Vortex-induced vibrations of a freely vibrating cylinder near a plane boundary: experimental investigation and theoretical modelling

This work reports on experiments that were performed with a freely vibrating cylinder exposed to currents and placed near a plane boundary parallel to the cylinder axis. It is observed that the proximity of the boundary affects the vertical response of the cylinder in two ways: (i) for gaps between 0.75 and 2 diameters (D), the amplitude of oscillation is reduced; (ii) for gaps smaller than 0.75D, the cylinder impacts the boundary, resulting in an increase of amplitudes and frequencies of oscillations as the flow is accelerated. The in-line force acting on the cylinder is also examined, and the dependency of its harmonic components on the flow velocity and distance to the boundary is evaluated. Besides the typical amplification of the mean component inside the lock-in region, it is also observed that as the cylinder is placed closer to the boundary, the harmonic component with the frequency of the vertical oscillations increases, while the component with twice that frequency decreases in similar amount. Based on the experimental observations, an existing wake-oscillator model for vortex-induced vibrations is enhanced in order to account for the effect of the boundary. The proposed model introduces an effective damper that is activated when the cylinder reaches a certain distance from the boundary, and a damper/spring set representing the rigidity of the boundary and the dissipation of energy due to impact

Fuzzy-logic controlled genetic algorithm for the rail-freight crew-scheduling problem

AbstractThis article presents a fuzzy-logic controlled genetic algorithm designed for the solution of the crew-scheduling problem in the rail-freight industry. This problem refers to the assignment of train drivers to a number of train trips in accordance with complex industrial and governmental regulations. In practice, it is a challenging task due to the massive quantity of train trips, large geographical span and significant number of restrictions. While genetic algorithms are capable of handling large data sets, they are prone to stalled evolution and premature convergence on a local optimum, thereby obstructing further search. In order to tackle these problems, the proposed genetic algorithm contains an embedded fuzzy-logic controller that adjusts the mutation and crossover probabilities in accordance with the genetic algorithm’s performance. The computational results demonstrate a 10% reduction in the cost of the schedule generated by this hybrid technique when compared with a genetic algorithm with fixed crossover and mutation rates

To be, or not to be, a non-native freshwater fish?

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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

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin