bluuebunny/crossref_metadata_2025_split huggingface dataset:
Online behavioural patterns for Coronavirus disease 2019 (COVID-19) in the United Kingdom
Authors: Walker M. D. , Sulyok M. 
Published: June 2020

Abstract
The current coronavirus (COVID-19) pandemic offers a unique opportunity to conduct an infodemiological study examining patterns in online searching activity about a specific disease and how this relates to news media within a specific country. Google Trends quantifies volumes of online activity. The relative search volume was obtained for ‘Coronavirus’, ‘handwashing’, ‘face mask’ and symptom related keywords, for the United Kingdom, from the date of the first confirmed case until numbers peaked in April. The relationship between online search traffic and confirmed case numbers was examined. Search volumes varied over time; peaks appear related to events in the progression of the epidemic which were reported in the media. Search activity on ‘Coronavirus’ correlated well against confirmed case number as did ‘face mask’ and symptom-related keywords. User-generated online data sources such as Google Trends may aid disease surveillance, being more responsive to changes in disease occurrence than traditional disease reporting. The relationship between media coverage and online searching activity is rarely examined, but may be driving online behavioural patterns.
Anxiety reduction after pre-procedure meetings in patients with CHD
Authors: Boyer Preston J. , Yell Joshua A. , Andrews Jennifer G. , Seckeler Michael D. 
Published: June 2020

AbstractBackground:Cardiac catheterisations for CHD produce anxiety for patients and families. Current strategies to mitigate anxiety and explain complex anatomy include pre-procedure meetings and educational tools (cardiac diagrams, echocardiograms, imaging, and angiography). More recently, three-dimensionally printed patient-specific models can be added to the armamentarium. The purpose of this study was to evaluate the efficacy of pre-procedure meetings and of different educational tools to reduce patient and parent anxiety before a catheterisation.Methods:Prospective study of patients ≥18 and parents of patients <18 scheduled for clinically indicated catheterisations. Patients completed online surveys before and after meeting with the interventional cardiologist, who was blinded to study participation. Both the pre- and post-meeting surveys measured anxiety using the State-Trait Anxiety Inventory. In addition, the post-meeting survey evaluated the subjective value (from 1 to 4) of individual educational tools: physician discussion, cardiac diagrams, echocardiograms, prior imaging, angiograms and three-dimensionally printed cardiac models. Data were compared using paired t-tests.Results:Twenty-three patients consented to participate, 16 had complete data for evaluation. Mean State-Trait Anxiety Inventory scores were abnormally elevated at baseline and decreased into the normal range after the pre-procedure meeting (39.8 versus 31, p = 0.008). Physician discussion, angiograms, and three-dimensional models were reported to be most effective at increasing understanding and reducing anxiety.Conclusion:In this pilot study, we have found that pre-catheterisation meetings produce a measurable decrease in patient and family anxiety before a procedure. Discussions of the procedure, angiograms, and three-dimensionally printed cardiac models were the most effective educational tools.
Atomic-Resolution Cryo-STEM Across Continuously Variable Temperatures
Authors: Goodge Berit H. , Bianco Elisabeth , Schnitzer Noah , Zandbergen Henny W. , Kourkoutis Lena F. 
Published: June 2020

AbstractAtomic-resolution cryogenic scanning transmission electron microscopy (cryo-STEM) has provided a path to probing the microscopic nature of select low-temperature phases in quantum materials. Expanding cryo-STEM techniques to broadly tunable temperatures will give access to the rich temperature-dependent phase diagrams of these materials. With existing cryo-holders, however, variations in sample temperature significantly disrupt the thermal equilibrium of the system, resulting in large-scale sample drift. The ability to tune the temperature without negative impact on the overall instrument stability is crucial, particularly for high-resolution experiments. Here, we test a new side-entry continuously variable temperature dual-tilt cryo-holder which integrates liquid nitrogen cooling with a 6-pin micro-electromechanical system (MEMS) sample heater to overcome some of these experimental challenges. We measure consistently low drift rates of 0.3–0.4 Å/s and demonstrate atomic-resolution cryo-STEM imaging across a continuously variable temperature range from ~100 K to well above room temperature. We conduct additional drift stability measurements across several commercial sample stages and discuss implications for further developments of ultra-stable, flexible cryo-stages.
Timescales and Processes of Methane Hydrate Formation and Breakdown, With Application to Geologic Systems
Authors: Ruppel C. D. , Waite W. F. 
Published: June 2020

AbstractGas hydrate is an ice‐like form of water and low molecular weight gas stable at temperatures of roughly −10°C to 25°C and pressures of ~3 to 30 MPa in geologic systems. Natural gas hydrates sequester an estimated one sixth of Earth's methane and are found primarily in deepwater marine sediments on continental margins, but also in permafrost areas and under continental ice sheets. When gas hydrate is removed from its stability field, its breakdown has implications for the global carbon cycle, ocean chemistry, marine geohazards, and interactions between the geosphere and the ocean‐atmosphere system. Gas hydrate breakdown can also be artificially driven as a component of studies assessing the resource potential of these deposits. Furthermore, geologic processes and perturbations to the ocean‐atmosphere system (e.g., warming temperatures) can cause not only dissociation, but also more widespread dissolution of hydrate or even formation of new hydrate in reservoirs. Linkages between gas hydrate and disparate aspects of Earth's near‐surface physical, chemical, and biological systems render an assessment of the rates and processes affecting the persistence of gas hydrate an appropriate Centennial Grand Challenge. This paper reviews the thermodynamic controls on methane hydrate stability and then describes the relative importance of kinetic, mass transfer, and heat transfer processes in the formation and breakdown (dissociation and dissolution) of gas hydrate. Results from numerical modeling, laboratory, and some field studies are used to summarize the rates of hydrate formation and breakdown, followed by an extensive treatment of hydrate dynamics in marine and cryospheric gas hydrate systems.
Characterization of the 2008 Phreatomagmatic Eruption of Okmok From ArcticDEM and InSAR: Deposition, Erosion, and Deformation
Authors: Dai Chunli , Howat Ian M. , Freymueller Jeffrey T. , Vijay Saurabh , Jia Yuanyuan 
Published: June 2020

AbstractOkmok volcano, one of the most active volcanoes in the Aleutian Islands, erupted between 12 July and 19 August 2008 and produced a new tephra cone (Ahmanilix) up to 253 m high. A coeruptive deposit thickness map and the posteruptive elevation change rate map are generated for this phreatomagmatic eruption using the new, high‐resolution (2 m) digital elevation model (DEM) time series provided by ArcticDEM. The total dense rock equivalent (DRE) volume over the proximal deposit field classified from the elevation change map is estimated as 0.147 ± 0.001 km3 DRE (bulk volume of 0.453 ± 0.003 km3). Combined with the distal deposit volume derived from field measurements, the total DRE is 0.25 km3 (bulk volume of 0.76 km3). The estimated erosion rate is up to −15 ± 3 m/year along the flanks of Ahmanilix, and the redeposition rate is about 1 ± 0.3 m/year at the base and 6 ± 1 m/year within the center of Ahmanilix. The surface elevation change also reveals a large ground surface collapse that disrupted the old Cone D lava bench, with a total collapse area of 0.15 km2 and a volume of (7.1 ± 0.4) × 10−3 km3. We also produce a coeruptive deformation map from satellite interferometric synthetic aperture radar (InSAR) using topography from both ArcticDEM and the Shuttle Radar Topography Mission (SRTM) and compare the results. Finally, based on historical eruption volumes, the magma supply rate at Okmok is estimated as (1.77 ± 0.1) × 10−3 km3/year.
Noise Characteristics of Operational Real‐Time High‐Rate GNSS Positions in a Large Aperture Network
Authors: Melgar Diego , Crowell Brendan W. , Melbourne Timothy I. , Szeliga Walter , Santillan Marcelo , Scrivner Craig 
Published: June 2020

AbstractLarge earthquakes are difficult to model in real‐time with traditional inertial seismic measurements. Several algorithms that leverage high‐rate real‐time Global Navigation Satellite Systems (HR‐GNSS) positions have been proposed, and it has been shown that they can supplement the earthquake monitoring effort. However, analyses of the long‐term noise behavior of high‐rate real‐time GNSS positions, which are important to understand how the data can be used operationally by monitoring agencies, have been limited to just a few sites and to short time spans. Here, we show results from an analysis of the noise characteristics of 1 year of positions at 213 GNSS sites spanning a large geographic region from Southern California to Alaska. We characterize the behavior of noise and propose several references noise models which can be used as baselines to compare against as technological improvements allow for higher precision solutions. We also show how to use the reference noise models to generate realistic synthetic noise that can be used in simulations of HR‐GNSS waveforms. We discuss spatiotemporal variations in the noise and their potential sources and significance. We also detail how noise analysis can be used in a dynamic quality control to determine which sites should or should not contribute positions to an earthquake modeling algorithm at a particular moment in time. We posit that while there remain important improvements yet to be made, such as reducing the number of outliers in the time series, the present quality of real‐time HR‐GNSS waveforms is more than sufficient for monitoring large earthquakes.
Joint Optimization of Measurement and Modeling Strategies With Application to Radial Flow in Stratified Aquifers
Authors: Maier R. , Gonzalez‐Nicolas A. , Leven C. , Nowak W. , Cirpka O. A. 
Published: June 2020

AbstractWhen applying environmental models, the choice of model complexity and the design of field campaigns depend on each other and on the modeling/prediction goal. We propose jointly optimizing model complexity and data collection (design) by maximizing the expected performance for the modeling goal. We use ensembles of highly resolved virtual realities and of less complex modeling variants that differ in their degrees of upscaling and simplified parameterization. For each design under consideration, we simulate hypothetical measurement data (subject to noise) with all realizations of all models. To mimic model calibration with hypothetical data, we identify pairs of best fitting realizations between virtual reality and each model variant for each design. Then, we emulate model choice by selecting (across the model variants, for each design and for each virtual reality) the pair that shows the best predictive match in the modeling goal. Finally, we identify the model/design combination that offers, on average over all virtual realities, the best predictive match. As a test application, we consider a heterogeneous, stratified aquifer, in which the stratification enhances hydraulic anisotropy on the macroscale. We define two different modeling goals: (a) estimating the hydraulic conductivity tensor upscaled to the full aquifer thickness and (b) predicting the pumping rate needed to dewater a construction pit. Our results indicate that jointly optimizing observation networks and model selection can reduce the prediction uncertainty of parameters at lower experimental costs. We also show that the involved trade‐offs between model complexity and required design depend on the target quantity.
Flightless-1 inhibits ER stress-induced apoptosis in colorectal cancer cells by regulating Ca2+ homeostasis
Authors: Choi Sun Sil , Lee Sang Kwon , Kim Joong Kwan , Park Hye-Kyung , Lee Eujin , Jang Jinho , Lee Yo Han , Khim Keon Woo , Hyun Ji-Min , Eom Hye-jin , Lee Semin , Kang Byuong Heon , Chae Young Chan , Myung Kyungjae , Myung Seung-Jae , Park Chan Young , Choi Jang Hyun 
Published: June 2020

AbstractThe endoplasmic reticulum (ER) stress response is an adaptive mechanism that is activated upon disruption of ER homeostasis and protects the cells against certain harmful environmental stimuli. However, critical and prolonged cell stress triggers cell death. In this study, we demonstrate that Flightless-1 (FliI) regulates ER stress-induced apoptosis in colon cancer cells by modulating Ca2+homeostasis. FliI was highly expressed in both colon cell lines and colorectal cancer mouse models. In a mouse xenograft model using CT26 mouse colorectal cancer cells, tumor formation was slowed due to elevated levels of apoptosis in FliI-knockdown (FliI-KD) cells. FliI-KD cells treated with ER stress inducers, thapsigargin (TG), and tunicamycin exhibited activation of the unfolded protein response (UPR) and induction of UPR-related gene expression, which eventually triggered apoptosis. FliI-KD increased the intracellular Ca2+concentration, and this upregulation was caused by accelerated ER-to-cytosolic efflux of Ca2+. The increase in intracellular Ca2+concentration was significantly blocked by dantrolene and tetracaine, inhibitors of ryanodine receptors (RyRs). Dantrolene inhibited TG-induced ER stress and decreased the rate of apoptosis in FliI-KD CT26 cells. Finally, we found that knockdown of FliI decreased the levels of sorcin and ER Ca2+and that TG-induced ER stress was recovered by overexpression of sorcin in FliI-KD cells. Taken together, these results suggest that FliI regulates sorcin expression, which modulates Ca2+homeostasis in the ER through RyRs. Our findings reveal a novel mechanism by which FliI influences Ca2+homeostasis and cell survival during ER stress.
Regulation of natural killer cell activity by glucocorticoids, serotonin, dopamine, and epinephrine
Authors: Capellino Silvia , Claus Maren , Watzl Carsten 
Published: June 2020

AbstractThe immune system and the nervous system are highly complex organs composed of various different cells that must interact with each other for proper function of the system. This communication can be mediated by soluble factors. The factors released by the nervous system (neurotransmitters) differ from those released by the immune system (cytokines). Nevertheless, the nervous and immune systems can influence each other’s activity because immune cells express neurotransmitter receptors, and neurons express cytokine receptors. Moreover, immune cells can synthesize and release neurotransmitters themselves, thus using neurotransmitter-mediated pathways via autocrine and paracrine mechanisms. Natural killer (NK) cells are innate lymphocytes that are important for early and effective immune reactions against infections and cancer. Many studies have shown the strong influence of stress and the nervous system on NK cell activity. This phenomenon may be one reason why chronic stress leads to a higher incidence of infections and cancer. Here, we review the effects of neuroendocrine factors on the different activities of NK cells. Understanding the effects of neuroendocrine factors on NK cell activities during physiological and pathophysiological conditions may result in novel therapeutic strategies to enhance NK cell functions against tumors.
Multi-trait analysis of rare-variant association summary statistics using MTAR
Authors: Luo Lan , Shen Judong , Zhang Hong , Chhibber Aparna , Mehrotra Devan V. , Tang Zheng-Zheng 
Published: June 2020

AbstractIntegrating association evidence across multiple traits can improve the power of gene discovery and reveal pleiotropy. Most multi-trait analysis methods focus on individual common variants in genome-wide association studies. Here, we introduce multi-trait analysis of rare-variant associations (MTAR), a framework for joint analysis of association summary statistics between multiple rare variants and different traits. MTAR achieves substantial power gain by leveraging the genome-wide genetic correlation measure to inform the degree of gene-level effect heterogeneity across traits. We apply MTAR to rare-variant summary statistics for three lipid traits in the Global Lipids Genetics Consortium. 99 genome-wide significant genes were identified in the single-trait-based tests, and MTAR increases this to 139. Among the 11 novel lipid-associated genes discovered by MTAR, 7 are replicated in an independent UK Biobank GWAS analysis. Our study demonstrates that MTAR is substantially more powerful than single-trait-based tests and highlights the value of MTAR for novel gene discovery.
The effect of flow on swimming bacteria controls the initial colonization of curved surfaces
Authors: Secchi Eleonora , Vitale Alessandra , Miño Gastón L. , Kantsler Vasily , Eberl Leo , Rusconi Roberto , Stocker Roman 
Published: June 2020

AbstractThe colonization of surfaces by bacteria is a widespread phenomenon with consequences on environmental processes and human health. While much is known about the molecular mechanisms of surface colonization, the influence of the physical environment remains poorly understood. Here we show that the colonization of non-planar surfaces by motile bacteria is largely controlled by flow. Using microfluidic experiments with Pseudomonas aeruginosa and Escherichia coli, we demonstrate that the velocity gradients created by a curved surface drive preferential attachment to specific regions of the collecting surface, namely the leeward side of cylinders and immediately downstream of apexes on corrugated surfaces, in stark contrast to where nonmotile cells attach. Attachment location and rate depend on the local hydrodynamics and, as revealed by a mathematical model benchmarked on the observations, on cell morphology and swimming traits. These results highlight the importance of flow on the magnitude and location of bacterial colonization of surfaces.
Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing
Authors: Stangl Christina , de Blank Sam , Renkens Ivo , Westera Liset , Verbeek Tamara , Valle-Inclan Jose Espejo , González Rocio Chamorro , Henssen Anton G. , van Roosmalen Markus J. , Stam Ronald W. , Voest Emile E. , Kloosterman Wigard P. , van Haaften Gijs , Monroe Glen R. 
Published: June 2020

AbstractFusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment. Fusion gene partner choice and breakpoint-position promiscuity restricts diagnostic detection, even for known and recurrent configurations. Here, we develop FUDGE (FUsion Detection from Gene Enrichment) to accurately and impartially identify fusions. FUDGE couples target-selected and strand-specific CRISPR-Cas9 activity for fusion gene driver enrichment — without prior knowledge of fusion partner or breakpoint-location — to long read nanopore sequencing with the bioinformatics pipeline NanoFG. FUDGE has flexible target-loci choices and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in one sequencing run. We observe on-average 665 fold breakpoint-site enrichment and identify nucleotide resolution fusion breakpoints within 2 days. The assay identifies cancer cell line and tumor sample fusions irrespective of partner gene or breakpoint-position. FUDGE is a rapid and versatile fusion detection assay for diagnostic pan-cancer fusion detection.
Spitzenkörper assembly mechanisms reveal conserved features of fungal and metazoan polarity scaffolds
Authors: Zheng Peng , Nguyen Tu Anh , Wong Jie Yun , Lee Michelle , Nguyen The-Anh , Fan Jing-Song , Yang Daiwen , Jedd Gregory 
Published: June 2020

AbstractThe Spitzenkörper (SPK) constitutes a collection of secretory vesicles and polarity-related proteins intimately associated with polarized growth of fungal hyphae. Many SPK-localized proteins are known, but their assembly and dynamics remain poorly understood. Here, we identify protein-protein interaction cascades leading to assembly of two SPK scaffolds and recruitment of diverse effectors in Neurospora crassa. Both scaffolds are transported to the SPK by the myosin V motor (MYO-5), with the coiled-coil protein SPZ-1 acting as cargo adaptor. Neither scaffold appears to be required for accumulation of SPK secretory vesicles. One scaffold consists of Leashin-2 (LAH-2), which is required for SPK localization of the signalling kinase COT-1 and the glycolysis enzyme GPI-1. The other scaffold comprises a complex of Janus-1 (JNS-1) and the polarisome protein SPA-2. Via its Spa homology domain (SHD), SPA-2 recruits a calponin domain-containing F-actin effector (CCP-1). The SHD NMR structure reveals a conserved surface groove required for effector binding. Similarities between SPA-2/JNS-1 and the metazoan GIT/PIX complex identify foundational features of the cell polarity apparatus that predate the fungal-metazoan divergence.
Reverse engineering synthetic antiviral amyloids
Authors: Michiels Emiel , Roose Kenny , Gallardo Rodrigo , Khodaparast Ladan , Khodaparast Laleh , van der Kant Rob , Siemons Maxime , Houben Bert , Ramakers Meine , Wilkinson Hannah , Guerreiro Patricia , Louros Nikolaos , Kaptein Suzanne J. F. , Ibañez Lorena Itatí , Smet Anouk , Baatsen Pieter , Liu Shu , Vorberg Ina , Bormans Guy , Neyts Johan , Saelens Xavier , Rousseau Frederic , Schymkowitz Joost 
Published: June 2020

AbstractHuman amyloids have been shown to interact with viruses and interfere with viral replication. Based on this observation, we employed a synthetic biology approach in which we engineered virus-specific amyloids against influenza A and Zika proteins. Each amyloid shares a homologous aggregation-prone fragment with a specific viral target protein. For influenza we demonstrate that a designer amyloid against PB2 accumulates in influenza A-infected tissue in vivo. Moreover, this amyloid acts specifically against influenza A and its common PB2 polymorphisms, but not influenza B, which lacks the homologous fragment. Our model amyloid demonstrates that the sequence specificity of amyloid interactions has the capacity to tune amyloid-virus interactions while allowing for the flexibility to maintain activity on evolutionary diverging variants.
Visualizing group II intron dynamics between the first and second steps of splicing
Authors: Manigrasso Jacopo , Chillón Isabel , Genna Vito , Vidossich Pietro , Somarowthu Srinivas , Pyle Anna Marie , De Vivo Marco , Marcia Marco 
Published: June 2020

AbstractGroup II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5’-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.