Comparing index-based vulnerability assessments in the Mississippi Delta: Implications of contrasting theories, indicators, and aggregation methodologies

There are many index-based approaches for assessing vulnerability to socio-natural hazards with differences in underlying theory, indicator selection and aggregation methodology. Spatially explicit output scores depend on these characteristics and contrasting approaches can therefore lead to very different policy implications. These discrepancies call for more critical reflection on index design and utility, a discussion that has not kept pace with the impetus for vulnerability assessments and respective index creation and application following the Hyogo Framework for Action 2005–2015. Comparing index outputs is an effective approach in this regard. Here, the Social Vulnerability Index (SoVI®) and the vulnerability component of the Global Delta Risk Index (GDRI) are applied at census tract level in the Mississippi Delta and visually and quantitatively compared. While the SoVI® is grounded in the hazard/risk research paradigm with primarily socio-economic indicators and an inductive principal component methodology, the GDRI incorporates advancements from sustainability science with ecosystem-based indicators and a modular hierarchical design. Maps, class rank changes, and correlations are used to assess the convergence and divergence of these indexes across the delta. Results show that while very different theoretical frameworks influence scores through indicator selection, methodology of index calculation has an even greater effect on output. Within aggregative methodology, the treatment of inter-indicator correlation is decisive. Implications include the need for an increased focus on index methodology and validation of results, transparency, and critical reflection regarding assessment limitations, as our results imply that contradictory risk reduction policies could be considered depending on the assessment methodology used

Assessing De Novo transcriptome assembly metrics for consistency and utility

Background: Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality. Results: We simulated sequencing transcripts of Drosophila melanogaster. By assembling these simulated reads using both a perfect and a modern transcriptome assembler while varying read length and sequencing depth, we evaluated quality metrics to determine whether they 1) revealed perfect assemblies to be of higher quality, and 2) revealed perfect assemblies to be more complete as data quantity increased. Several commonly used metrics were not consistent with these expectations, including average contig coverage and length, though they became consistent when singletons were included in the analysis. We found several annotation-based metrics to be consistent and informative, including contig reciprocal best hit count and contig unique annotation count. Finally, we evaluated a number of novel metrics such as reverse annotation count, contig collapse factor, and the ortholog hit ratio, discovering that each assess assembly quality in unique ways. Conclusions: Although much attention has been given to transcriptome assembly, little research has focused on determining how best to evaluate assemblies, particularly in light of the variety of options available for read length and sequencing depth. Our results provide an important review of these metrics and give researchers tools to produce the highest quality transcriptome assemblies.Keywords: Gene, Sanger, Genome, Discovery, Ests, Performanc

Uncertain voronoi cell computation based on space decomposition

LNCS v. 9239 entitled: Advances in Spatial and Temporal Databases: 14th International Symposium, SSTD 2015 ... ProceedingsThe problem of computing Voronoi cells for spatial objects whose locations are not certain has been recently studied. In this work, we propose a new approach to compute Voronoi cells for the case of objects having rectangular uncertainty regions. Since exact computation of Voronoi cells is hard, we propose an approximate solution. The main idea of this solution is to apply hierarchical access methods for both data and object space. Our space index is used to efficiently find spatial regions which must (not) be inside a Voronoi cell. Our object index is used to efficiently identify Delauny relations, i.e., data objects which affect the shape of a Voronoi cell. We develop three algorithms to explore index structures and show that the approach that descends both index structures in parallel yields fast query processing times. Our experiments show that we are able to approximate uncertain Voronoi cells much more effectively than the state-of-the-art, and at the same time, improve run-time performance.postprin

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

<p>Abstract</p> <p>Background</p> <p>Several recent studies have demonstrated the use of Roche 454 sequencing technology for <it>de novo </it>transcriptome analysis. Low error rates and high coverage also allow for effective SNP discovery and genetic diversity estimates. However, genetically diverse datasets, such as those sourced from natural populations, pose challenges for assembly programs and subsequent analysis. Further, estimating the effectiveness of transcript discovery using Roche 454 transcriptome data is still a difficult task.</p> <p>Results</p> <p>Using the Roche 454 FLX Titanium platform, we sequenced and assembled larval transcriptomes for two butterfly species: the Propertius duskywing, <it>Erynnis propertius </it>(Lepidoptera: Hesperiidae) and the Anise swallowtail, <it>Papilio zelicaon </it>(Lepidoptera: Papilionidae). The Expressed Sequence Tags (ESTs) generated represent a diverse sample drawn from multiple populations, developmental stages, and stress treatments.</p> <p>Despite this diversity, > 95% of the ESTs assembled into long (> 714 bp on average) and highly covered (> 9.6× on average) contigs. To estimate the effectiveness of transcript discovery, we compared the number of bases in the hit region of unigenes (contigs and singletons) to the length of the best match silkworm (<it>Bombyx mori</it>) protein--this "ortholog hit ratio" gives a close estimate on the amount of the transcript discovered relative to a model lepidopteran genome. For each species, we tested two assembly programs and two parameter sets; although CAP3 is commonly used for such data, the assemblies produced by Celera Assembler with modified parameters were chosen over those produced by CAP3 based on contig and singleton counts as well as ortholog hit ratio analysis. In the final assemblies, 1,413 <it>E. propertius </it>and 1,940 <it>P. zelicaon </it>unigenes had a ratio > 0.8; 2,866 <it>E. propertius </it>and 4,015 <it>P. zelicaon </it>unigenes had a ratio > 0.5.</p> <p>Conclusions</p> <p>Ultimately, these assemblies and SNP data will be used to generate microarrays for ecoinformatics examining climate change tolerance of different natural populations. These studies will benefit from high quality assemblies with few singletons (less than 26% of bases for each assembled transcriptome are present in unassembled singleton ESTs) and effective transcript discovery (over 6,500 of our putative orthologs cover at least 50% of the corresponding model silkworm gene).</p

The SKA Particle Array Prototype: The First Particle Detector at the Murchison Radio-astronomy Observatory

We report on the design, deployment, and first results from a scintillation detector deployed at the Murchison Radio-astronomy Observatory (MRO). The detector is a prototype for a larger array -- the Square Kilometre Array Particle Array (SKAPA) -- planned to allow the radio-detection of cosmic rays with the Murchison Widefield Array and the low-frequency component of the Square Kilometre Array. The prototype design has been driven by stringent limits on radio emissions at the MRO, and to ensure survivability in a desert environment. Using data taken from Nov.\ 2018 to Feb.\ 2019, we characterize the detector response while accounting for the effects of temperature fluctuations, and calibrate the sensitivity of the prototype detector to through-going muons. This verifies the feasibility of cosmic ray detection at the MRO. We then estimate the required parameters of a planned array of eight such detectors to be used to trigger radio observations by the Murchison Widefield Array.Comment: 17 pages, 14 figures, 3 table

Safe, Affordable, Nuclear Thermal Propulsion Systems

The fundamental capability of Nuclear Thermal Propulsion (NTP) is game changing for space exploration. A first generation Nuclear Cryogenic Propulsion Stage (NCPS) based on NTP could provide high thrust at a specific impulse above 900 s, roughly double that of state of the art chemical engines. Characteristics of fission and NTP indicate that useful first generation systems will provide a foundation for future systems with extremely high performance. The role of the NCPS in the development of advanced nuclear propulsion systems could be analogous to the role of the DC-3 in the development of advanced aviation. Progress made under the NCPS project could help enable both advanced NTP and advanced Nuclear Electric Propulsion (NEP)

Nuclear Cryogenic Propulsion Stage

The fundamental capability of Nuclear Thermal Propulsion (NTP) is game changing for space exploration. A first generation Nuclear Cryogenic Propulsion Stage (NCPS) based on NTP could provide high thrust at a specific impulse above 900 s, roughly double that of state of the art chemical engines. Characteristics of fission and NTP indicate that useful first generation systems will provide a foundation for future systems with extremely high performance. The role of the NCPS in the development of advanced nuclear propulsion systems could be analogous to the role of the DC-3 in the development of advanced aviation. Progress made under the NCPS project could help enable both advanced NTP and advanced NEP