De-wrinkling of pre-tensioned membranes

Thin membranes are used in the spacecraft industry as extremely lightweight structural components. They need to be stiffened, usually by applying discrete forces, and this increases their susceptibility to wrinkling in regions where high tensile stresses develop. We consider a regular polygonal membrane uniformly loaded at its corners by equal forces and we prevent wrinkle formation by trimming the edges of the polygon into very gentle curves. We confirm this performance through simple physical experiments using Kapton, a typical membrane material and, using computational analysis, we show how the distribution of compressive stresses, responsible for causing wrinkles, dissipates following trimming. Finally, we accurately predict the required level of trimming for any number of sides of polygon using a simple, linear model, which invokes a plate-bending analogy.This is the published manuscript. It was originally published in the International Journal of Solids and Structures here: http://www.sciencedirect.com/science/article/pii/S0020768314001875

Duckietown: An Innovative Way to Teach Autonomy

Teaching robotics is challenging because it is a multidisciplinary, rapidly evolving and experimental discipline that integrates cutting-edge hardware and software. This paper describes the course design and first implementation of Duckietown, a vehicle autonomy class that experiments with teaching innovations in addition to leveraging modern educational theory for improving student learning. We provide a robot to every student, thanks to a minimalist platform design, to maximize active learning; and introduce a role-play aspect to increase team spirit, by modeling the entire class as a fictional start-up (Duckietown Engineering Co.). The course formulation leverages backward design by formalizing intended learning outcomes (ILOs) enabling students to appreciate the challenges of: (a) heterogeneous disciplines converging in the design of a minimal self-driving car, (b) integrating subsystems to create complex system behaviors, and (c) allocating constrained computational resources. Students learn how to assemble, program, test and operate a self-driving car (Duckiebot) in a model urban environment (Duckietown), as well as how to implement and document new features in the system. Traditional course assessment tools are complemented by a full scale demonstration to the general public. The “duckie” theme was chosen to give a gender-neutral, friendly identity to the robots so as to improve student involvement and outreach possibilities. All of the teaching materials and code is released online in the hope that other institutions will adopt the platform and continue to evolve and improve it, so to keep pace with the fast evolution of the field.National Science Foundation (U.S.) (Award IIS #1318392)National Science Foundation (U.S.) (Award #1405259

PCA3 molecular urine assay for prostate cancer: association with pathologic features and impact of collection protocols

IntroductionPCA3 is a non-coding mRNA molecule that is overexpressed in prostate cancer. The purpose of this study is to evaluate the utility of the PCA3 molecular urine test scores to predict adverse pathologic features and catheterized specimen collection.MethodsHundred men with clinically localized prostate cancer scheduled to undergo robotic prostatectomy were enrolled in the study following a standard consent process. The study protocol consisted of providing four urine samples. Voided urine obtained following digital rectal examination (DRE) pre-operatively (Vl), catheterized urine without DRE (V2), and l0-day and 6-week postoperative voided (V3 and V4) urine samples were collected and analyzed. These four urine specimens underwent target capture, transcription-mediated amplification, and hybridization in order to quantify both PCA3 and PSA mRNA. The PCA3 score was calculated as the ratio of PCA3 to PSA.ResultsInformative rates (sufficient mRNA for analysis) for VI, V2, V3 and V4 were 91, 85, 0 and 2%, respectively. There was no significant associations with pathological stage, Gleason score >6. Higher PCA3 scores at V1 correlated with increased risk for perineural invasion (P = 0.0479).ConclusionsInformative PCA3 scores can be obtained from post-DRE voided urine as well as catheterized urine without a DRE. The PCA3 test does not seem to predict adverse pathologic features, though, may have an association with perineural invasion. The ability of PCA3 score to predict clinical outcome remains to be determined

Targeted Genome-Wide Enrichment of Functional Regions

Only a small fraction of large genomes such as that of the human contains the functional regions such as the exons, promoters, and polyA sites. A platform technique for selective enrichment of functional genomic regions will enable several next-generation sequencing applications that include the discovery of causal mutations for disease and drug response. Here, we describe a powerful platform technique, termed “functional genomic fingerprinting” (FGF), for the multiplexed genomewide isolation and analysis of targeted regions such as the exome, promoterome, or exon splice enhancers. The technique employs a fixed part of a uniquely designed Fixed-Randomized primer, while the randomized part contains all the possible sequence permutations. The Fixed-Randomized primers bind with full sequence complementarity at multiple sites where the fixed sequence (such as the splice signals) occurs within the genome, and multiplex amplify many regions bounded by the fixed sequences (e.g., exons). Notably, validation of this technique using cardiac myosin binding protein-C (MYBPC3) gene as an example strongly supports the application and efficacy of this method. Further, assisted by genomewide computational analyses of such sequences, the FGF technique may provide a unique platform for high-throughput sample production and analysis of targeted genomic regions by the next-generation sequencing techniques, with powerful applications in discovering disease and drug response genes

Contrasting signals from multiple markers illuminate population connectivity in a marine fish

Recent advances in molecular biology and bioinformatics have helped to unveil striking and previously unrecognized patterns of geographic genetic structure in marine populations. Largely driven by the pressing needs of fisheries management and conservation, studies on marine fish populations have played a pivotal role in testing the efficiency of a range of approaches to explore connectivity and dispersal at sea. Here, we employed nuclear and mitochondrial DNA markers and parasitic infestations to examine the nature and patterns of population structure in a warm-temperate coastal marine teleost across major putative biogeographic barriers in the Mediterranean Sea and Eastern Atlantic Ocean. We detected deep genetic divergence between mitochondrial lineages, likely caused by dramatic climatic and geological transformations before and during the Pleistocene. Such long-diverged lineages later came into secondary contact and can now be found in sympatry. More importantly, microsatellite data revealed that these lineages, after millions of years of independent evolution, now interbreed extensively. By combining genetic and parasite data, we were able to identify at least five independent demographic units. While the different genetic and parasite-based methods produce notably contrasting signals and may complicate the reconstruction of connectivity dynamics, we show that by tailoring the correct interpretation to each of the descriptors used, it is possible to achieve a deeper understanding of the micro-evolutionary process and, consequently, resolve population structure

Structure-based functional inference of hypothetical proteins from Mycoplasma hyopneumoniae

Enzootic pneumonia caused by Mycoplasma hyopneumoniae is a major constraint to efficient pork production throughout the world. This pathogen has a small genome with 716 coding sequences, of which 418 are homologous to proteins with known functions. However, almost 42% of the 716 coding sequences are annotated as hypothetical proteins. Alternative methodologies such as threading and comparative modeling can be used to predict structures and functions of such hypothetical proteins. Often, these alternative methods can answer questions about the properties of a model system faster than experiments. In this study, we predicted the structures of seven proteins annotated as hypothetical in M. hyopneumoniae, using the structure-based approaches mentioned above. Three proteins were predicted to be involved in metabolic processes, two proteins in transcription and two proteins where no function could be assigned. However, the modeled structures of the last two proteins suggested experimental designs to identify their functions. Our findings are important in diminishing the gap between the lack of annotation of important metabolic pathways and the great number of hypothetical proteins in the M. hyopneumoniae genome

Checking and bootstrapping lexical norms by means of word similarity indexes

In psychology, lexical norms related to the se- mantic properties of words, such as concreteness and va- lence, are important research resources. Collecting such norms by asking judges to rate the words is very time consuming, which strongly limits the number of words that compose them. In the present article, we present a technique for estimating lexical norms based on the latent semantic analysis of a corpus. The analyses conducted emphasize the technique’s effectiveness for several semantic dimensions. In addition to the extension of norms, this technique can be used to check human ratings to identify words for which the rating is very different from the corpus-based estimate