Using and Interpreting the Bayesian Optimization Algorithm to Improve Early Stage Design of Marine Structures.

Early stage naval structural design continues to advance as designers seek to improve the quality and speed of the design process. The early stages of design produce preliminary dimensions or scantlings which control the cost and structural performance of a vessel. Increased complexity in the evaluation of structural response has led to a need for efficient algorithms well suited to solving structural design specific optimization problems. As problem sizes increase, existing optimizers can become slow or inaccurate. The Bayesian Optimization Algorithm (BOA) is presented as one solution to efficiently solve problems in the structural design optimization process. The Bayesian optimization algorithm is an Estimation of Distribution Algorithm (EDA) that uses a statistical sample of potential design solutions to create and train a Bayesian network (BN). The application of BNs is well suited for nearly decomposable problem composition which closely matches rules based structural design evaluation. This makes the BOA well suited to solve complex early stage structural optimization problems. Additionally, the learning processes used to create and train the BNs can be analyzed and interpreted to capture design knowledge. This return of knowledge to the designer helps to improve designer intuition and model synthesis in the face of more complex and intricate models. The BNs are thus analyzed to augment design problem understanding and explore trade-offs within the design space. The result matches a paradigm shift in early stage optimization of naval structures. Designers gain better understanding of critical design variables and their interactions as compared to the previous focus on the single most optimal solution. This leads to efficient simulations which rapidly explore design spaces, document critical design variable relationships and enable the designer to create better early stage design solutions.PhDNaval Architecture and Marine EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/133317/1/tedevine_1.pd

Registration of ‘Purple Bounty’ and ‘Purple Prosperity’ hairy vetch

The hairy vetch (Vicia villosa Roth) cultivars ‘Purple Bounty’ (Reg. no. CV-12, PI 648342) and ‘Purple Prosperity’ (Reg. no. CV-11, PI 654047) were released in 2007 and 2008, respectively, by the USDA–ARS in collaboration with the Rodale Institute and the agricultural experiment stations of Pennsylvania State University and Cornell University. Hairy vetch is a commonly used annual legume cover crop grown for its cold tolerance, fast growth, large biomass production, and ability to fix N2. However, this species has not been selected for the traits needed to optimize its use as a cover crop. Our breeding program focused on developing a cultivar that was both early flowering and had adequate winter survival and therefore adapted to mechanical termination in organic no-till production in the U.S. Northeast and Mid-Atlantic. Purple Bounty and Purple Prosperity were developed between 1998 and 2005 using recurrent selection at nurseries in Beltsville and Keedysville, MD. In 2005–2006, selections were evaluated against commercial checks for flowering time in Maryland and Pennsylvania, and in the 2006–2007 and 2007–2008 seasons they were evaluated in 10 locations (12 total site-years) across the United States for winter survival. Purple Bounty and Purple Prosperity both flowered earlier than the commercial material against which they were tested (significance depended on the date and site); Purple Bounty was the earlier flowering of the two cultivars. Purple Bounty and Purple Prosperity also had equivalent or improved winter survival compared with ‘AU Early Cover’, an early-maturing cultivar developed in the southern United States, at all test locations. Purple Prosperity is no longer commercially available, but Purple Bounty is currently licensed and distributed by Allied Seed (Nampa, ID)

Rocaglates induce gain-of-function alterations to eIF4A and eIF4F

Rocaglates are a diverse family of biologically active molecules that have gained tremendous interest in recent years due to their promising activities in pre-clinical cancer studies. As a result, this family of compounds has been significantly expanded through the development of efficient synthetic schemes. However, it is unknown whether all of the members of the rocaglate family act through similar mechanisms of action. Here, we present a comprehensive study comparing the biological activities of >200 rocaglates to better understand how the presence of different chemical entities influences their biological activities. Through this, we find that most rocaglates preferentially repress the translation of mRNAs containing purine-rich 5' leaders, but certain rocaglates lack this bias in translation repression. We also uncover an aspect of rocaglate mechanism of action in which the pool of translationally active eIF4F is diminished due to the sequestration of the complex onto RNA.P50 GM067041 - NIGMS NIH HHS; R24 GM111625 - NIGMS NIH HHS; R35 GM118173 - NIGMS NIH HHSPublished versio

Toward a Socialism for the Future, in the Wake of the Demise of the Socialism of the Past

http://deepblue.lib.umich.edu/bitstream/2027.42/51230/1/464.pd

Effects of the neonicotinoid pesticide thiamethoxam at field-realistic levels on microcolonies of Bombus terrestris worker bumble bees

Copyright © 2013 Elsevier. Notice: this is the author’s version of a work that was accepted for publication in Ecotoxicology and Environmental Safety. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Ecotoxicology and Environmental Safety, 2014, Vol. 100, pp. 153-158 at: http://dx.doi.org/10.1016/j.ecoenv.2013.10.027Neonicotinoid pesticides are currently implicated in the decline of wild bee populations. Bumble bees, Bombus spp., are important wild pollinators that are detrimentally affected by ingestion of neonicotinoid residues. To date, imidacloprid has been the major focus of study into the effects of neonicotinoids on bumble bee health, but wild populations are increasingly exposed to alternative neonicotinoids such as thiamethoxam. To investigate whether environmentally realistic levels of thiamethoxam affect bumble bee performance over a realistic exposure period, we exposed queenless microcolonies of Bombus terrestris L. workers to a wide range of dosages up to 98 μg kg−1 in dietary syrup for 17 days. Results showed that bumble bee workers survived fewer days when presented with syrup dosed at 98 μg thiamethoxam kg−1, while production of brood (eggs and larvae) and consumption of syrup and pollen in microcolonies were significantly reduced by thiamethoxam only at the two highest concentrations (39, 98 μg kg−1). In contrast, we found no detectable effect of thiamethoxam at levels typically found in the nectars of treated crops (between 1 and 11 μg kg−1). By comparison with published data, we demonstrate that during an exposure to field-realistic concentrations lasting approximately two weeks, brood production in worker bumble bees is more sensitive to imidacloprid than thiamethoxam. We speculate that differential sensitivity arises because imidacloprid produces a stronger repression of feeding in bumble bees than thiamethoxam, which imposes a greater nutrient limitation on production of brood.Natural Environment Research Council (NERC

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Can a Multifaceted Intervention Including Motivational Interviewing Improve Medication Adherence, Quality of Life, and Mortality Rates in Older Patients Undergoing Coronary Artery Bypass Surgery? A Multicenter, Randomized Controlled Trial with 18-Month Follow-Up.

BACKGROUND: Patients undergoing coronary artery bypass graft (CABG) surgery are required to take a complex regimen of medications for extended periods, and they may have negative outcomes because they struggle to adhere to this regimen. Designing effective interventions to promote medication adherence in this patient group is therefore important. OBJECTIVE: The present study aimed to evaluate the long-term effects of a multifaceted intervention (psycho-education, motivational interviewing, and short message services) on medication adherence, quality of life (QoL), and mortality rates in older patients undergoing CABG surgery. METHODS: Patients aged over 65 years from 12 centers were assigned to the intervention (EXP; n = 144) or treatment-as-usual (TAU; n = 144) groups using cluster randomization at center level. Medication adherence was evaluated using the Medication Adherence Rating Scale (MARS), pharmacy refill rate, and lipid profile; QoL was evaluated using Short Form-36. Data were collected at baseline; 3, 6, and 18 months after intervention. Survival status was followed up at 18 months. Multi-level regressions and survival analyses for hazard ratio (HR) were used for analyses. RESULTS: Compared with patients who received TAU, the MARS, pharmacy refill rate, and lipid profile of patients in the EXP group improved 6 months after surgery (p < 0.01) and remained so 18 months after surgery (p < 0.01). QoL also increased among patients in the EXP group as compared with those who received TAU at 18 months post-surgery (physical component summary score p = 0.02; mental component summary score p = 0.04). HR in the EXP group compared with the TAU group was 0.38 (p = 0.04). CONCLUSION: The findings suggest that a multifaceted intervention can improve medication adherence in older patients undergoing CABG surgery, with these improvements being maintained after 18 months. QoL and survival rates increased as a function of better medication adherence. ClinicalTrials.gov NCT02109523