Investigating the efficacy of network visualizations for intelligence tasks

There is an increasing requirement for advanced analytical methodologies to help military intelligence analysts cope with the growing amount of data they are saturated with on a daily basis. Specifically, within the context of terror network analysis, one of the largest problems is the transformation of raw tabular data into a visualization that is easily and effectively exploited by intelligence analysts. Currently, the primary method within the intelligence do-main is the node-link visualization, which encodes data sets by depicting the ties between nodes as lines between objects in a plane. This method, although useful, has limitations when the size and complexity of data grows. The matrix offers an alternate perspective because the two dimensions of the matrix are arrayed as an actors x actors matrix. This paper describes an experiment investigating node-link and matrix visualization techniques within social network analysis, and their effectiveness for the intelligence tasks of: 1) identifying leaders and 2) identifying clusters. The sixty participants in the experiment were all Air Force intelligence analysts and we provide recommendations for building visualization tools for this specialized group of users.Lincoln LaboratoryNational Science Foundation (U.S.) (Grant 1136996

Effect of Combination Folic Acid, Vitamin B6 , and Vitamin B12 Supplementation on Fracture Risk in Women: A Randomized, Controlled Trial.

Epidemiologic studies have demonstrated an association of elevated plasma homocysteine levels with greater bone resorption and fracture risk. Vitamins B12 , B6 , and folic acid are cofactors in homocysteine metabolism, and supplementation with B vitamins is effective in lowering homocysteine levels in humans. However, randomized trials of supplemental B vitamins for reduction of fracture risk have been limited. Therefore, we performed an ancillary study to the Women's Antioxidant and Folic Acid Cardiovascular Study (WAFACS), a large randomized trial of women with preexisting cardiovascular disease or three or more coronary risk factors, to test whether a daily B vitamin intervention including folic acid (2.5 mg/day), vitamin B6 (50 mg/day), and vitamin B12 (1 mg/day) reduces nonspine fracture risk over 7.3 years of treatment and follow-up. Among 4810 women, we confirmed 349 nonspine fracture cases by centralized review of medical records. In a substudy of 300 women (150 in treatment group and 150 controls) with paired plasma samples at randomization and follow-up (7.3 years later), we measured two bone turnover markers, including C-terminal cross-linking telopeptide of type I collagen (CTX) and intact type I procollagen N-propeptide (P1NP). In Cox proportional hazards models based on intention-to-treat, we found no significant effects of B vitamin supplementation on nonspine fracture risk (relative hazard = 1.08; 95% confidence interval, 0.88 to 1.34). In a nested case-cohort analysis, there were no significant effects of B vitamins on fracture risk among women with elevated plasma homocysteine levels, or low levels of vitamins B12 or B6 , or folate at baseline. Furthermore, treatment with B vitamins had no effect on change in markers of bone turnover. We found no evidence that daily supplementation with B vitamins reduces fracture risk or rates of bone metabolism in middle-aged and older women at high risk of cardiovascular disease. © 2017 American Society for Bone and Mineral Research

Parameters, practices, and preferences for regulatory review of emerging biotechnology products in food and agriculture

This paper evaluates the U.S. regulatory review of three emerging biotechnology products according to parameters, practices, and endpoints of assessments that are important to stakeholders and publics. First, we present a summary of the literature on variables that are important to non-expert publics in governing biotech products, including ethical, social, policy process, and risk and benefit parameters. Second, we draw from our USDA-funded project results that surveyed stakeholders with subject matter expertise about their attitudes towards important risk, benefit, sustainability, and societal impact parameters for assessing novel agrifood technologies, including biotech. Third, we evaluate the regulatory assessments of three food and agricultural biotechnology case studies that have been reviewed under U.S. regulatory agencies and laws of the Coordinated Framework for the Regulation of Biotechnology, including gene-edited soybeans, beef cattle, and mustard greens. Evaluation of the regulatory review process was based on parameters identified in steps 1 and 2 which were deemed important to both publics and stakeholders. Based on this review, we then propose several policy options for U.S. federal agencies to strengthen their oversight processes to better align with a broader range of parameters to support sustainable agrifood products that rely on novel technologies. These policy options include 1) those that would not require new institutions or legal foundations (such as conducting Environmental Impact Statements and/or requiring a minimal level of safety data), 2) those that would require a novel institutional or cross-institutional framework (such as developing a publicly-available website and/or performing holistic sustainability assessments), and 3) those that would require the agencies to have additional legal authorities (such as requiring agencies to review biotech products according to a minimal set of health, environmental, and socio-economic parameters). Overall, the results of this analysis will be important for guiding policy practice and formulation in the regulatory assessment of emerging biotechnology products that challenge existing legal and institutional frameworks

Further Analyses of the Safety of Verubecestat in the Phase 3 EPOCH Trial of Mild-To-Moderate Alzheimer’s Disease

Background: Verubecestat, a BACE1 inhibitor that reduces Aβ levels in the cerebrospinal fluid of humans, was not effective in a phase 3 trial (EPOCH) of mild-to-moderate AD and was associated with adverse events. To assist in the development of BACE1 inhibitors, we report detailed safety findings from EPOCH. Methods: EPOCH was a randomized, double-blind, placebo-controlled 78-week trial evaluating verubecestat 12 mg and 40 mg in participants with mild-to-moderate AD diagnosed clinically. The trial was terminated due to futility close to its scheduled completion. Of 1957 participants who were randomized and took treatment, 652 were assigned to verubecestat 12 mg, 652 to verubecestat 40 mg, and 653 to placebo. Adverse events and relevant laboratory, vital sign, and ECG findings were assessed. Results: Verubecestat 12 mg and 40 mg were associated with an increase in the percentage of participants reporting adverse events versus placebo (89 and 92% vs. 82%), although relatively few participants discontinued treatment due to adverse events (8 and 9% vs. 6%). Adverse events that were increased versus placebo included falls and injuries, suicidal ideation, weight loss, sleep disturbance, rash, and hair color change. Most were mild to moderate in severity. Treatment differences in suicidal ideation emerged within the first 3 months but did not appear to increase after 6 months. In contrast, treatment differences in falls and injuries continued to increase over time. Conclusions: Verubecestat was associated with increased risk for several types of adverse events. Falls and injuries were notable for progressive increases over time. While the mechanisms underlying the increased adverse events are unclear, they may be due to BACE inhibition and should be considered in future clinical development programs of BACE1 inhibitors

Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168

Phase-variable restriction-modification systems are a feature of a diverse range of bacterial species. Stochastic, reversible switches in expression of the methyltransferase produces variation in methylation of specific sequences. Phase-variable methylation by both Type I and Type III methyltransferases is associated with altered gene expression and phenotypic variation. One phase-variable gene of Campylobacter jejuni encodes a homologue of an unusual Type IIG restriction-modification system in which the endonuclease and methyltransferase are encoded by a single gene. Using both inhibition of restriction and PacBio-derived methylome analyses of mutants and phase-variants, the cj0031c allele in C. jejuni strain NCTC11168 was demonstrated to specifically methylate adenine in 5′CCCGA and 5′CCTGA sequences. Alterations in the levels of specific transcripts were detected using RNA-Seq in phase-variants and mutants of cj0031c but these changes did not correlate with observed differences in phenotypic behaviour. Alterations in restriction of phage growth were also associated with phase variation (PV) of cj0031c and correlated with presence of sites in the genomes of these phages. We conclude that PV of a Type IIG restriction-modification system causes changes in site-specific methylation patterns and gene expression patterns that may indirectly change adaptive traits

The amyloid-β pathway in Alzheimer's disease: a plain language summary

WHAT IS THIS SUMMARY ABOUT?: This plain language summary of an article published in Molecular Psychiatry, reviews the evidence supporting the role of the amyloid-β (Aβ) pathway and its dysregulation in Alzheimer's disease (AD), and highlights the rationale for drugs targeting the Aβ pathway in the early stages of the disease. WHY IS THIS IMPORTANT?: Aβ is a protein fragment (or peptide) that exists in several forms distinguished by their size, shape/structure, degree of solubility and disease relevance. The accumulation of Aβ plaques is a hallmark of AD. However, smaller, soluble aggregates of Aβ - including Aβ protofibrils - also play a role in the disease. Because Aβ-related disease mechanisms are complex, the diagnosis, treatment and management of AD should be reflective of and guided by up-to-date scientific knowledge and research findings in this area. This article describes the Aβ protein and its role in AD, summarizing the evidence showing that altered Aβ clearance from the brain may lead to the imbalance, toxic buildup and misfolding of the protein - triggering a cascade of cellular, molecular and systematic events that ultimately lead to AD. WHAT ARE THE KEY TAKEAWAYS?: The physiological balance of brain Aβ levels in the context of AD is complex. Despite many unanswered questions, mounting evidence indicates that Aβ has a central role in driving AD progression. A better understanding of the Aβ pathway biology will help identify the best therapeutic targets for AD and inform treatment approaches

Archeological Significance Testing at 41BX17/271, the Granberg Site: A Multi-Component Site along the Salado Creek in Bexar County, Texas

The Center for Archaeological Research (CAR) of The University of Texas at San Antonio conducted archeological significance testing at 41BX17, the Granberg Site, from January to March 2006. The testing was conducted for the Texas Department of Transportation, Environmental Affairs Division (TxDOT-ENV). The Granberg Site sits on the eastern flood terrace of the Salado Creek south of Loop 410 in San Antonio, Bexar County, Texas. Planned road improvements including installation of a storm sewer line and a water main prompted the need to assess whether (1) cultural deposits including human remains still exist after previous testing and (2) if the deposits contribute to the site’s National Register of Historic Places eligibility. The archeological work was conducted under Texas Antiquities Permit No. 4010. Steve A. Tomka served as Principal Investigator and Jennifer Thompson served as Project Archeologist. Fieldwork included mechanical auger boring and backhoe trenching to determine the horizontal extent of the site boundaries within the median of Loop 410 eastbound. Sixteen 1-x-1-m units were excavated to determine the distribution and integrity of the cultural deposits and to locate any possible burials that may still exist at the site. Materials recovered included burned rock features, chipped stone artifacts, animal bone, snail and mussel shell and charred plant remains. The distribution of the artifacts, the geomorphic investigations, the radiocarbon assays, and temporally diagnostic artifacts indicate the presence of Middle and Late Archaic archeological materials with good stratigraphic integrity. The Granberg Site was determined to be ineligible for the National Register of Historic Places. Following the completion of eligibility testing efforts, the TxDOT directed the CAR to develop a research design linking the data recovered from the various excavations at the Granberg Site with research goals. The CAR developed the research design (Munoz et al. 2007) under Work Authorization No. 57513SA005 with Cynthia M. Munoz serving as Project Archeologist. At roughly the time of the research design implementation, the CAR was the recipient of a donation of a collection of commingled human skeletal remains recovered from the Granberg Site. These remains were recovered from 41BX17/271 in 1962 by Harvey Kohnitz, an avocational archeologist, without knowledge or permission from the Texas Highway Department. The remains were stored at the Kohnitz home until his son, Mark Kohnitz, donated them to the CAR in 2007. An osteological analysis was conducted at the CAR laboratory during February 2008 for TxDOT, under Work Authorization No. 57513SA005 Supplemental Work Authorization No. 4. The results of this analysis are reported in Appendix H of this report. The commingled remains will be curated the CAR and all required documents, including an inventory, will be submitted to the National Park Service National NAGPRA Program to fulfill all obligations pertaining to the NAGPRA laws. All artifacts collected during this project and all project-associated documentation are permanently curated at the CAR according to Texas Historical Commission guidelines

Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis

The preterm gut microbiome is a complex dynamic community influenced by genetic and environmental factors and is implicated in the pathogenesis of necrotising enterocolitis (NEC) and sepsis. We aimed to explore the longitudinal development of the gut microbiome in preterm twins to determine how shared environmental and genetic factors may influence temporal changes and compared this to the expressed breast milk (EBM) microbiome. Stool samples (n = 173) from 27 infants (12 twin pairs and 1 triplet set) and EBM (n = 18) from 4 mothers were collected longitudinally. All samples underwent PCR-DGGE (denaturing gradient gel electrophoresis) analysis and a selected subset underwent 454 pyrosequencing. Stool and EBM shared a core microbiome dominated by Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae. The gut microbiome showed greater similarity between siblings compared to unrelated individuals. Pyrosequencing revealed a reduction in diversity and increasing dominance of Escherichia sp. preceding NEC that was not observed in the healthy twin. Antibiotic treatment had a substantial effect on the gut microbiome, reducing Escherichia sp. and increasing other Enterobacteriaceae. This study demonstrates related preterm twins share similar gut microbiome development, even within the complex environment of neonatal intensive care. This is likely a result of shared genetic and immunomodulatory factors as well as exposure to the same maternal microbiome during birth, skin contact and exposure to EBM. Environmental factors including antibiotic exposure and feeding are additional significant determinants of community structure, regardless of host genetics