A New IEEE 802.15.4 Simulation Model for OMNeT++ / INET

This paper introduces a new IEEE 802.15.4 simulation model for OMNeT++ / INET. 802.15.4 is an important underlying standard for wireless sensor networks and Internet of Things scenarios. The presented implementation is designed to be compatible with OMNeT++ 4.x and INET 2.x and laid-out to be expandable for newer revisions of the 802.15.4 standard. The source code is available online https://github.com/michaelkirsche/IEEE802154INET-StandaloneComment: Published in: A. F\"orster, C. Sommer, T. Steinbach, M. W\"ahlisch (Eds.), Proc. of 1st OMNeT++ Community Summit, Hamburg, Germany, September 2, 2014, arXiv:1409.0093, 201

Computational Methods for Structural Variation Analysis in Populations

Recent advances in long-read sequencing have given us an unprecedented view of structural variants (SVs). However, much of their role in disease and evolution remains unknown due to a number of technical and biological challenges, including the high error rate of most long-read sequencing data, the additional complexity of aligning around large variants, and biological differences in how the same SV can manifest in different individuals. In this thesis we introduce novel methods for structural variant analysis and demonstrate how they overcome many of these obstacles. First, we apply recent advances in data structures to the substring search problem and show how learned index structures can enable accelerated alignment of genomic reads. Next, we present an optimized SV calling pipeline that integrates improvements to existing software alongside two novel SV-processing methods, Iris and Jasmine, which improve the accuracy of SV breakpoints and sequences in individual samples and compare and integrate SV calls from multiple samples. Finally, we show how the introduction of CHM13, the first gap-free telomere-to-telomere human reference genome, enables for the first time variant calling in over 100 Mbp of newly resolved sequence and mitigates long-standing issues in variant calling that were attributed to gaps, errors, and minor alleles in the prior GRCh38 reference. We demonstrate the broad applicability of our advancements in SV inference by uncovering novel associations with gene expression in 444 human individuals from the 1000 Genomes Project, by detecting SVs in the tomato genome which affect fruit size and yield, and by comparing SVs between tumor and normal cells in organoids derived from the SKBR3 breast cancer cell line

Introduction of electric vehicle charging stations to university campuses : A case study for the university of Georgia from 2014 to 2017

Electric vehicles (EVs) are becoming increasingly popular in the United States of America (USA). EVs attract buyers with benefits including energy efficiency and environmental friendliness. As EV usage grows, more public spaces are installing EV charging stations. This paper presents a comprehensive analysis of EV charging station usage at the University of Georgia (UGA) in Athens, Georgia. Three ChargePoint EV charging stations at UGA were used to collect data about each of 3204 charging events that occurred from 10 April 2014 to 20 June 2017. The charging event data included start date, start time, length of parking time, length of charging time, amount of energy delivered, and the postal code entered by the user during ChargePoint account registration. Analytical methods were proposed to obtain information about EV charging behavior, charging station occupancy, and geolocation of charging station users. The methodology presented here was time- and cost-effective, as well as scalable to other organizations that own charging stations. Because this study took place at a university, the results presented here can be used as a reference for EV charging station usage in other college towns in the USA that do not have EV charging stations but are planning to develop EV infrastructure

Textile sensors for stab and cut detection

Manufacturers are aiming for more flexible and lightweight protective clothing to increase wearing comfort. A cardigan with a knitted stab-resistant inlay and an alarm system is presented. The stab-resistant inlay is based on a multilayer ultra-high molecular weight poly ethylene (UHMW-PE) fabric. Stab resistance was evaluated according to the standard of the Association of Test Laboratories for Bullet, Stab or Pike Resistant Materials and Construction Standard (VPAM 2011). Furthermore sensors for the detection of cuts and pressure were integrated. Both sensors can trigger alarms if the wearer is attacked. Normal pressure occurring through leaning on a wall or sitting is filtered out and does not trigger an alarm

Jasmine: Population-scale structural variant comparison and analysis

The increasing availability of long-reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine (https://github.com/mkirsche/Jasmine ), a fast and accurate method for SV refinement, comparison, and population analysis. Using an SV proximity graph, Jasmine outperforms five widely-used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than five-fold, and reveals a set of high confidence de novo SVs confirmed by multiple long-read technologies. We also present a harmonized callset of 205,192 SVs from 31 samples of diverse ancestry sequenced with long reads. We genotype these SVs in 444 short read samples from the 1000 Genomes Project with both DNA and RNA sequencing data and assess their widespread impact on gene expression, including within several medically relevant genes

Visualizing the ultra-structure of microorganisms using table-top extreme ultraviolet imaging

Table-top extreme ultraviolet (EUV) microscopy offers unique opportunities for label-free investigation of biological samples. Here, we demonstrate ptychographic EUV imaging of two dried, unstained model specimens: germlings of a fungus (Aspergillus nidulans), and bacteria (Escherichia coli) cells at 13.5 nm wavelength. We find that the EUV spectral region, which to date has not received much attention for biological imaging, offers sufficient penetration depths for the identification of intracellular features. By implementing a position-correlated ptychography approach, we demonstrate a millimeter-squared field of view enabled by infrared illumination combined with sub-60 nm spatial resolution achieved with EUV illumination on selected regions of interest. The strong element contrast at 13.5 nm wavelength enables the identification of the nanoscale material composition inside the specimens. Our work will advance and facilitate EUV imaging applications and enable further possibilities in life science

Paragraph: A graph-based structural variant genotyper for short-read sequence data

Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an accurate genotyper that models SVs using sequence graphs and SV annotations. We demonstrate the accuracy of Paragraph on whole-genome sequence data from three samples using long-read SV calls as the truth set, and then apply Paragraph at scale to a cohort of 100 short-read sequenced samples of diverse ancestry. Our analysis shows that Paragraph has better accuracy than other existing genotypers and can be applied to population-scale studies. © 2019 The Author(s)

Olfactory bulb projections in the bullfrog Rana catesbeiana

The projections of the accessory and main olfactory bulbs of the bullfrog are described as part of a long term analysis of the morphological differences in amphibian and reptilian telencephalons. Unilateral aspiration of the accessory olfactory bulb results in an ipsilateral projection to the pars lateralis of the amygdala via the accessory olfactory tract. Degenerating fibers from the accessory olfactory bulb are tracable into the cell-free zone between the dorsal striatum and the lateral pallium, and projections to these neural populations may also exist. Unilateral lesions of the main olfactory bulb reveal two major secondary pathways: an ipsilateral medial olfactory tract that projects to the rostral ventromedial portion of the medial pallium, the postolfactory eminence and the rostral, lateral and medial septal nuclei; and an ipsilateral lateral olfactory tract that projects to the dorsal striatum, the lateral pallium and the ventral half of the dorsal pallium. Two crossed secondary olfactory pathways to the contralateral telencephalon decussate via the habenular commissure after entering the ipsilateral stria medullaris. A crossed lateral pathway terminates in the dorsal striatum, the caudal, lateral pallium and the ventral portion of the dorsal pallium. A crossed medial pathway terminates in the internal granule layer of the main olfactory bulb.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/50258/1/1051450302_ftp.pd