Question-answering, relevance feedback and summarisation : TREC-9 interactive track report

In this paper we report on the effectiveness of query-biased summaries for a question-answering task. Our summarisation system presents searchers with short summaries of documents, composed of a series of highly matching sentences extracted from the documents. These summaries are also used as evidence for a query expansion algorithm to test the use of summaries as evidence for interactive and automatic query expansion

Implications of solar flare hard X-ray "knee" spectra observed by RHESSI

We analyse the RHESSI photon spectra of four flares that exhibit significant deviations from power laws - i.e. changes in the "local" Hard X-ray spectral index. These spectra are characterised by two regions of constant power law index connected by a region of changing spectral index - the "knee". We develop theoretical and numerical methods of describing such knees in terms of variable photon spectral indices and we study the results of their inversions for source mean thin target and collisional thick target injection electron spectra. We show that a particularly sharp knee can produce unphysical negative values in the electron spectra, and we derive inequalities that can be used to test for this without the need for an inversion to be performed. Such unphysical features would indicate that source model assumptions were being violated, particularly strongly for the collisional thick target model which assumes a specific form for electron energy loss. For all four flares considered here we find that the knees do not correspond to unphysical electron spectra. In the three flares that have downward knees we conclude that the knee can be explained in terms of transport effects through a region of non-uniform ionisation. In the other flare, which has an upward knee, we conclude that it is most likely a feature of the accelerated spectrum

Investigation of mixed element hybrid grid-based CFD methods for rotorcraft flow analysis

Accurate first-principles flow prediction is essential to the design and development of rotorcraft, and while current numerical analysis tools can, in theory, model the complete flow field, in practice the accuracy of these tools is limited by various inherent numerical deficiencies. An approach that combines the first-principles physical modeling capability of CFD schemes with the vortex preservation capabilities of Lagrangian vortex methods has been developed recently that controls the numerical diffusion of the rotor wake in a grid-based solver by employing a vorticity-velocity, rather than primitive variable, formulation. Coupling strategies, including variable exchange protocols are evaluated using several unstructured, structured, and Cartesian-grid Reynolds Averaged Navier-Stokes (RANS)/Euler CFD solvers. Results obtained with the hybrid grid-based solvers illustrate the capability of this hybrid method to resolve vortex-dominated flow fields with lower cell counts than pure RANS/Euler methods

Nitrogen superfractionation in dense cloud cores

We report new calculations of interstellar 15N fractionation. Previously, we have shown that large enhancements of 15N/14N can occur in cold, dense gas where CO is frozen out, but that the existence of an NH + N channel in the dissociative recombination of N2H+ severely curtails the fractionation. In the light of recent experimental evidence that this channel is in fact negligible, we have reassessed the 15N chemistry in dense cloud cores. We consider the effects of temperatures below 10 K, and of the presence of large amounts of atomic nitrogen. We also show how the temporal evolution of gas-phase isotope ratios is preserved as spatial heterogeneity in ammonia ice mantles, as monolayers deposited at different times have different isotopic compositions. We demonstrate that the upper layers of this ice may have 15N/14N ratios an order of magnitude larger than the underlying elemental value. Converting our ratios to delta-values, we obtain delta(15N) > 3,000 per mil in the uppermost layer, with values as high as 10,000 per mil in some models. We suggest that this material is the precursor to the 15N `hotspots' recently discovered in meteorites and IDPsComment: accepted by MNRA

Problems and Progress in Flare Fast Particle Diagnostics

Recent progress in the diagnosis of flare fast particles is critically discussed with the main emphasis on high resolution Hard X-Ray (HXR) data from RHESSI and coordinated data from other instruments. Spectacular new photon data findings are highlighted as are advances in theoretical aspects of their use as fast particle diagnostics, and some important comparisons made with interplanetary particle data. More specifically the following topics are addressed (a) RHESSI data on HXR (electron) versus gamma-ray line (ion) source locations. (b) RHESSI hard X-ray source spatial structure in relation to theoretical models and loop density structure. (c) Energy budget of flare electrons and the Neupert effect. (d) Spectral deconvolution methods including blind target testing and results for RHESSI HXR spectra, including the reality and implications of dips inferred in electron spectra (e) The relation between flare in-situ and interplanetary particle data.Comment: 15 pages, 13 figures, submitted to Advances in Space Researc

Keeping it light: (re)analyzing community-wide datasets without major infrastructure

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Alexander, H., Johnson, L. K., & Brown, C. T.. Keeping it light: (re)analyzing community-wide datasets without major infrastructure. Gigascience, 8(2),(2019): giy159, doi:10.1093/gigascience/giy159.DNA sequencing technology has revolutionized the field of biology, shifting biology from a data-limited to data-rich state. Central to the interpretation of sequencing data are the computational tools and approaches that convert raw data into biologically meaningful information. Both the tools and the generation of data are actively evolving, yet the practice of re-analysis of previously generated data with new tools is not commonplace. Re-analysis of existing data provides an affordable means of generating new information and will likely become more routine within biology, yet necessitates a new set of considerations for best practices and resource development. Here, we discuss several practices that we believe to be broadly applicable when re-analyzing data, especially when done by small research groups.Funding was provided by the Gordon and Betty Moore Foundation (award GBMF4551 to C.T.B.)

Five minutes with Jeffrey C. Alexander: “Southern European countries are not just experiencing an economic crisis, but also an identity crisis”

Is there a ‘dark side’ to European modernity? As part of our ‘Thinkers on Europe’ series, EUROPP’s editors Stuart A Brown and Chris Gilson spoke to Jeffrey C. Alexander about his views on modernity, the European integration process, and the importance of cultural and political symbols to European democracy

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, L. K., Alexander, H., & Brown, C. T. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience, 8(4), (2019): giy158, doi: 10.1093/gigascience/giy158.Background: De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or “pipelines,” on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. Results: New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. Conclusions: Given current bioinformatics approaches, there is no single “best” reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.Funding was provided by the Gordon and Betty Moore Foundation under award number GBMF4551 to C.T.B. Jetstream cloud platform was used with XSEDE allocation TG-BIO160028 [66, 67]

Use of Denosumab in Children With Osteoclast Bone Dysplasias: Report of Three Cases.

Denosumab has been used successfully to treat disease-associated osteoclast overactivity, including giant cell tumor of bone. Given its mechanism of action, denosumab is a potent potential treatment of other osteoclast bone dysplasias including central giant cell granuloma (CGCG), aneurysmal bone cyst (ABC), and cherubism. Relatively little is known about the safety and efficacy of denosumab in patients with these conditions, especially in children. We report on 3 pediatric patients treated with denosumab over a 3-year period at UCLA Medical Center (Los Angeles and Santa Monica, CA, USA): a 12-year-old with recurrent ABC of the pelvis, a 14-year-old with CGCG of the mandible, and a 12-year-old with cherubism. All were started on a 1-year course of 15 doses 120 mg s.c., given monthly with two loading doses on day 8 and 15. All patients demonstrated rapid and pronounced clinical improvement while on denosumab, including a significant reduction in pain and sclerosis of lytic lesions on radiographs. Within 1 month of initiating therapy, 2 patients experienced hypocalcemia (Common Terminology Criteria for Adverse Events [CTCAE] grade 2) and hypophosphatemia, with 1 patient experiencing symptoms. One patient went on to experience symptomatic rebound hypercalcemia (CTCAE grade 4) 5 months after completing therapy, requiring bisphosphonates and calcitonin. For the second patient, we developed a schedule to wean denosumab involving the progressive lengthening of time between doses from 1 to 4 months in 1-month increments before cessation. We found that denosumab therapy results in significant clinical and radiographic improvement for pediatric patients with nonresectable ABC, CGCG, and cherubism. Problems with serum calcium may be more common in younger patients, with symptomatic and protracted rebound hypercalcemia after cessation of therapy the most significant. We present a potential solution to this problem with progressive spacing of doses. Potential serious adverse events from alterations in calcium homeostasis should be explored in prospective clinical trials. © 2019 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research

A short diastereoselective total synthesis of (±)-vibralactone

A total synthesis of the (±)-vibralactone has been achieved in 11 steps and 16% overall yield from malonic acid. Key steps include a highly diastereoselective allylation of an α-formyl ester containing an all carbon α-quaternary center, a Pd-catalyzed deallylative β-lactonization, and an aldehyde-selective Wacker oxidation of a terminal alkene