bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large‐Eddy Simulation Model for the Effect of Gas Bubble Dissolution on the Dynamics of Hydrocarbon Plume from Deep‐Water Blowout
Authors: Peng Chen , Xiao Shuolin , Yang Di 
Published: May 2020

AbstractDuring a deep‐water wellhead blowout incident, the dynamics of the released hydrocarbon plume is strongly affected by the gas dissolution process that weakens the bubble‐induced buoyancy for driving the plume. In this study, a new modeling strategy is developed to efficiently incorporate the gas dissolution effect into a fast Eulerian‐Eulerian large‐eddy simulation (LES) model. By simultaneously simulating the evolutions of the bubble mass concentration and number density functions, the average bubble size in each LES computational cell can be calculated locally. Based on the cell‐averaged bubble diameter, the local gas dissolution rate and bubble rise velocity are parameterized, which are then used in the gas transport equations to model the evolution of the gas bubble field due to turbulent transport and gas dissolution. This LES model is applied to simulate several blowout scenarios with different initial bubble sizes. The results show that the plumes that have smaller initial bubble size exhibit faster relative bubble dissolution rate compared to the plumes with larger initial bubble size. As a result, the plumes with smaller bubbles also have lower peel and trap heights than those with larger bubbles. For comparison, a second set of LES runs with identical conditions but without including the gas dissolution effect are also performed. The data analysis shows that the omission of gas dissolution can cause overestimations of the plume peel and trap heights for up to 151% and 127%, respectively, suggesting the importance of including the gas dissolution effect for accurately modeling the near‐field hydrocarbon plumes.
Sensitivity of Streamflow Metrics to Infiltration‐Based Stormwater Management Networks
Authors: Avellaneda P. M. , Jefferson A. J. 
Published: May 2020

AbstractAs stormwater control measures (SCMs) capture surface runoff from impervious areas, a shift in the water balance and flow regime components may emerge in urban watersheds, but the amount of SCM treatment needed to detectably shift these components may vary. We used the Soil and Water Assessment Tool (SWAT) hydrologic model to assess the sensitivity of 16 hydrologic metrics as an increasingly dense rain garden SCM network was applied across the West Creek watershed, near Cleveland, Ohio (USA). As the area treated by SCMs increased, annual baseflow increases matched decreases in surface runoff, while water yield and evapotranspiration changes remained small. The stream's peak response to rainfall decreased with SCM implementation across storm sizes, ranging from the threshold rainfall depth (4.8 mm) to values higher than the design storm of a single rain garden (19 mm). SCM networks draining >20% of directly connected impervious area (DCIA) significantly decreased the magnitude of discharges with a return period of less than 1 year, the percentage of time above mean flow, and flashiness. Recession slopes and annual 1‐ and 7‐day low flows exhibited a slight response that fell within uncertainty limits of the model. Water balance and rainfall response metrics exhibited the greatest sensitivity to different intensities of stormwater management, while infrequent high and low flows were resistant to detectable change even at high levels of SCM treatment when model uncertainty was included.
Earlier parasite arrival reduces the repeatability of host adaptive radiation
Authors: Tan Jiaqi , Yang Xian , He Qixin , Hua Xia , Jiang Lin 
Published: May 2020

Abstract
Although parasites are known to have various effects on their hosts, we know little about their role in the assembly of diversifying host populations. Using an experimental bacterium (Pseudomonas fluorescens SBW25)-bacteriophage (ϕ2) system, we show that earlier parasite arrival significantly reduced the repeatability of host diversification. Earlier parasite arrival amplified the priority effects associated with the stochastic emergence of novel SBW25 phenotypes, translating into greater historical contingency in SBW25 diversification. Our results highlight the important role of parasite-host interactions in driving host adaptive radiation.
Extreme active matter at high densities
Authors: Mandal Rituparno , Bhuyan Pranab Jyoti , Chaudhuri Pinaki , Dasgupta Chandan , Rao Madan 
Published: May 2020

AbstractWe study the remarkable behaviour of dense active matter comprising self-propelled particles at large Péclet numbers, over a range of persistence times, from τp → 0, when the active fluid undergoes a slowing down of density relaxations leading to a glass transition as the active propulsion force f reduces, to τp → ∞, when as f reduces, the fluid jams at a critical point, with stresses along force-chains. For intermediate τp, a decrease in f drives the fluid through an intermittent phase before dynamical arrest at low f. This intermittency is a consequence of periods of jamming followed by bursts of plastic yielding associated with Eshelby deformations. On the other hand, an increase in f leads to an increase in the burst frequency; the correlated plastic events result in large scale vorticity and turbulence. Dense extreme active matter brings together the physics of glass, jamming, plasticity and turbulence, in a new state of driven classical matter.
High-throughput functional evaluation of BRCA2 variants of unknown significance
Authors: Ikegami Masachika , Kohsaka Shinji , Ueno Toshihide , Momozawa Yukihide , Inoue Satoshi , Tamura Kenji , Shimomura Akihiko , Hosoya Noriko , Kobayashi Hiroshi , Tanaka Sakae , Mano Hiroyuki 
Published: May 2020

AbstractNumerous nontruncating missense variants of theBRCA2gene have been identified, but there is a lack of convincing evidence, such as familial data, demonstrating their clinical relevance and they thus remain unactionable. To assess the pathogenicity of variants of unknown significance (VUSs) withinBRCA2, here we develop a method, the MANO-B method, for high-throughput functional evaluation utilizingBRCA2-deficient cells and poly (ADP-ribose) polymerase (PARP) inhibitors. The estimated sensitivity and specificity of this assay compared to those of the International Agency for Research on Cancer classification system is 95% and 95% (95% confidence intervals: 77–100% and 82–99%), respectively. We classify the functional impact of 186BRCA2VUSs with our computational pipeline, resulting in the classification of 126 variants as normal/likely normal, 23 as intermediate, and 37 as abnormal/likely abnormal. We further describe a simplified, on-demand annotation system that could be used as a companion diagnostic for PARP inhibitors in patients with unknownBRCA2VUSs.
Near-field transmission matrix microscopy for mapping high-order eigenmodes of subwavelength nanostructures
Authors: Seo Eunsung , Jin Young-Ho , Choi Wonjun , Jo Yonghyeon , Lee Suyeon , Song Kyung-Deok , Ahn Joonmo , Park Q.-Han , Kim Myung-Ki , Choi Wonshik 
Published: May 2020

AbstractAs nanoscale photonic devices are densely integrated, multiple near-field optical eigenmodes take part in their functionalization. Inevitably, these eigenmodes are highly multiplexed in their spectra and superposed in their spatial distributions, making it extremely difficult for conventional near-field scanning optical microscopy (NSOM) to address individual eigenmodes. Here, we develop a near-field transmission matrix microscopy for mapping the high-order eigenmodes of nanostructures, which are invisible with conventional NSOM. At an excitation wavelength where multiple modes are superposed, we measure the near-field amplitude and phase maps for various far-field illumination angles, from which we construct a fully phase-referenced far- to near-field transmission matrix. By performing the singular value decomposition, we extract orthogonal near-field eigenmodes such as anti-symmetric mode and quadruple mode of multiple nano-slits whose gap size (50 nm) is smaller than the probe aperture (150 nm). Analytic model and numerical mode analysis validated the experimentally observed modes.
Fracture toughness of a metal–organic framework glass
Authors: To Theany , Sørensen Søren S. , Stepniewska Malwina , Qiao Ang , Jensen Lars R. , Bauchy Mathieu , Yue Yuanzheng , Smedskjaer Morten M. 
Published: May 2020

AbstractMetal-organic framework glasses feature unique thermal, structural, and chemical properties compared to traditional metallic, organic, and oxide glasses. So far, there is a lack of knowledge of their mechanical properties, especially toughness and strength, owing to the challenge in preparing large bulk glass samples for mechanical testing. However, a recently developed melting method enables fabrication of large bulk glass samples (>25 mm3) from zeolitic imidazolate frameworks. Here, fracture toughness (KIc) of a representative glass, namely ZIF-62 glass (Zn(C3H3N2)1.75(C7H5N2)0.25), is measured using single-edge precracked beam method and simulated using reactive molecular dynamics. KIc is determined to be ~0.1 MPa m0.5, which is even lower than that of brittle oxide glasses due to the preferential breakage of the weak coordinative bonds (Zn-N). The glass is found to exhibit an anomalous brittle-to-ductile transition behavior, considering its low fracture surface energy despite similar Poisson’s ratio to that of many ductile metallic and organic glasses.
Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis
Authors: Thomas Quentin Angelo , Ard Ryan , Liu Jinghan , Li Bingnan , Wang Jingwen , Pelechano Vicent , Marquardt Sebastian 
Published: May 2020

AbstractRNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that ~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.
Probing multiphoton light-induced molecular potentials
Authors: Kübel M. , Spanner M. , Dube Z. , Naumov A. Yu. , Chelkowski S. , Bandrauk A. D. , Vrakking M. J. J. , Corkum P. B. , Villeneuve D. M. , Staudte A. 
Published: May 2020

AbstractThe strong coupling between intense laser fields and valence electrons in molecules causes distortions of the potential energy hypersurfaces which determine the motion of the nuclei and influence possible reaction pathways. The coupling strength varies with the angle between the light electric field and valence orbital, and thereby adds another dimension to the effective molecular potential energy surface, leading to the emergence of light-induced conical intersections. Here, we demonstrate that multiphoton couplings can give rise to complex light-induced potential energy surfaces that govern molecular behavior. In the laser-induced dissociation of H2+, the simplest of molecules, we measure a strongly modulated angular distribution of protons which has escaped prior observation. Using two-color Floquet theory, we show that the modulations result from ultrafast dynamics on light-induced molecular potentials. These potentials are shaped by the amplitude, duration and phase of the dressing fields, allowing for manipulating the dissociation dynamics of small molecules.
Chemical multi-fingerprinting of exogenous ultrafine particles in human serum and pleural effusion
Authors: Lu Dawei , Luo Qian , Chen Rui , Zhuansun Yongxun , Jiang Jie , Wang Weichao , Yang Xuezhi , Zhang Luyao , Liu Xiaolei , Li Fang , Liu Qian , Jiang Guibin 
Published: May 2020

AbstractAmbient particulate matter pollution is one of the leading causes of global disease burden. Epidemiological studies have revealed the connections between particulate exposure and cardiovascular and respiratory diseases. However, until now, the real species of ambient ultrafine particles (UFPs) in humans are still scarcely known. Here we report the discovery and characterization of exogenous nanoparticles (NPs) in human serum and pleural effusion (PE) samples collected from non-occupational subjects in a typical polluted region. We show the wide presence of NPs in human serum and PE samples with extreme diversity in chemical species, concentration, and morphology. Through chemical multi-fingerprinting (including elemental fingerprints, high-resolution structural fingerprints, and stable iron isotopic fingerprints) of NPs, we identify the sources of the NPs to be abiogenic, particularly, combustion-derived particulate emission. Our results provide evidence for the translocation of ambient UFPs into the human circulatory system, and also provide information for understanding their systemic health effects.
Intestinal fungi are causally implicated in microbiome assembly and immune development in mice
Authors: van Tilburg Bernardes Erik , Pettersen Veronika Kuchařová , Gutierrez Mackenzie W. , Laforest-Lapointe Isabelle , Jendzjowsky Nicholas G. , Cavin Jean-Baptiste , Vicentini Fernando A. , Keenan Catherine M. , Ramay Hena R. , Samara Jumana , MacNaughton Wallace K. , Wilson Richard J. A. , Kelly Margaret M. , McCoy Kathy D. , Sharkey Keith A. , Arrieta Marie-Claire 
Published: May 2020

AbstractThe gut microbiome consists of a multi-kingdom microbial community. Whilst the role of bacteria as causal contributors governing host physiological development is well established, the role of fungi remains to be determined. Here, we use germ-free mice colonized with defined species of bacteria, fungi, or both to differentiate the causal role of fungi on microbiome assembly, immune development, susceptibility to colitis, and airway inflammation. Fungal colonization promotes major shifts in bacterial microbiome ecology, and has an independent effect on innate and adaptive immune development in young mice. While exclusive fungal colonization is insufficient to elicit overt dextran sulfate sodium-induced colitis, bacterial and fungal co-colonization increase colonic inflammation. Ovalbumin-induced airway inflammation reveals that bacterial, but not fungal colonization is necessary to decrease airway inflammation, yet fungi selectively promotes macrophage infiltration in the airway. Together, our findings demonstrate a causal role for fungi in microbial ecology and host immune functionality, and therefore prompt the inclusion of fungi in therapeutic approaches aimed at modulating early life microbiomes.
Guessing probability in quantum key distribution
Authors: Wang Xiang-Bin , Wang Jing-Tao , Qin Ji-Qian , Jiang Cong , Yu Zong-Wen 
Published: May 2020

AbstractOn the basis of the existing trace distance result, we present a simple and efficient method to tighten the upper bound of the guessing probability. The guessing probability of the final key k can be upper bounded by the guessing probability of another key $${\bf{k}}^{\prime}$$

k

′

, if $${\bf{k}}^{\prime}$$

k

′

can be mapped from the final key k. Compared with the known methods, our result is more tightened by thousands of orders of magnitude. For example, given a 10−9-secure key from the sifted key, the upper bound of the guessing probability obtained using our method is 2 × 10−3277. This value is smaller than the existing result 10−9 by more than 3000 orders of magnitude. Our result shows that from the perspective of guessing probability, the performance of the existing trace distance security is actually much better than what was assumed in the past.
Complete sleep and local field potential analysis regarding estrus cycle, pregnancy, postpartum and post-weaning periods and homeostatic sleep regulation in female rats
Authors: Tóth Attila , Pethő Máté , Keserű Dóra , Simon Dorina , Hajnik Tünde , Détári László , Dobolyi Árpád 
Published: May 2020

AbstractSleep and local field potential (LFP) characteristics were addressed during the reproductive cycle in female rats using long-term (60–70 days) recordings. Changes in homeostatic sleep regulation was tested by sleep deprivation (SDep). The effect of mother-pup separation on sleep was also investigated during the postpartum (PP) period. First half of the pregnancy and early PP period showed increased wakefulness (W) and higher arousal indicated by elevated beta and gamma activity. Slow wave sleep (SWS) recovery was suppressed while REM sleep replacement was complete after SDep in the PP period. Pup separation decreased maternal W during early-, but increased during middle PP while did not affect during late PP. More W, less SWS, higher light phase beta activity but lower gamma activity was seen during the post-weaning estrus cycle compared to the virgin one. Maternal sleep can be governed by the fetuses/pups needs and their presence, which elevate W of mothers. Complete REM sleep- and incomplete SWS replacement after SDep in the PP period may reflect the necessity of maternal REM sleep for the offspring while SWS increase may compete with W essential for maternal care. Maternal experience may cause sleep and LFP changes in the post-weaning estrus cycle.
Characterization of radioresistant epithelial stem cell heterogeneity in the damaged mouse intestine
Authors: Sato Taku , Sase Miwako , Ishikawa Shun , Kajita Mihoko , Asano Jumpei , Sato Toshiro , Mori Yoshiyuki , Ohteki Toshiaki 
Published: May 2020

AbstractThe small intestine has a robust regenerative capacity, and various cell types serve as “cells-of-origin” in the epithelial regeneration process after injury. However, how much each population contributes to regeneration remains unclear. Using lineage tracing, we found that Lgr5-expressing cell derivatives contained radioresistant intestinal stem cells (ISCs) crucial for epithelial regeneration in the damaged intestine after irradiation. Single-cell qRT-PCR analysis showed that surviving Lgr5-expressing cell derivatives in the damaged intestine are remarkably heterogeneous, and that the expression levels of a YAP-target gene Sca1 were inversely correlated with their “stemness”, suggesting that the YAP/Wnt signal balance in surviving crypt epithelial cells determines the cellular contribution to epithelial regeneration. Single-cell RNA sequencing of Sca1–Lgr5-derivatives revealed that expression of a tetraspanin family member CD81 correlated well with the expression of ISC- and proliferation-related genes. Consistent with these findings, organoid-forming ability was confined to the CD81hiSca1– fraction within the damaged crypt epithelial cells. Characterization of radioresistant epithelial stem cell heterogeneity in the damaged intestine may contribute to therapeutic strategies for gastrointestinal diseases.
Inhibition of urease activity by different compounds provides insight into the modulation and association of bacterial nickel import and ureolysis
Authors: Svane Simon , Sigurdarson Jens Jakob , Finkenwirth Friedrich , Eitinger Thomas , Karring Henrik 
Published: May 2020

AbstractThe nickel-dependent urease enzyme is responsible for the hydrolysis of urea to ammonia and carbon dioxide. A number of bacteria produce urease (ureolytic bacteria) and are associated with various infectious diseases and ammonia emissions from agriculture. We report the first comprehensive comparison of the inhibition of urease activity by compounds analysed under the same conditions. Thus, 71 commercially available compounds were screened for their anti-ureolytic properties against both the ureolytic bacterium Klebsiella pneumoniae and purified jack bean urease. Of the tested compounds, 30 showed more than 25% inhibition of the ureolytic activity of Klebsiella pneumoniae or jack bean urease, and among these, carbon disulfide, N-phenylmaleimide, diethylenetriaminepentaacetic acid, sodium pyrrolidinedithiocarbamate, 1,2,4-butanetricarboxylic acid, tannic acid, and gallic acid have not previously been reported to possess anti-ureolytic properties. The diverse effects of metal ion chelators on ureolysis were investigated using a cellular nickel uptake assay. Ethylenediaminetetraacetic acid (EDTA) and dimethylglyoxime (DMG) clearly reduced the nickel import and ureolytic activity of cells, oxalic acid stimulated nickel import but reduced the ureolytic activity of cells, 1,2,4-butanetricarboxylic acid strongly stimulated nickel import and slightly increased the ureolytic activity of cells, while L-cysteine had no effect on nickel import but efficiently reduced the ureolytic activity of cells.
A Cell-based Screen in Actinomyces oris to Identify Sortase Inhibitors
Authors: Gosschalk Jason E. , Chang Chungyu , Sue Christopher K. , Siegel Sara D. , Wu Chenggang , Kattke Michele D. , Yi Sung Wook , Damoiseaux Robert , Jung Michael E. , Ton-That Hung , Clubb Robert T. 
Published: May 2020

AbstractSortase enzymes are attractive antivirulence drug targets that attach virulence factors to the surface ofStaphylococcus aureusand other medically significant bacterial pathogens. Prior efforts to discover a useful sortase inhibitor have relied upon anin vitroactivity assay in which the enzyme is removed from its native site on the bacterial surface and truncated to improve solubility. To discover inhibitors that are effective in inactivating sortasesin vivo, we developed and implemented a novel cell-based screen usingActinomyces oris, a key colonizer in the development of oral biofilms.A.orisis unique because it exhibits sortase-dependent growth in cell culture, providing a robust phenotype for high throughput screening (HTS). Three molecules representing two unique scaffolds were discovered by HTS and disrupt surface protein display in intact cells and inhibit enzyme activityin vitro. This represents the first HTS for sortase inhibitors that relies on the simple metric of cellular growth and suggests thatA.orismay be a useful platform for discovery efforts targeting sortase.