Kinetics of Competing Reactions of N-aryl-4-chloro-1,8-naphthalimides with Primary Amines

Color poster with text, diagrams, tables, and graphs.This study presented the mechanistic implications of the kinetics of competing reactions of N-aryl-4-chloro-1,8-naphthalimides with primary amines.University of Wisconsin--Eau Claire Office of Research and Sponsored Programs; Petroleum Research Fund

Matching pursuit-based compressive sensing in a wearable biomedical accelerometer fall diagnosis device

There is a significant high fall risk population, where individuals are susceptible to frequent falls and obtaining significant injury, where quick medical response and fall information are critical to providing efficient aid. This article presents an evaluation of compressive sensing techniques in an accelerometer-based intelligent fall detection system modelled on a wearable Shimmer biomedical embedded computing device with Matlab. The presented fall detection system utilises a database of fall and activities of daily living signals evaluated with discrete wavelet transforms and principal component analysis to obtain binary tree classifiers for fall evaluation. 14 test subjects undertook various fall and activities of daily living experiments with a Shimmer device to generate data for principal component analysis-based fall classifiers and evaluate the proposed fall analysis system. The presented system obtains highly accurate fall detection results, demonstrating significant advantages in comparison with the thresholding method presented. Additionally, the presented approach offers advantageous fall diagnostic information. Furthermore, transmitted data accounts for over 80% battery current usage of the Shimmer device, hence it is critical the acceleration data is reduced to increase transmission efficiency and in-turn improve battery usage performance. Various Matching pursuit-based compressive sensing techniques have been utilised to significantly reduce acceleration information required for transmission.Scopu

PMLB: A Large Benchmark Suite for Machine Learning Evaluation and Comparison

The selection, development, or comparison of machine learning methods in data mining can be a difficult task based on the target problem and goals of a particular study. Numerous publicly available real-world and simulated benchmark datasets have emerged from different sources, but their organization and adoption as standards have been inconsistent. As such, selecting and curating specific benchmarks remains an unnecessary burden on machine learning practitioners and data scientists. The present study introduces an accessible, curated, and developing public benchmark resource to facilitate identification of the strengths and weaknesses of different machine learning methodologies. We compare meta-features among the current set of benchmark datasets in this resource to characterize the diversity of available data. Finally, we apply a number of established machine learning methods to the entire benchmark suite and analyze how datasets and algorithms cluster in terms of performance. This work is an important first step towards understanding the limitations of popular benchmarking suites and developing a resource that connects existing benchmarking standards to more diverse and efficient standards in the future.Comment: 14 pages, 5 figures, submitted for review to JML

Automating biomedical data science through tree-based pipeline optimization

Over the past decade, data science and machine learning has grown from a mysterious art form to a staple tool across a variety of fields in academia, business, and government. In this paper, we introduce the concept of tree-based pipeline optimization for automating one of the most tedious parts of machine learning---pipeline design. We implement a Tree-based Pipeline Optimization Tool (TPOT) and demonstrate its effectiveness on a series of simulated and real-world genetic data sets. In particular, we show that TPOT can build machine learning pipelines that achieve competitive classification accuracy and discover novel pipeline operators---such as synthetic feature constructors---that significantly improve classification accuracy on these data sets. We also highlight the current challenges to pipeline optimization, such as the tendency to produce pipelines that overfit the data, and suggest future research paths to overcome these challenges. As such, this work represents an early step toward fully automating machine learning pipeline design.Comment: 16 pages, 5 figures, to appear in EvoBIO 2016 proceeding

Jurassic Greenways: Planning a Dinosaur Trail for the Connecticut River Valley

Greenways often combine natural, historic/cultural, and recreational resources (Fábos 1995). However, there has been less integration with scientific interpretation, particularly in the area of paleontology and geology, except for a few notable examples. The current threat of global climate compels a look back in geologic time to how different landscapes, ecosystems, and human settlements evolved and adapted to rapidly changing climatic and environmental conditions. This study involves research and project development of a greenway and trail network that connects the important historical and cultural sites related to dinosaurs in New England’s Connecticut River Valley of Massachusetts and Connecticut (USA). The project is a partnership of museums, cultural sites, and tourist businesses related to the discovery of dinosaur tracks and other significant paleo-geologic sites (www.jurassicroadshow.com). The lead organization, the Pocumtuck Valley Memorial Association, a historic museum in Deerfield, MA (www.deerfieldma. org), is developing an interactive web-site called the Impressions from a Lost World that is the beginning point for this project, which was conducted as part of a graduate landscape architecture studio at the University of Massachusetts, Amherst under the direction of Professor Robert L. Ryan

Preliminary results using a P300 brain-computer interface speller: a possible interaction effect between presentation paradigm and set of stimuli

Fernández-Rodríguez Á., Medina-Juliá M.T., Velasco-Álvarez F., Ron-Angevin R. (2019) Preliminary Results Using a P300 Brain-Computer Interface Speller: A Possible Interaction Effect Between Presentation Paradigm and Set of Stimuli. In: Rojas I., Joya G., Catala A. (eds) Advances in Computational Intelligence. IWANN 2019. Lecture Notes in Computer Science, vol 11506. Springer, ChamSeveral proposals to improve the performance controlling a P300-based BCI speller have been studied using the standard row-column presentation (RCP) par-adigm. However, this paradigm could not be suitable for those patients with lack of gaze control. To solve that, the rapid serial visual presentation (RSVP) para-digm, which presents the stimuli located in the same position, has been proposed in previous studies. Thus, the aim of the present work is to assess if a stimuli set of pictures that improves the performance in RCP, could also improve the per-formance in a RSVP paradigm. Six participants have controlled four conditions in a calibration task: letters in RCP, pictures in RCP, letters in RSVP and pictures in RSVP. The results showed that pictures in RCP obtained the best accuracy and information transfer rate. The improvement effect given by pictures was greater in the RCP paradigm than in RSVP. Therefore, the improvements reached under RCP may not be directly transferred to the RSVP.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

The Kinematic Evolution of Strong MgII Absorbers

We consider the evolution of strong (W_r(2796) > 0.3A) MgII absorbers, most of which are closely related to luminous galaxies. Using 20 high resolution quasar spectra from the VLT/UVES public archive, we examine 33 strong MgII absorbers in the redshift range 0.3 < z < 2.5. We compare and supplement this sample with 23 strong MgII absorbers at 0.4 < z < 1.4 observed previously with HIRES/Keck. We find that neither equivalent width nor kinematic spread (the optical depth weighted second moment of velocity) of MgII2796 evolve. However, the kinematic spread is sensitive to the highest velocity component, and therefore not as sensitive to additional weak components at intermediate velocities relative to the profile center. The fraction of absorbing pixels within the full velocity range of the system does show a trend of decreasing with decreasing redshift. Most high redshift systems (14/20) exhibit absorption over the entire system velocity range, which differs from the result for low redshift systems (18/36) at the 95% level. This leads to a smaller number of separate subsystems for high redshift systems because weak absorping components tend to connect the stronger regions of absorption. We hypothesize that low redshift MgII profiles are more likely to represent well formed galaxies, many of which have kinematics consistent with a disk/halo structure. High redshift MgII profiles are more likely to show evidence of complex protogalactic structures, with multiple accretion or outflow events. Although these results are derived from measurements of gas kinematics, they are consistent with hierarchical galaxy formation evidenced by deep galaxy surveys.Comment: Accepted to the Astrophysical Journa

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.

Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism

A novel mixed-method approach to assess children's sedentary behaviours

Purpose: Accurately measuring sedentary behavior (SB) in children is challenging by virtue of its complex nature. While self-report questionnaires are susceptible to recall errors, accelerometer data lacks contextual information. This study aimed to explore the efficacy of using accelerometry combined with the Digitising Children’s Data Collection (DCDC) for Health application (app), to capture SB comprehensively. Methods: 74 children (9–10 years old) wore ActiGraph GT9X accelerometers for 7 days. Each received a SAMSUNG Galaxy Tab4 (SM-T230) tablet, with the DCDC app installed and a specially designed sedentary behavior study downloaded. The app uses four data collection tools: 1) Questionnaire, 2) Take a photograph, 3) Draw a picture, and 4) Record my voice. Children self-reported their SB daily. Accelerometer data were analyzed using R-package GGIR. App data were downloaded and individual participant profiles created. SBs reported were grouped into categories and reported as frequencies. Results: Participants spent, on average, 629 min (i.e., 73% of their waking time) sedentary. App data revealed most of their out-of-school SB consisted of screen time (112 photos, 114 drawings, and screen time mentioned 135 times during voice recordings). Playing with toys, reading, arts and crafts, and homework were also reported across all four data capturing tools on the app. On an individual level, data from the app often explained irregular patterns in physical activity and SB observed in accelerometer data. Conclusion: This mixed methods approach to assessing SB adds context to accelerometer data, providing researchers with information needed for intervention design