional amount incurred appears to be statistically independent of acquisition phase, branch of service, commodity, contract type or any other factor except for the basic contract amount and the number of contract line item numbers; both of these later variables equally affected the contract percentage increase because of an ECP. The combined model overall bested current anecdotal approaches to ECP withhold

Time-dependent appearance of myofibroblasts in granulation tissue of human skin wounds

Human skin wounds (66) inflicted between 20 h and 7 months prior to biopsy were studied. In order to identify the type of cellular differentiation of the fibroblastic cells in the granulation tissue, alpha-smooth muscle actin and desmin were immunohistochemically localized. The value of any presumed time-dependent appearance and/or disappearance of positively stained cells was tested for the estimation of wound age. In skin specimens with a wound age less than 5 days (n =15) no typical granulation tissue had developed and no alpha-actin-positive myofibroblasts could be detected. The first appearance of positively reacting myofibroblasts was noted in a 5-day-old wound. In 57% of the lesions with a wound age between 5 and 31 days (25 out of 44 cases) typical granulation tissue formation was present and myofibroblasts with positive reaction for alpha-smooth muscle actin could be identified. Numerous positively reacting cells could generally be found in wounds aged between 16 and 31 days, but also in wounds less than 16 days old. In 29% of the cases with a wound age of more than 31 days (2 out of 7 cases) alpha-sma-positive myofibroblasts also occured. Fibroblastic cells positive for desmin could not be seen at all in our series. Our results demonstrate the appearance of alpha-sma-positive myofibroblasts with the initial formation of typical granulation tissue in human skin lesions as early as approximately 5 days after wounding. In contrast to recent experimental results these cells remained detectable in wounds aged more than 2 months in some cases. The immunohistochemical detection of actin-positive cells, therefore, demonstrates whether an unknown skin wound is aged approximately 5 days or more. Even though a time-dependent decrease of myofibroblasts in human granulation tissue after 31 days in human wounds seems probable, the extended presence (up to about 2 months) of these cells allows no further exact age determination of older wounds

BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies

Genome-wide association studies (GWAS) have discovered many loci associated with common disease and quantitative traits. However, most GWAS have not studied the gene–gene interactions (epistasis) that could be important in complex trait genetics. A major challenge in analysing epistasis in GWAS is the enormous computational demands of analysing billions of SNP combinations. Several methods have been developed recently to address this, some using computers equipped with particular graphical processing units, most restricted to binary disease traits and all poorly suited to general usage on the most widely used operating systems. We have developed the BiForce Toolbox to address the demand for high-throughput analysis of pairwise epistasis in GWAS of quantitative and disease traits across all commonly used computer systems. BiForce Toolbox is a stand-alone Java program that integrates bitwise computing with multithreaded parallelization and thus allows rapid full pairwise genome scans via a graphical user interface or the command line. Furthermore, BiForce Toolbox incorporates additional tests of interactions involving SNPs with significant marginal effects, potentially increasing the power of detection of epistasis. BiForce Toolbox is easy to use and has been applied in multiple studies of epistasis in large GWAS data sets, identifying interesting interaction signals and pathways

Towards resolving the phosphorus chaos created by food systems

© 2019, The Author(s). The chaotic distribution and dispersal of phosphorus (P) used in food systems (defined here as disorderly disruptions to the P cycle) is harming our environment beyond acceptable limits. An analysis of P stores and flows across Europe in 2005 showed that high fertiliser P inputs relative to productive outputs was driving low system P efficiency (38 % overall). Regional P imbalance (P surplus) and system P losses were highly correlated to total system P inputs and animal densities, causing unnecessary P accumulation in soils and rivers. Reducing regional P surpluses to zero increased system P efficiency (+ 16 %) and decreased total P losses by 35 %, but required a reduction in system P inputs of ca. 40 %, largely as fertiliser. We discuss transdisciplinary and transformative solutions that tackle the P chaos by collective stakeholder actions across the entire food value chain. Lowering system P demand and better regional governance of P resources appear necessary for more efficient and sustainable food systems

Ethanol Pharmacokinetics in Neonates Secondary to Medication Administration

Purpose: Ethanol serves as a solvent and microbial preservative in oral liquid medications and is the second most commonly used solvent in liquid medications following water. Despite widespread use of ethanol in liquid medications for neonates, the pharmacokinetics and toxicity of ethanol in young children are not well described. The aim of the current study is to quantify blood ethanol levels in neonates secondary to oral ethanol containing medications. Methods: Neonates who received either oral phenobarbital (15% ethanol) and/or oral dexamethasone (30% ethanol) per standard of care were eligible for enrollment. A maximum of 6 blood samples per patient (4.5 mL total) were taken over the study period. Blood samples were collected via heel stick at the time of clinical laboratory collections or following a specific collection for study purposes. In addition, blood samples were collected from neonates receiving sublingual buprenorphine (30% ethanol) for neonatal abstinence syndrome from a separate clinical study. Blood ethanol levels were measured using a validated headspace gas chromatography-mass spectrometry method utilizing micro-volume ( ̴100uL) plasma samples. The limit of detection and lower limit of quantification for the assay were 0.1 mg/L and 0.5 mg/L respectively. Results: A total of 39 plasma samples from 15 neonates who were on ethanol containing medications were collected over the study period. Four neonates were exposed to phenobarbital and/or dexamethasone, while eleven neonates were exposed to buprenorphine alone or in combination with phenobarbital. Patients were exposed to an average of 71.6 mg/kg (range 13.1 to 215 mg/kg) of ethanol after a single dose of an ethanol containing medication. Blood ethanol levels were detectable in 98% (38/39) of samples, quantifiable in 67% (26/39) of samples, and ranged from below detection to 85.4 mg/L. Ethanol was rapidly cleared and did not accumulate with current dosing regimens. Conclusion: Ethanol intake secondary to medication administration varied widely. Blood ethanol levels in neonates were low and ethanol was eliminated rapidly after a single dose of oral medications that contained a sizable fraction of ethanol.https://jdc.jefferson.edu/petposters/1000/thumbnail.jp

Investigation of genetically regulated gene expression and response to treatment in rheumatoid arthritis highlights an association between IL18RAP expression and treatment response.

This article has been accepted for publication in Annals of the Rheumatic Diseases, 2020 following peer review, and the Version of Record can be accessed online at http://dx.doi.org/10.1136/annrheumdis-2020-217204OBJECTIVES: In this study, we sought to investigate whether there was any association between genetically regulated gene expression (as predicted using various reference panels) and anti-tumour necrosis factor (anti-TNF) treatment response (change in erythrocyte sedimentation rate (ESR)) using 3158 European ancestry patients with rheumatoid arthritis. METHODS: The genetically regulated portion of gene expression was estimated in the full cohort of 3158 subjects (as well as within a subcohort consisting of 1575 UK patients) using the PrediXcan software package with three different reference panels. Estimated expression was tested for association with anti-TNF treatment response. As a replication/validation experiment, we also investigated the correlation between change in ESR with measured gene expression at the Interleukin 18 Receptor Accessory Protein (IL18RAP) gene in whole blood and synovial tissue, using an independent replication data set of patients receiving conventional synthetic disease modifying anti-rheumatic drugs, with directly measured (via RNA sequencing) gene expression. RESULTS: We found that predicted expression of IL18RAP showed a consistent signal of association with treatment response across the reference panels. In our independent replication data set, IL18RAP expression in whole blood showed correlation with the change in ESR between baseline and follow-up (r=-0.35, p=0.0091). Change in ESR was also correlated with the expression of IL18RAP in synovial tissue (r=-0.28, p=0.02). CONCLUSION: Our results suggest that IL18RAP expression is worthy of further investigation as a potential predictor of treatment response in rheumatoid arthritis that is not specific to a particular drug type

Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS

This is a post-peer-review, pre-copyedit version of an article published in Lecture Notes in Computer Science. The final authenticated version is available online at: https://doi.org/10.1007/978-3-319-09873-9_57[Abstract] High-throughput genotyping technologies allow the collection of up to a few million genetic markers (such as SNPs) of an individual within a few minutes of time. Detecting epistasis, such as 2-SNP interactions, in Genome-Wide Association Studies is an important but time consuming operation since statistical computations have to be performed for each pair of measured markers. In this work we present EpistSearch, a parallelized tool that, following the log-linear model approach, uses a novel filter to determine the interactions between all SNP-pairs. Our tool is parallelized using a hybrid combination of Pthreads and CUDA in order to take advantage of CPU/GPU architectures. Experimental results with simulated and real datasets show that EpistSearch outperforms previous approaches, either using GPUs or only CPU cores. For instance, an exhaustive analysis of a real-world dataset with 500,000 SNPs and 5,000 individuals requires less than 42 minutes on a machine with 6 CPU cores and a GTX Titan GPU

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

Primary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined10(-8)) and used pathway analysis to identify JAK-STAT/IL12/IL27 signalling and cytokine-cytokine pathways, for which relevant therapies exist