Contributors: Pradip Hayu, M.S., Nima Zahadat, Ph.D.
Contributors: Srilatha Lakka
... Data Visualization Individual Project-1 Analysis of Military, Health and Education Spending
Benchmarking Octave, R and Python platforms for code prototyping in Data Analytics and Machine Learning applications programming
Contributors: Harris Georgiou
... Abstract Octave, R and Python identical codes are tested in terms of in terms of end-user execution speed, using a very low-end "embedded" hardware system and a standard office workstation. The codes include algorithmic primitives common in Data Analytics and Machine Learning, i.e., matrix manipulation (inversion, product), linear Algebra, linear regression, Singular Value Decomposition (SVD), fast Fourier transformation (FFT) and a baseline Bubblesort implementation for testing flow control structures. Description In Data Analytics and Machine Learning, code prototyping is an integral part of the Research & Development (R&D) process, especially in data exploration and algorithm design. The programming tools and platforms used for these tasks are selected for rich API/library base, high-level expression syntax, very compact code, interactive on-the-fly code input, abstract data management and best-possible execution speed. Thus, traditional programming languages are usually inappropriate for such heavily iterative and exploratory coding evolutions. Today, by far the three most popular and appropriate choices are Octave, R and Python. In this work, these three programming environments are assessed in terms of end-user execution speed. More specifically, some common algorithmic primitives are implemented and tested in each language separately, including matrix manipulation (inversion, product), linear Algebra, linear regression, Singular Value Decomposition (SVD), as well as fast Fourier transformation (FFT) as a standard procedure in a signal processing pipeline. Additionally, a baseline implementation of the Bubblesort algorithm is employed for testing the efficiency of flow control structures and execution performance in code branching. The results present the performance of the three identical source codes in terms of end-user execution speed (elapsed time) in three different hardware platforms, namely: (1) simulating very low-end processing and resources machine similar to embedded systems (Linux, 2GB RAM, N20 Atom single-core CPU), (2) a standard/enhanced office workstation (Win10, 16GB RAM, dual-core i7 CPU) and (3) a high-end workstation or small office server (Win10, 32GB RAM, quad-core i7 CPU).
Contributors: Lingyi Meng M.S., Nima Zahadat, Ph.D.
... This project is related to relationship between river’s Injury and Passenger Characteristics through analyzing on Python-Pandas and Plotly. The coding is stored in file "Lingyi Meng.ipynb" and diagrams created by coding is kept as png form. There are totally two main part of datasets: "2016OhioCrash.xlsx" is the core data for analyzing and the left mini table are designed for analyzing the overlook together.
Contributors: Kincaid, Rodney P., Lam, Victor L., Randall, Glenn, Sullivan, Christopher S.
... These are the primary data files including uncropped gel images, raw data for replicon and virus replication experiments and code for image processing.
Contributors: Leonardo Diaco, Luca Garofalo, Davide Marchesini
... Dimensionamento e verifica di una rete di fognatura a Romagnano in Provincia Autonoma di Trento (IT)
Data from: Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)
Contributors: Kordonowy, Lauren L., MacManes, Matthew D.
... Rodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. Well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. Therefore, this study characterizes the transcriptome of three male reproductive tissues (testes, epididymis and vas deferens) of Peromyscus eremicus (Cactus mouse), a desert specialist. The transcriptome assembly process was optimized in order to produce a high quality and substantially complete annotated transcriptome. This composite transcriptome was generated to characterize the expressed transcripts in the male reproductive tract of P. eremicus, which will serve as a crucial resource for future research investigating our hypothesis that the male Cactus mouse possesses an adaptive reproductive phenotype to mitigate water-loss from ejaculate. This study reports genes under positive selection in the male Cactus mouse reproductive transcriptome relative to transcriptomes from Peromyscus maniculatus (deer mouse) and Mus musculus. Thus, this study expands upon existing genetic research in this species, and we provide a high quality transcriptome to enable further explorations of our proposed hypothesis for male Cactus mouse reproductive adaptations to minimize seminal fluid loss.
Replication Data for: Which Matters Most: Party Strategic Exit or Voter Strategic Voting? A Laboratory Experiment
Contributors: Bol, Damien, Blais, André, Labbé St-Vincent, Simon
... There is abundant empirical evidence that the plurality rule constrains party competition and favors two-party systems. This reduction of party system fragmentation may be due to parties deciding not to enter elections for which they are not viable and/or voters voting strategically. Yet no prior research has attempted to estimate the respective role of parties and voters in this process. To fill this gap, we conducted a unique laboratory experiment where some subjects played the role of parties and others played the role of voters, and where the two were able to respond to each other just as in real-life elections. We find that the reduction due to party strategic exit is higher than that due to strategic voting. We conclude that parties play a key role in the effect of the plurality rule on party system fragmentation.
Data from: The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes
Contributors: Eves-van den Akker, Sebastian, Lilley, Catherine J., Danchin, Etienne G. J., Rancurel, Corinne, Cock, Peter J. A., Urwin, Peter E., Jones, John T.
... Within the phylum Nematoda, plant-parasitism is hypothesized to have arisen independently on at least four occasions. The most economically damaging plant-parasitic nematode species, and consequently the most widely studied, are those that feed as they migrate destructively through host roots causing necrotic lesions (migratory endoparasites) and those that modify host root tissue to create a nutrient sink from which they feed (sedentary endoparasites). The false root-knot nematode Nacobbus aberrans is the only known species to have both migratory endoparasitic and sedentary endoparasitic stages within its life cycle. Moreover, its sedentary stage appears to have characteristics of both the root-knot and the cyst nematodes. We present the first large-scale genetic resource of any false-root knot nematode species. We use RNAseq to describe relative abundance changes in all expressed genes across the life cycle to provide interesting insights into the biology of this nematode as it transitions between modes of parasitism. A multigene phylogenetic analysis of N. aberrans with respect to plant-parasitic nematodes of all groups confirms its proximity to both cyst and root-knot nematodes. We present a transcriptome-wide analysis of both lateral gene transfer events and the effector complement. Comparing parasitism genes of typical root-knot and cyst nematodes to those of N. aberrans has revealed interesting similarities. Importantly, genes that were believed to be either cyst nematode, or root-knot nematode, “specific” have both been identified in N. aberrans. Our results provide insights into the characteristics of a common ancestor and the evolution of sedentary endoparasitism of plants by nematodes.
Contributors: Motoyasu Satou, Hiroyuki Kaiya, Yoshihiro Nishi, Akio Shinohara, Shin-ichiro Kawada, Mikiya Miyazato, Kenji Kangawa, Hiroyuki Sugimoto
... Here, we describe cDNA cloning and purification of the ghrelin gene sequences and ghrelin peptides from the Japanese true mole, Mogera imaizumii. The gene spans >2.9kbp, has four exons and three introns, and shares structural similarity with those of terrestrial animals. Mature mole ghrelin peptide was predicted to be 28 amino acids long (GSSFLSPEHQKVQQRKESKKPPSKPQPR) and processed from a prepropeptide of 116 amino acids. To further elucidate molecular characteristics, we purified ghrelin peptides from mole stomach. By mass spectrometry, we found that the mole ghrelin peptides had higher ratios of the odd-number fatty acids (C9 and C11 as much as C8) attached to the third serine residue than other vertebrate ghrelin. Truncated forms of ghrelins such as [1–27], [1–19], [1–16] and [1–15], and that lacked the 14th glutamine residue (des-Gln14 ghrelin) were produced in the stomach. Marked expression of ghrelin mRNA in lung was observed as in stomach and brain. Phylogenetic analysis indicated that the branch of M. imaizumii has slightly higher dN/dS ratios (the nucleotide substitution rates at non-synonymous and synonymous sites) than did other eulipotyphlans. Peptide length was positively correlated with human ghrelin receptor activation, whereas the length of fatty-acyl chains showed no obvious functional correlation. The basal higher luciferase activities of the 5′-proximal promoter region of mole ghrelin were detected in ghrelin-negative C2C12 cells and hypoxic culture conditions impaired transcriptional activity. These results indicated that moles have acquired diverse species of ghrelin probably through distinctive fatty acid metabolism because of their food preferences. The results provide a gateway to understanding ghrelin metabolism in fossorial animals.