bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modernization of Atmospheric Physics Parameterization in Canadian NWP
Authors: McTaggart‐Cowan R. , Vaillancourt P. A. , Zadra A. , Chamberland S. , Charron M. , Corvec S. , Milbrandt J. A. , Paquin‐Ricard D. , Patoine A. , Roch M. , Separovic L. , Yang J. 
Published: September 2019

AbstractAtmospheric physics is represented in numerical models by parameterizations that use resolved‐scale information to estimate the effects of physical processes on the atmospheric state. Over time, our understanding of these processes improves, new techniques are introduced to represent physics in a numerical model, and increased resolution changes the relative importance of different parameterizations within the system. As a result, the physical parameterization packages of numerical weather prediction (NWP) models undergo regular updates as older schemes are replaced with newer ones that offer an improved, and often more complex, depiction of relevant physical processes. Such changes are typically combined with a rebalancing of the physics suite because of strong interactions between parameterization schemes and the presence of compensating errors in the system. In this study, a major update to the package of physical parameterizations used in Canadian operational NWP is introduced. The primary goals of this effort were to improve the global energy budget and to facilitate an increase in the vertical resolution of operational configurations. Both of these objectives were achieved, along with a significant improvement in guidance quality for global and regional prediction systems.
Early Mesozoic Magmatism Within the Tibetan Plateau: Implications for the Paleo‐Tethyan Tectonic Evolution and Continental Amalgamation
Authors: Li Shan , Chung Sun‐Lin , Hou Zengqian , Chew David , Wang Tao , Wang Baodi , Wang Yanbin 
Published: September 2019

AbstractNumerous early Mesozoic magmatic rocks within the Tibetan Plateau ultimately have a geodynamic controll caused by the Paleo‐Tethyan tectonic evolution and the assembly of Pangea. Based on their temporal variation and the timing of closure (235 ± 10 Ma) of the Paleo‐Tethys Ocean, they can be broadly divided into two groups by zircon U‐Pb geochronology: an Early to Middle Triassic (252–235 Ma) group and a Late Triassic to Early Jurassic (ca. 235–190 Ma) group. Early magmatic rocks are mainly found in the middle northern Tibetan Plateau, whereas late magmatic rocks are more widespread in the whole Tibetan Plateau. Nd and Hf isotope mapping suggests that the eastern segment of the Qiangtang is underlain by old (late Archean to early Paleoproterozoic) basement, while Southern Lhasa is underlain by juvenile lower crust, which yields Neoproterozoic to early Paleozoic model ages. Early Mesozoic tectonomagmatism was likely caused by episodic southward opening of multi‐Tethys oceans, punctuated by episodes of subduction and collision. The Middle to Late Permian tectonomagmatic history of Paleo‐Tethys was dominated by continental arc‐related systems. During the Early to Middle Triassic, the tectonomagmatic history was associated with the ongoing closure of the Paleo‐Tethys Ocean and a tectonic transition from subduction to collision. Late Triassic tectonomagmatism formed in a post‐collisional setting following the closure of the Paleo‐Tethys Ocean and the ultimate assembly of Pangea. Early Mesozoic magmatism within the Tibetan Plateau thus provides crucial information on the history of oceanic‐continental evolution and helps constrain the tectonic transition from subduction/accretion through to collision/postcollision for East Paleo‐Tethys.
Exhuming the Top End of North America: Episodic Evolution of the Eurekan Belt and Its Potential Relationships to North Atlantic Plate Tectonics and Arctic Climate Change
Authors: Vamvaka Agni , Pross Jörg , Monien Patrick , Piepjohn Karsten , Estrada Solveig , Lisker Frank , Spiegel Cornelia 
Published: September 2019

AbstractWe present the first low‐temperature thermochronology data from northernmost Ellesmere Island (Canadian Arctic), along with palynological data from Paleogene sediments. Our study area is part of the >2,500‐km‐long Eurekan deformation belt that formed across the High Arctic during the Eocene. The aim of this study is to investigate the exhumation of the Eurekan belt and potential relationships with the opening of the North Atlantic, as well as with environmental changes of the Arctic. Our data show that the Canadian Arctic margin was characterized by stretching and basin formation during the Paleocene. Sediment deposition occurred in a coastal swamp environment under a warm and humid climate that lasted into the early Eocene. Exhumation of northern Ellesmere Island was episodic and was presumably controlled by strike‐slip movements along the De Geer Fracture Zone between Svalbard and Greenland. Enhanced exhumation of northern Ellesmere Island occurred ~66–60 Ma, ~55–48 Ma, 44–38 Ma, and 34–26 Ma. These exhumation periods largely correlate with changes of spreading rates and movement directions of the Norwegian‐Greenland Sea. Main topographic growth along the Eurekan belt was temporally coincident with deposition of ice‐rafted debris off eastern Greenland. We suggest that Eurekan topography growth was an important trigger for glacier formation in Greenland. The cessation of rapid exhumation at ~26 Ma can be explained by continental separation between Greenland and Svalbard, which decoupled northern Ellesmere Island from strike‐slip movements along the De Geer Fracture Zone, eventually leading to the opening of the Fram Strait.
Local delivery of arsenic trioxide nanoparticles for hepatocellular carcinoma treatment
Authors: Hu Jian , Dong Yi , Ding Li , Dong Yang , Wu Zhihua , Wang Wenping , Shen Ming , Duan Yourong 
Published: September 2019

AbstractHepatocellular carcinoma (HCC) is a malignancy with a poor prognosis. Surgery combined with chemotherapy has been recommended as a curative regimen for HCC. Nevertheless, the anticancer mechanisms of chemicals in hepatocellular carcinoma remain unclear. Pyroptosis is a type of programmed necrosis, and its mechanism in hepatocellular carcinoma is poorly understood. The efficacy and mechanism of arsenic trioxide nanoparticles in the treatment of HCC were explored in this research. Arsenic trioxide alone and arsenic trioxide nanoparticles were conveniently administered to mice intratumorally using a needle. Compared with As2O3, As2O3nanoparticles (As2O3-NPs) showed better inhibition, promoted greater LDH release, and induced cell morphology indicative of pyroptosis in vitro. Compared with the free drug, As2O3-NPs increased GSDME-N expression and decreased Dnmt3a, Dnmt3b, and Dnmt1 expression in Huh7 cells. In vivo, As2O3-NPs induced a significant decrease in the expression of Dnmt3a, Dnmt3b and Dnmt1, but significantly upregulated the expression of GSDME-N (gasdermin E (GSDME) was originally found to be related to deafness; recently, it has been defined as a gasdermin family member associated with pyroptosis). As2O3-NPs inhibited tumor growth more strongly than As2O3or control, a finding likely attributed to the downregulation of PCNA and DNMT-related proteins and the upregulation of GSDME-N.
The Dutch Y-chromosomal landscape
Authors: Altena Eveline , Smeding Risha , van der Gaag Kristiaan J. , Larmuseau Maarten H. D. , Decorte Ronny , Lao Oscar , Kayser Manfred , Kraaijenbrink Thirsa , de Knijff Peter 
Published: September 2019

AbstractPrevious studies indicated existing, albeit limited, genetic-geographic population substructure in the Dutch population based on genome-wide data and a lack of this for mitochondrial SNP based data. Despite the aforementioned studies, Y-chromosomal SNP data from the Netherlands remain scarce and do not cover the territory of the Netherlands well enough to allow a reliable investigation of genetic-geographic population substructure. Here we provide the first substantial dataset of detailed spatial Y-chromosomal haplogroup information in 2085 males collected across the Netherlands and supplemented with previously published data from northern Belgium. We found Y-chromosomal evidence for genetic–geographic population substructure, and several Y-haplogroups demonstrating significant clinal frequency distributions in different directions. By means of prediction surface maps we could visualize (complex) distribution patterns of individual Y-haplogroups in detail. These results highlight the value of a micro-geographic approach and are of great use for forensic and epidemiological investigations and our understanding of the Dutch population history. Moreover, the previously noted absence of genetic-geographic population substructure in the Netherlands based on mitochondrial DNA in contrast to our Y-chromosome results, hints at different population histories for women and men in the Netherlands.
Cellular responses to beating hydrogels to investigate mechanotransduction
Authors: Chandorkar Yashoda , Castro Nava Arturo , Schweizerhof Sjören , Van Dongen Marcel , Haraszti Tamás , Köhler Jens , Zhang Hang , Windoffer Reinhard , Mourran Ahmed , Möller Martin , De Laporte Laura 
Published: September 2019

AbstractCells feel the forces exerted on them by the surrounding extracellular matrix (ECM) environment and respond to them. While many cell fate processes are dictated by these forces, which are highly synchronized in space and time, abnormal force transduction is implicated in the progression of many diseases (muscular dystrophy, cancer). However, material platforms that enable transient, cyclic forces in vitro to recreate an in vivo-like scenario remain a challenge. Here, we report a hydrogel system that rapidly beats (actuates) with spatio-temporal control using a near infra-red light trigger. Small, user-defined mechanical forces (~nN) are exerted on cells growing on the hydrogel surface at frequencies up to 10 Hz, revealing insights into the effect of actuation on cell migration and the kinetics of reversible nuclear translocation of the mechanosensor protein myocardin related transcription factor A, depending on the actuation amplitude, duration and frequency.
Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells
Authors: Hao Yi , Fan Xinqi , Shi Yujie , Zhang Che , Sun De-en , Qin Ke , Qin Wei , Zhou Wen , Chen Xing 
Published: September 2019

AbstractUnnatural monosaccharides such as azidosugars that can be metabolically incorporated into cellular glycans are currently used as a major tool for glycan imaging and glycoproteomic profiling. As a common practice to enhance membrane permeability and cellular uptake, the unnatural sugars are per-O-acetylated, which, however, can induce a long-overlooked side reaction, non-enzymatic S-glycosylation. Herein, we develop 1,3-di-esterified N-azidoacetylgalactosamine (GalNAz) as next-generation chemical reporters for metabolic glycan labeling. Both 1,3-di-O-acetylated GalNAz (1,3-Ac2GalNAz) and 1,3-di-O-propionylated GalNAz (1,3-Pr2GalNAz) exhibit high efficiency for labeling protein O-GlcNAcylation with no artificial S-glycosylation. Applying 1,3-Pr2GalNAz in mouse embryonic stem cells (mESCs), we identify ESRRB, a critical transcription factor for pluripotency, as an O-GlcNAcylated protein. We show that ESRRB O-GlcNAcylation is important for mESC self-renewal and pluripotency. Mechanistically, ESRRB is O-GlcNAcylated by O-GlcNAc transferase at serine 25, which stabilizes ESRRB, promotes its transcription activity and facilitates its interactions with two master pluripotency regulators, OCT4 and NANOG.
Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
Authors: Tycko Josh , Wainberg Michael , Marinov Georgi K. , Ursu Oana , Hess Gaelen T. , Ego Braeden K. , Aradhana  , Li Amy , Truong Alisa , Trevino Alexandro E. , Spees Kaitlyn , Yao David , Kaplow Irene M. , Greenside Peyton G. , Morgens David W. , Phanstiel Douglas H. , Snyder Michael P. , Bintu Lacramioara , Greenleaf William J. , Kundaje Anshul , Bassik Michael C. 
Published: September 2019

AbstractPooled CRISPR-Cas9 screens are a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we investigate Cas9, dCas9, and CRISPRi/a off-target activity in screens for essential regulatory elements. The sgRNAs with the largest effects in genome-scale screens for essential CTCF loop anchors in K562 cells were not single guide RNAs (sgRNAs) that disrupted gene expression near the on-target CTCF anchor. Rather, these sgRNAs had high off-target activity that, while only weakly correlated with absolute off-target site number, could be predicted by the recently developed GuideScan specificity score. Screens conducted in parallel with CRISPRi/a, which do not induce double-stranded DNA breaks, revealed that a distinct set of off-targets also cause strong confounding fitness effects with these epigenome-editing tools. Promisingly, filtering of CRISPRi libraries using GuideScan specificity scores removed these confounded sgRNAs and enabled identification of essential regulatory elements.
Forecasting the magnitude of the largest expected earthquake
Authors: Shcherbakov Robert , Zhuang Jiancang , Zöller Gert , Ogata Yosihiko 
Published: September 2019

AbstractThe majority of earthquakes occur unexpectedly and can trigger subsequent sequences of events that can culminate in more powerful earthquakes. This self-exciting nature of seismicity generates complex clustering of earthquakes in space and time. Therefore, the problem of constraining the magnitude of the largest expected earthquake during a future time interval is of critical importance in mitigating earthquake hazard. We address this problem by developing a methodology to compute the probabilities for such extreme earthquakes to be above certain magnitudes. We combine the Bayesian methods with the extreme value theory and assume that the occurrence of earthquakes can be described by the Epidemic Type Aftershock Sequence process. We analyze in detail the application of this methodology to the 2016 Kumamoto, Japan, earthquake sequence. We are able to estimate retrospectively the probabilities of having large subsequent earthquakes during several stages of the evolution of this sequence.
A lipid-binding protein mediates rhoptry discharge and invasion in Plasmodium falciparum and Toxoplasma gondii parasites
Authors: Suarez Catherine , Lentini Gaëlle , Ramaswamy Raghavendran , Maynadier Marjorie , Aquilini Eleonora , Berry-Sterkers Laurence , Cipriano Michael , Chen Allan L. , Bradley Peter , Striepen Boris , Boulanger Martin J. , Lebrun Maryse 
Published: September 2019

AbstractMembers of the Apicomplexa phylum, including Plasmodium and Toxoplasma, have two types of secretory organelles (micronemes and rhoptries) whose sequential release is essential for invasion and the intracellular lifestyle of these eukaryotes. During invasion, rhoptries inject an array of invasion and virulence factors into the cytoplasm of the host cell, but the molecular mechanism mediating rhoptry exocytosis is unknown. Here we identify a set of parasite specific proteins, termed rhoptry apical surface proteins (RASP) that cap the extremity of the rhoptry. Depletion of RASP2 results in loss of rhoptry secretion and completely blocks parasite invasion and therefore parasite proliferation in both Toxoplasma and Plasmodium. Recombinant RASP2 binds charged lipids and likely contributes to assembling the machinery that docks/primes the rhoptry to the plasma membrane prior to fusion. This study provides important mechanistic insight into a parasite specific exocytic pathway, essential for the establishment of infection.
Emergent honeycomb network of topological excitations in correlated charge density wave
Authors: Park Jae Whan , Cho Gil Young , Lee Jinwon , Yeom Han Woong 
Published: September 2019

AbstractWhen two periodic potentials compete in materials, one may adopt the other, which straightforwardly generates topological defects. Of particular interest are domain walls in charge-, dipole-, and spin-ordered systems, which govern macroscopic properties and important functionality. However, detailed atomic and electronic structures of domain walls have often been uncertain and the microscopic mechanism of their functionality has been elusive. Here, we clarify the complete atomic and electronic structures of the domain wall network, a honeycomb network connected by Z3 vortices, in the nearly commensurate Mott charge-density wave (CDW) phase of 1T-TaS2. Scanning tunneling microscopy resolves characteristic charge orders within domain walls and their vortices. Density functional theory calculations disclose their unique atomic relaxations and the metallic in-gap states confined tightly therein. A generic theory is constructed, which connects this emergent honeycomb network of conducting electrons to the enhanced superconductivity.
A streamlined and predominantly diploid genome in the tiny marine green alga Chloropicon primus
Authors: Lemieux Claude , Turmel Monique , Otis Christian , Pombert Jean-François 
Published: September 2019

AbstractTiny marine green algae issued from two deep branches of the Chlorophyta, the Mamiellophyceae and Chloropicophyceae, dominate different regions of the oceans and play key roles in planktonic communities. Considering that the Mamiellophyceae is the sole lineage of prasinophyte algae that has been intensively investigated, the extent to which these two algal groups differ in their metabolic capacities and cellular processes is currently unknown. To address this gap of knowledge, we investigate here the nuclear genome sequence of a member of the Chloropicophyceae, Chloropicon primus. Among the main biological insights that emerge from this 17.4 Mb genome, we find an unexpected diploid structure for most chromosomes and a propionate detoxification pathway in green algae. Our results support the notion that separate events of genome minimization, which entailed differential losses of genes/pathways, have occurred in the Chloropicophyceae and Mamiellophyceae, suggesting different strategies of adaptation to oceanic environments.
CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation
Authors: Tuladhar Rubina , Yeu Yunku , Tyler Piazza John , Tan Zhen , Rene Clemenceau Jean , Wu Xiaofeng , Barrett Quinn , Herbert Jeremiah , Mathews David H. , Kim James , Hyun Hwang Tae , Lum Lawrence 
Published: September 2019

AbstractThe introduction of insertion-deletions (INDELs) by non-homologous end-joining (NHEJ) pathway underlies the mechanistic basis of CRISPR-Cas9-directed genome editing. Selective gene ablation using CRISPR-Cas9 is achieved by installation of a premature termination codon (PTC) from a frameshift-inducing INDEL that elicits nonsense-mediated decay (NMD) of the mutant mRNA. Here, by examining the mRNA and protein products of CRISPR targeted genes in a cell line panel with presumed gene knockouts, we detect the production of foreign mRNAs or proteins in ~50% of the cell lines. We demonstrate that these aberrant protein products stem from the introduction of INDELs that promote internal ribosomal entry, convert pseudo-mRNAs (alternatively spliced mRNAs with a PTC) into protein encoding molecules, or induce exon skipping by disruption of exon splicing enhancers (ESEs). Our results reveal challenges to manipulating gene expression outcomes using INDEL-based mutagenesis and strategies useful in mitigating their impact on intended genome-editing outcomes.
An ultrahigh resolution pressure sensor based on percolative metal nanoparticle arrays
Authors: Chen Minrui , Luo Weifeng , Xu Zhongqi , Zhang Xueping , Xie Bo , Wang Guanghou , Han Min 
Published: September 2019

AbstractTunneling conductance among nanoparticle arrays is extremely sensitive to the spacing of nanoparticles and might be applied to fabricate ultra-sensitive sensors. Such sensors are of paramount significance for various application, such as automotive systems and consumer electronics. Here, we represent a sensitive pressure sensor which is composed of a piezoresistive strain transducer fabricated from closely spaced nanoparticle films deposited on a flexible membrane. Benefited from this unique quantum transport mechanism, the thermal noise of the sensor decreases significantly, providing the opportunity for our devices to serve as high-performance pressure sensors with an ultrahigh resolution as fine as about 0.5 Pa and a high sensitivity of 0.13 kPa−1. Moreover, our sensor with such an unprecedented response capability can be operated as a barometric altimeter with an altitude resolution of about 1 m. The outstanding behaviors of our devices make nanoparticle arrays for use as actuation materials for pressure measurement.
A termination-insensitive and robust electron gas at the heterointerface of two complex oxides
Authors: Zhang Meng , Du Kai , Ren Tianshuang , Tian He , Zhang Ze , Hwang Harold Y. , Xie Yanwu 
Published: September 2019

AbstractThe single-crystal SrTiO3 (001) has two different surface terminations, TiO2 and SrO. One most remarkable observation in previous studies is that only the heterointerfaces with TiO2-terminated SrTiO3, which usually combines with polar oxides such as LaAlO3, host an electron gas. Here we show that a robust electron gas can be generated between a non-polar oxide, CaHfO3, and SrTiO3 (001) with either termination. Unlike the well-known electron gas of LaAlO3/SrTiO3, the present one of CaHfO3/SrTiO3 essentially has no critical thickness of CaHfO3, can survive a long-time oxygen annealing at high temperature, and its transport properties are stable under exposure to water and other polar solvents. By electrostatic gating through CaHfO3, field-effect devices are demonstrated using CaHfO3/SrTiO3 heterointerfaces with both terminations. These results show that the electron gas reported in the present study is unique and promising for applications in oxide electronics.
Multifunctional nanoagents for ultrasensitive imaging and photoactive killing of Gram-negative and Gram-positive bacteria
Authors: Tang Jiali , Chu Binbin , Wang Jinhua , Song Bin , Su Yuanyuan , Wang Houyu , He Yao 
Published: September 2019

AbstractSimultaneous imaging and treatment of infections remains a major challenge, with most current approaches being effective against only one specific group of bacteria or not being useful for diagnosis. Here we develop multifunctional nanoagents that can potentially be used for imaging and treatment of infections caused by diverse bacterial pathogens. The nanoagents are made of fluorescent silicon nanoparticles (SiNPs) functionalized with a glucose polymer (e.g., poly[4-O-(α-D-glucopyranosyl)-D-glucopyranose]) and loaded with chlorin e6 (Ce6). They are rapidly internalized into Gram-negative and Gram-positive bacteria by a mechanism dependent on an ATP-binding cassette (ABC) transporter pathway. The nanoagents can be used for imaging bacteria by tracking the green fluorescence of SiNPs and the red fluorescence of Ce6, allowing in vivo detection of as few as 105 colony-forming units. The nanoagents exhibit in vivo photodynamic antibacterial efficiencies of 98% against Staphylococcus aureus and 96% against Pseudomonas aeruginosa under 660 nm irradiation.