Processing Submillisecond Timing Differences in a Model Electrosensory System

Perception of sensory cues requires peripheral encoding followed by extraction of behaviorally relevant signal components by central neurons. Some sensory systems can detect temporal information with submillisecond accuracy, despite these signals occurring faster than the approximately 1 ms timescale of neuronal firing. In sound localization, the best studied example of this phenomenon, there are at least two distinct mechanisms for detecting submillisecond timing differences, indicating that multiple solutions to this fundamental problem exist. I investigated mechanisms for processing submillisecond timing differences by studying electrosensory processing in a time coding expert, mormyrid weakly electric fish, which can detect submillisecond differences in the duration of electric signals. First, I measured responses of peripheral receptors to stimuli of different durations. I found that each unit responded preferentially to longer stimuli, but with response thresholds that varied among units within the behaviorally relevant range of durations. This variability establishes a population code operating at near threshold intensities in which the number and identity of responding receptors represents duration. At higher stimulus intensities all units respond independent of duration, rendering the population code obsolete. Importantly, peripheral receptors respond either to the start or end of a signal. Thus, stimulus duration is also represented by a temporal code, as a difference in spike times between receptors. Next, I investigated the central mechanism for detection of submillisecond spike time differences by recording from time comparator neurons (Small Cells) in the midbrain. Recording from Small Cells is challenging because their somas are small and relatively inaccessible. I therefore designed a novel method using retrograde labeling to directly visualize and record from Small Cells in vivo. I showed that patterns of duration tuning vary among Small Cells due to a combination of blanking inhibition corresponding to one edge of a stimulus and variably delayed excitation corresponding to one or both edges of a stimulus. Other circuits that detect submillisecond timing differences rely either on precisely-timed inhibition or delay-line coincidence detection. I demonstrate a novel mechanism by which mormyrids combine delay-line coincidence detection with precisely-timed blanking inhibition to establish diverse patterns of duration tuning among a population of time comparators

Developing measures for valuing changes in biodiversity : final report

This document reports the findings from the DEFRA funded research project 'Developing measures for valuing changes in biodiversity'. The aim of the research was to develop an appropriate framework that will enable cost-effective and robust valuations of the total economic value of changes to biodiversity in the UK countryside. The research involved a review of ecological and economic literature on the valuation of biodiversity changes. The information gathered from this review, along with the findings from a series of public focus groups and an expert review of valuation methodologies, were used to develop a suite of valuation instruments that were used to measure the economic value of different aspects of biodiversity. Contingent valuation and choice experiment studies were administered to households in Cambridgeshire and Northumberland, while valuation workshops were conducted in Northumberland only. The data from these studies were also used to test for benefits transfer

The New Naval Architecture Degree Program at UNSW Canberra

We are open for business with the new Naval Architecture degree program of UNSW Canberra at the Australian Defence Force Academy. We are excited about the future and look forward to welcoming the first cohort of undergraduate students who will engage with us in 2022. Through this paper we will provide insight into our planning and aspirations for our activities in teaching and research. Given the history of naval architecture at UNSW Sydney, this might be seen as a transfer geographically of the discipline from Sydney to Canberra, but it also represents a conscious effort to tailor the program for Navy in support of the current Defence White Paper, the continuous naval shipbuilding policy, and the requisite foundational skills development in the discipline. The Australian Defence Force Academy is a unique institution in the context of the Australian higher education landscape and positioning the program here provides opportunities for it to thrive

Evaluating the Value of Dynamic Terrain Simulation on Training Quality

Warfighters perform a variety of civilian duties, such as construction. For example, in Iraq, from 2004-2011, the US Army carried out over 5,000 construction projects. Training warfighters on heavy construction equipment is a timeconsuming task that contrasts with shrinking military budgets. Simulation-based training offers improved training for fewer resources. Simulators can decrease time to task proficiency by up to 90%. Identifying the pertinent features needed for a construction equipment trainer is challenging. For example, a critical skill is identifying different soil types. Lifting too much soil can damage equipment while not taking enough can cause significant delays. An experimental study investigated the effectiveness of a virtual excavator trainer with particular attention to the use of a high-fidelity soil simulation and its effect on learning. The experiments included two soil types: clay (hard to handle, high mechanical integrity) and sand (easy to handle, reduced mechanical integrity). Participants used the Dynamic Environments (DE) Testbed with the Construction Equipment Virtual Trainer (CEVT) for the experiments. Randomly assigned participants worked with clay, sand, or both materials as well as using the CEVT or watching video for their training tasks. Participants attended three separate training sessions and completed decision tasks to assess their level of knowledge in identifying different soils and operating a virtual excavator correctly. Results showed that while the high-fidelity simulation did not dramatically improve learning, use of the simulation-based trainer did allow participants to estimate better the time required to conduct tasks based on different terrain types. The authors recommend: (1) designing training scenarios that limit the effect of contamination by prior experience, (2) improved simulator controls, (3) enhanced simulator graphic fidelity, and (4) an increased number of participants provide results with the desired consistency in improving training quality

Cultural Participation: A Survey about Arts & Cultural Activities on Chicago’s South Side

Each year our graduate research class at the University of Chicago’s Harris School of Public Policy undertakes a project to address a major issue in cultural policy. In 2013, our project was locally-based, but focused on an issue with global implications: charting the multiple and varied ways that people are now engaging in cultural activities and experiences beyond the focus in recent decades on arts attendance at established cultural venues. Conducted periodically since 1982, the National Endowment for the Arts’ Survey of Public Participation in the Arts (SPPA) serves as the preeminent source of arts participation data in the US. Historically, the most widely reported summary statistic from the SPPA has been attendance at the seven benchmark arts events.1 The 2008 SPPA found that only 34.6 percent of American adults had attended any benchmark arts performance or exhibit in the preceding 12 months. This finding, along with the general downward trend in attendance across all art forms and among all age cohorts, sent shock waves through the cultural community of artists, arts professionals, audiences and supporters. And the persistent finding that the majority of cultural attenders tend to be white, well-educated, and older than the median age of Americans was also cause for concern and questioning. New questions have subsequently arisen about the nature of arts and cultural participation: What arts experiences are most relevant to people’s daily lives? Through what means and in what settings do people feel that they are participating in creative or cultural activity? Does the SPPA adequately capture these activities? Such issues about the extent and scope of cultural participation are now being addressed in countries around the world. A 2012 UNESCO study compiled the kinds of survey questions that are now being asked internationally, including “did you go to a library, attend the cinema, or play videogames in the past 12 months?” “How often do you read books, newspapers, magazines, or listen to the radio?” “How often, if ever, have you taken photographs, or made videos or movies?; played a musical instrument, sung, acted or danced?) [UNESCO 2012]. Increasingly, arts are not perceived as a luxury, but as an inherent cultural right to self-expression and community participation (Ivey 2008). Acts of individual creative expression, as well as attendance, are vital aspects of a healthy arts ecology. Our project to investigate the ways and means by which individuals participate in arts and cultural experiences took shape as a pilot project in Chicago’s South Side community, where the University of Chicago is located. With the help of the University-sponsored South Side Arts and Humanities Network, we brought a local focus to the questions of: What “counts” as cultural participation? How often do people participate? What are the physical and social contexts for participation? How and why do people participate in the way they do Ten cultural organizations of varying sizes and membership, all of which actively engage people in a range of cultural activities and experiences, agreed to participate in our pilot study. Our students conducted interviews with staff and volunteer members of South Side arts and cultural organizations on the topic of cultural participation, then developed and conducted an online survey to gauge what kinds of cultural participation take place in this local context. Although our sample of respondents is an online convenience sample, not representative of the South Side as a whole, it does allow analysis of participation patterns within our sample of 263 respondents. It also generates a snapshot view of our local cultural landscape that can be used to encourage researchers and policymakers to think much more expansively about what cultural participation in the 21st century means. The opportunity to address the question of “what’s happening culturally?” in our local neighborhood proved inspiring, particularly at this time when the latest 2012 NEA Survey of Public Participation in the Arts results are forthcoming. In conjunction with the NEA’s recent efforts to energize research to understand arts and cultural engagement, we present our survey results and report with the hope that it can make a contribution to a new and broadened understanding of cultural participation. Jennifer Novak-Leonard and Betty Farrell Instructors, PPHA 39703 Harris School of Public Policy, The University of Chicago March 201

Ultracontinuous single haplotype genome assemblies for the domestic cat (Felis catus) and Asian leopard cat (Prionailurus bengalensis)

In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the offspring of a domestic cat (Felis catus) x Asian leopard cat (Prionailurus bengalensis) cross, with PacBio long sequence reads and used Illumina sequence reads from the parents to phase \u3e99.9% of the reads into the two species’ haplotypes. De novo assembly of the phased reads produced highly continuous haploid genome assemblies for the domestic cat and Asian leopard cat, with contig N50 statistics exceeding 83 Mb for both genomes. Whole genome alignments reveal the Felis and Prionailurus genomes are colinear, and the cytogenetic differences between the homologous F1 and E4 chromosomes represent a case of centromere repositioning in the absence of a chromosomal inversion. Both assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in one or two large contigs. We further demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available. These novel genome resources will empower studies of feline precision medicine, adaptation and speciation

Screening synteny blocks in pairwise genome comparisons through integer programming

<p>Abstract</p> <p>Background</p> <p>It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events.</p> <p>Results</p> <p>We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota-based screening can eliminate ambiguous synteny blocks and focus on specific genomic evolutionary events, like the divergence of lineages (in cross-species comparisons) and the most recent WGD (in self comparisons).</p> <p>Conclusions</p> <p>The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons. There are two major contributions of QUOTA-ALIGN: 1) reducing the block screening task to a BIP problem, which is novel; 2) providing an efficient software pipeline starting from all-against-all BLAST to the screened synteny blocks with dot plot visualizations. Python codes and full documentations are publicly available <url>http://github.com/tanghaibao/quota-alignment</url>. QUOTA-ALIGN program is also integrated as a major component in SynMap <url>http://genomevolution.com/CoGe/SynMap.pl</url>, offering easier access to thousands of genomes for non-programmers.</p

Melting and differentiation of early-formed asteroids: The perspective from high precision oxygen isotope studies

A number of distinct methodologies are available for determining the oxygen isotope composition of minerals and rocks, these include laser-assisted fluorination, secondary ion mass spectrometry (SIMS)and UV laser ablation. In this review we focus on laser-assisted fluorination, which currently achieves the highest levels of precision available for oxygen isotope analysis. In particular, we examine how results using this method have furthered our understanding of early-formed differentiated meteorites. Due to its rapid reaction times and low blank levels, laser-assisted fluorination has now largely superseded the conventional externally-heated Ni “bomb” technique for bulk analysis. Unlike UV laser ablation and SIMS analysis, laser-assisted fluorination is not capable of focused spot analysis. While laser fluorination is now a mature technology, further analytical improvements are possible via refinements to the construction of sample chambers, clean-up lines and the use of ultra-high resolution mass spectrometers. High-precision oxygen isotope analysis has proved to be a particularly powerful technique for investigating the formation and evolution of early-formed differentiated asteroids and has provided unique insights into the interrelationships between various groups of achondrites. A clear example of this is seenin samples that lie close to the terrestrial fractionation line (TFL). Based on the data from conventional oxygen isotope analysis, it was suggested that the main-group pallasites, the howardite eucrite diogenite suite (HEDs) and mesosiderites could all be derived from a single common parent body. However,high precision analysis demonstrates that main-group pallasites have a Δ17O composition that is fully resolvable from that of the HEDs and mesosiderites, indicating the involvement of at least two parent bodies. The range of Δ17O values exhibited by an achondrite group provides a useful means of assessing the extent to which their parent body underwent melting and isotopic homogenization. Oxygen isotope analysis can also highlight relationships between ungrouped achondrites and the more well-populated groups. A clear example of this is the proposed link between the evolved GRA 06128/9 meteorites and the brachinites. The evidence from oxygen isotopes, in conjunction with that from other techniques, indicates that we have samples from approximately 110 asteroidal parent bodies (∼60 irons, ∼35 achondrites and stony-iron, and ∼15 chondrites) in our global meteorite collection. However, compared to the likely size of the original protoplanetary asteroid population, this is an extremely low value. In addition, almost all of the differentiated samples (achondrites, stony-iron and irons) are derived from parent bodies that were highly disrupted early in their evolution. High-precision oxygen isotope analysis of achondrites provides some important insights into the origin of mass-independent variation in the early Solar System. In particular, the evidence from various primitive achondrite groups indicates that both the slope 1 (Y&R) and CCAM lines are of primordial significance. Δ17O differences between water ice and silicate-rich solids were probably the initial source of the slope 1 anomaly. These phases most likely acquired their isotopic composition as a result of UV photo-dissociation of CO that took place either in the early solar nebula or precursor giant molecular cloud. Such small-scale isotopic heterogeneities were propagated into larger-sized bodies, such as asteroids and planets, as a result of early Solar System processes, including dehydration, aqueous alteration,melting and collisional interactions

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination

High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catusv8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location