bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anisotropic viscoacoustic wave modelling in VTI media using frequency-dependent complex velocity
Authors: Zhang Yabing , Liu Yang , Xu Shigang 
Published: June 2020

Abstract
Under the conditions of acoustic approximation and isotropic attenuation, we derive the pseudo- and pure-viscoacoustic wave equations from the complex constitutive equation and the decoupled P-wave dispersion relation, respectively. Based on the equations, we investigate the viscoacoustic wave propagation in vertical transversely isotropic media. The favourable advantage of these formulas is that the phase dispersion and the amplitude dissipation terms are inherently separated. As a result, we can conveniently perform the decoupled viscoacoustic wavefield simulations by choosing different coefficients. In the computational process, a generalised pseudo-spectral method and a low-rank decomposition scheme are adopted to calculate the wavenumber-domain and mixed-domain propagators, respectively. Because low-rank decomposition plays an important role in the simulated procedure, we evaluate the approximation accuracy for different operators using a linear velocity model. To demonstrate the effectiveness and the accuracy of our method, several numerical examples are carried out based on the new pseudo- and pure-viscoacoustic wave equations. Both equations can effectively describe the viscoacoustic wave propagation characteristics in vertical transversely isotropic media. Unlike the pseudo-viscoacoustic wave equation, the pure-viscoacoustic wave equation can produce stable viscoacoustic wavefields without any SV-wave artefacts.
Global apparent resistivity definition for a high-performance TEM excitation source
Authors: Li He , Li Wenhan , Qi Zhipeng , Li Xiu , Lu Kailiang 
Published: June 2020

AbstractThe high-performance transient electromagnetic method (TEM) excitation source is a new type of source that has been proposed for urban underground space exploration. This source is composed of two trapezoid plates. To ensure that the radiation field was focused in a certain direction, the two trapezoid plate-shaped antennas were arranged into a horn shape. This new source is characterised by high power, directional excitation and high resolution. The corresponding multi-component global apparent resistivity definition method is established for a high-performance transient electromagnetic excitation source. This method is studied using the inverse function theorem. Then, the monotonic relationship between components of the electromagnetic field and resistivity is analysed. For the fields that satisfy the monotonic relationship with half-space resistivity, the apparent resistivity can be calculated correctly to ignore the time period and location in the space. This means that this definition method can eliminate the limitation of early and late times, and the near and far zones. The apparent resistivity calculation results of the theoretical layered model reveal that global apparent resistivity curves show a regular change, which smoothly and comprehensively reflects the change of electrical information in the model. The experimental results of the 3D model show that the five-layer low-resistivity anomaly contained in the urban underground space designed in this paper exhibits an obvious response in the global apparent resistivity profile. It is concluded that a high-performance TEM excitation source possesses a high resolution, clearly reflecting all of the anomalies of a complex urban underground space model.
An extraction method of dispersion curve from vertical seismic profiling data
Authors: Hu Zhi , Gao Jinghuai , He Yanbin , Zhang Guowei 
Published: June 2020

Abstract
The dispersion curve describes the relationship between velocities and frequencies. The group velocity is a kind of dispersion, which presents the velocities of the energy with different frequencies. Although many studies have shown methods for estimating group velocity from a surface wave, the estimation of group velocity from body-wave data is still hard. In this paper, we propose a method to calculate the group velocity from vertical seismic profiling (VSP) data that is a kind of body-wave data. The generalised S-transform (GST) is used to map the seismic signal to the time-frequency (TF) domain and then the group delay (GD) can be extracted from the TF domain. The GD shows the travelling time of different frequency components. The group velocity can be calculated by the GD and the distance between receivers. Unfortunately, the GD is hard to measure accurately because of the noise. Inaccurate GD introduces errors in estimating the velocity. To reduce the errors, we make use of the multiple traces and the iterative least-squares fitting to extract the relationship line between GD and depths. The slope of the line is the reciprocal of the group velocity. Two numerical examples prove the effectiveness of the method. We also derive the formula of group velocity in diffusive-viscous media. In the field data example, the dispersion intensity at different depths and the geological layers can be well matched. These examples illustrate the proposed method is an alternative method for dispersion estimation from VSP.
Seismic reflectivity inversion using an L1-norm basis-pursuit method and GPU parallelisation
Authors: Wang Ruo , Wang Yanghua , Rao Ying 
Published: June 2020

Abstract
Seismic reflectivity inversion problem can be formulated using a basis-pursuit method, aiming to generate a sparse reflectivity series of the subsurface media. In the basis-pursuit method, the reflectivity series is composed by large amounts of even and odd dipoles, thus the size of the seismic response matrix is huge and the matrix operations involved in seismic inversion are very time-consuming. In order to accelerate the matrix computation, a basis-pursuit method-based seismic inversion algorithm is implemented on Graphics Processing Unit (GPU). In the basis-persuit inversion algorithm, the problem is imposed with a L1-norm model constraint for sparsity, and this L1-norm basis-pursuit inversion problem is reformulated using a linear programming method. The core problems in the inversion are large-scale linear systems, which are resolved by a parallelised conjugate gradient method. The performance of this fully parallelised implementation is evaluated and compared to the conventional serial coding. Specifically, the investigation using several field seismic data sets with different sizes indicates that GPU-based parallelisation can significantly reduce the computational time with an overall factor up to 145. This efficiency improvement demonstrates a great potential of the basis-pursuit inversion method in practical application to large-scale seismic reflectivity inversion problems.
Cloning, Expression, and Immunological Characterization of Formosan Subterranean Termite (Blattodea: Rhinotermitidae) Arginine Kinase
Authors: Mattison Christopher P , Tungtrongchitr Anchalee , Tille Katherine S , Cottone Carrie B , Riegel Claudia 
Published: June 2020

Abstract
Several parts of the world regularly consume termites. Arthropod arginine kinase proteins often cross-react with human immunoblobulin E (IgE) antibodies and they are considered pan-allergens. The Formosan subterranean termite Coptotermes formosanus (C. formosanus (Shiraki) [Isoptera: Rhinotermitidae]), along with cockroaches, belong to the order Blattodea and they are common household pests in tropical and subtropical parts of the world. An sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) band migrating at approximately 37 kDa in C. formosanus termite extracts cross-reacted with IgE from five cockroach allergic patient samples by immunoblot. Liquid chromatography-mass spectrometry analysis of gel slices from the corresponding region of a gel indicated several peptides from the excised region were identical to the American cockroach arginine kinase allergen, Per a 9. The sequence of the full-length C. formosanus arginine kinase gene indicates the protein it encodes is 96% identical to American cockroach Per a 9, 94% identical to German cockroach Bla g 9, and 82–84% identical to shrimp arginine kinase proteins Pen m 2, Lit v 2, and Cra c 2. Full-length C. formosanus arginine kinase was fused to a glutathione S-transferase tag and recombinantly expressed and purified from Escherichia coli by affinity chromatography. The recombinant protein was recognized by IgE from 11 of 12 cockroach or shrimp allergic samples, but did not cross-react with dust mite allergic or peanut/tree nut allergic samples. The results of this study indicate the C. formosanus arginine kinase cross-reacts with cockroach and shrimp allergic IgE, and if consumed would likely act as an allergen.
SARS–CoV-2 isolation from an appendix
Authors: Ahmad Shahzaib , Ahmed Rahim Nadeem , Jani Poonam , Ullah Mattee , Aboulgheit Hossam 
Published: June 2020

Abstract
Efforts to recognize SARS–CoV-2 infection have focused on respiratory symptoms such as cough and shortness of breath. Although it is also well known that SARS–CoV-2 infection can cause gastrointestinal symptoms such as abdominal pain, nausea, vomiting and diarrhoea, there are emerging reports of SARS–CoV-2 infection causing surgical pathology. We present the first case report of SARS–CoV-2 infection directly causing acute appendicitis, first suspected due to highly atypical histological features and later confirmed as polymerase chain reaction positive appendicular tissue sample.
Two bladders, two colons and two uteruses
Authors: Geoghegan Luke , Ahuja Manish , Sheth Hemant 
Published: June 2020

Abstract
Complete colonic duplication is rare and frequently asymptomatic. We present an interesting case of tubular colonic duplication with associated uterine didelphys and a longitudinal sagittal septum in the bladder, noted incidentally on cross-sectional imaging. The patient was later diagnosed with ulcerative colitis affecting the duplicated colon and is currently in remission following medical therapy.
Reporting Sysmex XN Absolute Neutrophil Count in Samples with Leukocyte Analyzer Flagging
Authors: Linko-Parvinen Anna-Maria , Turkia Heidi 
Published: June 2020

Abstract

Objective
To provide faster laboratory data reporting, we evaluated the accuracy of Sysmex XN (Sysmex Inc, Kobe, Japan) absolute neutrophil count (ANC) in the presence of analyzer flagging.

Methods
Sysmex XN and manual microscopy ANC were compared with 80 autovalidated control specimens and with 280 study specimens with analyzer flagging regarding immature granulocytes (IG) &gt;3% or other leukocyte abnormalities. Specimens with ambiguous neutrophil clusters were excluded.

Results
A slight positive overall method bias was seen for Sysmex XN compared to manual microscopy (n = 280), 0.025 (95% confidence interval [CI], –0.023 to 0.069) × 109/L. With IG &gt; 10% (n = 123) the bias was larger, but not clinically significant, 0.17 (95% CI, 0.060–0.25) × 109/L. No clinically significant difference was seen in neutropenic (ANC &lt; 1.5 × 109/L) specimens (n = 91), 0.070 (95% CI, –0.013 to 0.14) × 109/L.

Conclusion
These data indicate that Sysmex XN ANC can be reported in the presence of certain analyzer flagging to improve patient care.
Evaluation of Self-Collection as a Method of Extragenital STI Screening
Authors: Chohonis Kelly , Davis Kepler , Calvano Tatjana 
Published: June 2020

Abstract

Introduction
The goal of this study is to improve overall screening, detection, and treatment of Neisseria gonorrhea (GC) and Chlamydia trachomatis (CT) at our institution.

Materials and Methods
An observational study with two phases was conducted at a U.S. Army Medical Center. Previously collected samples from January 2014 through December 2015 were compared to prospectively collected data from March 2016 through December 2017. All data were collected from a convenience sample of active duty, HIV-positive men who have sex with men. Concordance between provider-collected and self-collected extragenital screening (EGS) samples was evaluated.

Results
The rate of detection using EGS was higher than previously found using urogenital screening alone. Our prospective analysis revealed that expanding screening to include extragenital sites increased rates of detection of GC and CT. Our rates of GC detection at the pharynx and rectum, and CT detection at the rectum, were higher than those reported in the literature for men who have sex with men. Rates of CT infection at the pharynx were comparable with those reported in the literature. Detection of GC at the pharynx was exactly concordant between self-collected and provider-collected samples. Concordance of GC and CT detection at the rectum was very good. The kappa coefficient for detection of CT at the pharynx was zero, which corresponded to 44 out of 45 concordant observations.

Conclusions
Prior to implementation of EGS at our institution, we missed the opportunity to detect a substantial number of GC/CT infections with urogenital screening alone. Our results suggest that self-collection is a reliable method of EGS as compared to provider collection of samples.
Invasive Meningococcal Disease at Fort Ord and San Diego Naval Training Center, 1962–1964
Authors: Christopher George W 
Published: June 2020

Abstract
Meningococcal epidemics at 2 training facilities were early examples of outbreaks fueled by military demographics and because of lethal drug-resistant bacteria for which there are no vaccines or chemoprophylaxis. Positive outcomes included the elucidation of the natural history of meningococcal colonization and disease and the initiation of vaccine development.
Native and nonnative bivalve settlement: potential competition for spatial resources in a northeast Florida estuary
Authors: Raabe Jennifer M , Gilg Matthew R 
Published: June 2020

ABSTRACT
Introduced species often have negative effects on native species that occupy the same habitats in the area of introduction. Habitat preferences of organisms can therefore play a large role in determining the severity of interactions such as competition or predation. Previous laboratory studies have shown that the introduced mussel species Perna viridis can decrease the settlement and early survival of the native oyster species Crassostrea virginica. Both species can often be found in the same general areas, but it is unknown whether this habitat overlap is complete, or whether there are certain locations that may act as refuges for native bivalve species. The present study investigated the settlement patterns of the introduced P. viridis and two groups of native bivalves, oysters (C. virginica and Ostrea equestris) and mussels (Ischadium recurvum, Brachidontes exustus and Geukensia demissa), to determine whether preferential settlement depths and habitats differed among the groups. Most of these groups showed significantly greater settlement on deeper substrates that were located in the main channel of the Atlantic Intracoastal Waterway of northeast Florida. While native oysters also settled in adjacent feeder creeks in fairly large numbers, settlement of P. viridis in these areas was relatively rare. In main channel locations, the overlap in settlement depth is likely to result in competition between introduced and native bivalve species, but feeder creeks may provide areas of refuge for native oysters. The spatial and temporal overlap of all three groups suggests that competition among nonnative and native bivalves may occur in nature.
The structural ensemble of a Holliday junction determined by X-ray scattering interference
Authors: Zettl Thomas , Shi Xuesong , Bonilla Steve , Sedlak Steffen M , Lipfert Jan , Herschlag Daniel 
Published: June 2020

Abstract
The DNA four-way (Holliday) junction is the central intermediate of genetic recombination, yet key aspects of its conformational and thermodynamic properties remain unclear. While multiple experimental approaches have been used to characterize the canonical X-shape conformers under specific ionic conditions, the complete conformational ensemble of this motif, especially at low ionic conditions, remains largely undetermined. In line with previous studies, our single-molecule Förster resonance energy transfer (smFRET) measurements of junction dynamics revealed transitions between two states under high salt conditions, but smFRET could not determine whether there are fast and unresolvable transitions between distinct conformations or a broad ensemble of related states under low and intermediate salt conditions. We therefore used an emerging technique, X-ray scattering interferometry (XSI), to directly probe the conformational ensemble of the Holliday junction across a wide range of ionic conditions. Our results demonstrated that the four-way junction adopts an out-of-plane geometry under low ionic conditions and revealed a conformational state at intermediate ionic conditions previously undetected by other methods. Our results provide critical information to build toward a full description of the conformational landscape of the Holliday junction and underscore the utility of XSI for probing conformational ensembles under a wide range of solution conditions.
Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment
Authors: Nechooshtan Gal , Yunusov Dinar , Chang Kenneth , Gingeras Thomas R 
Published: June 2020

Abstract
Extracellular RNAs participate in intercellular communication, and are being studied as promising minimally invasive diagnostic markers. Several studies in recent years showed that tRNA halves and distinct Y RNA fragments are abundant in the extracellular space, including in biofluids. While their regulatory and diagnostic potential has gained a substantial amount of attention, the biogenesis of these extracellular RNA fragments remains largely unexplored. Here, we demonstrate that these fragments are produced by RNase 1, a highly active secreted nuclease. We use RNA sequencing to investigate the effect of a null mutation of RNase 1 on the levels of tRNA halves and Y RNA fragments in the extracellular environment of cultured human cells. We complement and extend our RNA sequencing results with northern blots, showing that tRNAs and Y RNAs in the non-vesicular extracellular compartment are released from cells as full-length precursors and are subsequently cleaved to distinct fragments. In support of these results, formation of tRNA halves is recapitulated by recombinant human RNase 1 in our in vitro assay. These findings assign a novel function for RNase 1, and position it as a strong candidate for generation of tRNA halves and Y RNA fragments in biofluids.
RNA aptamer capture of macromolecular complexes for mass spectrometry analysis
Authors: Ray Judhajeet , Kruse Angela , Ozer Abdullah , Kajitani Takuya , Johnson Richard , MacCoss Michael , Heck Michelle , Lis John T 
Published: June 2020

AbstractSpecific genomic functions are dictated by macromolecular complexes (MCs) containing multiple proteins. Affinity purification of these complexes, often using antibodies, followed by mass spectrometry (MS) has revolutionized our ability to identify the composition of MCs. However, conventional immunoprecipitations suffer from contaminating antibody/serum-derived peptides that limit the sensitivity of detection for low-abundant interacting partners using MS. Here, we present AptA–MS (aptamer affinity–mass spectrometry), a robust strategy primarily using a specific, high-affinity RNA aptamer against Green Fluorescent Protein (GFP) to identify interactors of a GFP-tagged protein of interest by high-resolution MS. Utilizing this approach, we have identified the known molecular chaperones that interact with human Heat Shock Factor 1 (HSF1), and observed an increased association with several proteins upon heat shock, including translation elongation factors and histones. HSF1 is known to be regulated by multiple post-translational modifications (PTMs), and we observe both known and new sites of modifications on HSF1. We show that AptA–MS provides a dramatic target enrichment and detection sensitivity in evolutionarily diverse organisms and allows identification of PTMs without the need for modification-specific enrichments. In combination with the expanding libraries of GFP-tagged cell lines, this strategy offers a general, inexpensive, and high-resolution alternative to conventional approaches for studying MCs.
NF1 optic pathway glioma: analyzing risk factors for visual outcome and indications to treat
Authors: Azizi Amedeo A , Walker David A , Liu Jo-Fen , Sehested Astrid , Jaspan Timothy , Pemp Berthold , Simmons Ian , Ferner Rosalie , Grill Jacques , Hargrave Darren , Driever Pablo Hernáiz , Evans D Gareth , Opocher Enrico ,   SIOPE NF1 OPG Nottingham, UK, Workshop 2014
Published: June 2020

Abstract

Background
The aim of the project was to identify risk factors associated with visual progression and treatment indications in pediatric patients with neurofibromatosis type 1 associated optic pathway glioma (NF1-OPG).

Methods
A multidisciplinary expert group consisting of ophthalmologists, pediatric neuro-oncologists, neurofibromatosis specialists, and neuro-radiologists involved in therapy trials assembled a cohort of children with NF1-OPG from 6 European countries with complete clinical, imaging, and visual outcome datasets. Using methods developed during a consensus workshop, visual and imaging data were reviewed by the expert team and analyzed to identify associations between factors at diagnosis with visual and imaging outcomes.

Results
Eighty-three patients (37 males, 46 females, mean age 5.1 ± 2.6 y; 1–13.1 y) registered in the European treatment trial SIOP LGG-2004 (recruited 2004–2012) were included. They were either observed or treated (at diagnosis/after follow-up).
In multivariable analysis, factors present at diagnosis associated with adverse visual outcomes included: multiple visual signs and symptoms (adjusted odds ratio [adjOR]: 8.33; 95% CI: 1.9–36.45), abnormal visual behavior (adjOR: 4.15; 95% CI: 1.20–14.34), new onset of visual symptoms (adjOR: 4.04; 95% CI: 1.26–12.95), and optic atrophy (adjOR: 3.73; 95% CI: 1.13–12.53). Squint, posterior visual pathway tumor involvement, and bilateral pathway tumor involvement showed borderline significance. Treatment appeared to reduce tumor size but improved vision in only 10/45 treated patients. Children with visual deterioration after primary observation are more likely to improve with treatment than children treated at diagnosis.

Conclusions
The analysis identified the importance of symptomatology, optic atrophy, and history of vision loss as predictive factors for poor visual outcomes in children with NF1-OPG.