bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assimilation of GPM Rain Rate Products With GSI Data Assimilation System for Heavy and Light Precipitation Events
Authors: Li Xuanli , Mecikalski John R. , Srikishen Jayanthi , Zavodsky Bradley , Petersen Walter A. 
Published: January 2020

AbstractThe National Aeronautics and Space Administration‐Japan Aerospace Exploration Agency Global Precipitation Measurement (GPM) mission consists of a multisatellite constellation that provides real‐time or near‐real‐time global observations of rain and snow. In this study, GPM Level 3 Integrated Multi‐satellitE Retrievals for GPM (IMERG) and Level 2 GPM Microwave Imager Goddard Profiling rainfall products have been assimilated into the Weather Research and Forecasting model using the community Gridpoint Statistical Interpolation (GSI) data assimilation system. Experiments have been conducted and compared to demonstrate the impact of rain rate data assimilation on forecasts of heavy rainfall related to Hurricane Harvey (2017) and moderate to light rainfall observed during the GPM Integrated Precipitation and Hydrology Experiment field campaign. The results indicate that both GPM Microwave Imager Goddard Profiling and IMERG data could generate apparent increments in moisture, temperature, wind, and pressure fields for Hurricane Harvey, which led to significant improvement in the precipitation forecast. Frequent (every 3 hr) assimilation of IMERG data also positively impacted the short‐term precipitation forecast skill for the Integrated Precipitation and Hydrology Experiment moderate to light rain events. However, results also indicate that the impact of rain data assimilation was limited for a system that had a small horizontal dimension with low rain rates and within a relatively stable synoptic environment.
Holocene Hydrographic Variations From the Baltic‐North Sea Transitional Area (IODP Site M0059)
Authors: Ni S. , Quintana Krupinski N. B. , Groeneveld J. , Fanget A. S. , Böttcher M. E. , Liu B. , Lipka M. , Knudsen K. L. , Naeraa T. , Seidenkrantz M.‐S. , Filipsson H. L. 
Published: January 2020

AbstractDeoxygenation affects many continental shelf seas across the world today and results in increasing areas of hypoxia (dissolved oxygen concentration ([O2]) <1.4 ml/L). The Baltic Sea is increasingly affected by deoxygenation. Deoxygenation correlates with other environmental variables such as changing water temperature and salinity and is directly linked to ongoing global climate change. To place the ongoing environmental changes into a larger context and to further understand the complex Baltic Sea history and its impact on North Atlantic climate, we investigated a high accumulation‐rate brackish‐marine sediment core from the Little Belt (Site M0059), Danish Straits, NW Europe, retrieved during the Integrated Ocean Drilling Program (IODP) Expedition 347. We combined benthic foraminiferal geochemistry, faunal assemblages, and pore water stable isotopes to reconstruct seawater conditions (e.g., oxygenation, temperature, and salinity) over the past 7.7 thousand years (ka). Bottom water salinity in the Little Belt reconstructed from modeled pore water oxygen isotope data increased between 7.7 and 7.5 ka BP as a consequence of the transition from freshwater to brackish‐marine conditions. Salinity decreased gradually (from 30 to 24) from 4.1 to ~2.5 ka BP. By using the trace elemental composition (Mg/Ca, Mn/Ca, and Ba/Ca) and stable carbon and oxygen isotopes of foraminiferal species Elphidium selseyensis and E. clavatum, we identified that generally warming and hypoxia occurred between about 7.5 and 3.3 ka BP, approximately coinciding in time with the Holocene Thermal Maximum (HTM). These changes of bottom water conditions were coupled to the North Atlantic Oscillation (NAO) and relative sea level change.
The circadian rhythm in intervertebral disc degeneration: an autophagy connection
Authors: Zhang Tai-Wei , Li Ze-Fang , Dong Jian , Jiang Li-Bo 
Published: January 2020

AbstractThere is one circadian clock in the central nervous system and another in the peripheral organs, and the latter is driven by an autoregulatory molecular clock composed of several core clock genes. The height, water content, osmotic pressure and mechanical characteristics of intervertebral discs (IVDs) have been demonstrated to exhibit a circadian rhythm (CR). Recently, a molecular clock has been shown to exist in IVDs, abolition of which can lead to stress in nucleus pulposus cells (NPCs), contributing to intervertebral disc degeneration (IDD). Autophagy is a fundamental cellular process in eukaryotes and is essential for individual cells or organs to respond and adapt to changing environments; it has also been demonstrated to occur in human NPCs. Increasing evidence supports the hypothesis that autophagy is associated with CR. Thus, we review the connection between CR and autophagy and the roles of these mechanisms in IDD.
A new microchannel capillary flow assay (MCFA) platform with lyophilized chemiluminescence reagents for a smartphone-based POCT detecting malaria
Authors: Ghosh Sthitodhi , Aggarwal Kashish , U. Vinitha T. , Nguyen Thinh , Han Jungyoup , Ahn Chong H. 
Published: January 2020

AbstractThere has been a considerable development in microfluidic based immunodiagnostics over the past few years which has greatly favored the growth of novel point-of-care-testing (POCT). However, the realization of an inexpensive, low-power POCT needs cheap and disposable microfluidic devices that can perform autonomously with minimum user intervention. This work, for the first time, reports the development of a new microchannel capillary flow assay (MCFA) platform that can perform chemiluminescence based ELISA with lyophilized chemiluminescent reagents. This new MCFA platform exploits the ultra-high sensitivity of chemiluminescent detection while eliminating the shortcomings associated with liquid reagent handling, control of assay sequence and user intervention. The functionally designed microchannels along with adequate hydrophilicity produce a sequential flow of assay reagents and autonomously performs the ultra-high sensitive chemiluminescence based ELISA for the detection of malaria biomarker such as PfHRP2. The MCFA platform with no external flow control and simple chemiluminescence detection can easily communicate with smartphone via USB-OTG port using a custom-designed optical detector. The use of the smartphone for display, data transfer, storage and analysis, as well as the source of power allows the development of a smartphone based POCT analyzer for disease diagnostics. This paper reports a limit of detection (LOD) of 8 ng/mL by the smartphone analyzer which is sensitive enough to detect active malarial infection. The MCFA platform developed with the smartphone analyzer can be easily customized for different biomarkers, so a hand-held POCT for various infectious diseases can be envisaged with full networking capability at low cost.
A digital microfluidic system with 3D microstructures for single-cell culture
Authors: Zhai Jiao , Li Haoran , Wong Ada Hang-Heng , Dong Cheng , Yi Shuhong , Jia Yanwei , Mak Pui-In , Deng Chu-Xia , Martins Rui P. 
Published: January 2020

AbstractDespite the precise controllability of droplet samples in digital microfluidic (DMF) systems, their capability in isolating single cells for long-time culture is still limited: typically, only a few cells can be captured on an electrode. Although fabricating small-sized hydrophilic micropatches on an electrode aids single-cell capture, the actuation voltage for droplet transportation has to be significantly raised, resulting in a shorter lifetime for the DMF chip and a larger risk of damaging the cells. In this work, a DMF system with 3D microstructures engineered on-chip is proposed to form semi-closed micro-wells for efficient single-cell isolation and long-time culture. Our optimum results showed that approximately 20% of the micro-wells over a 30 × 30 array were occupied by isolated single cells. In addition, low-evaporation-temperature oil and surfactant aided the system in achieving a low droplet actuation voltage of 36V, which was 4 times lower than the typical 150 V, minimizing the potential damage to the cells in the droplets and to the DMF chip. To exemplify the technological advances, drug sensitivity tests were run in our DMF system to investigate the cell response of breast cancer cells (MDA-MB-231) and breast normal cells (MCF-10A) to a widely used chemotherapeutic drug, Cisplatin (Cis). The results on-chip were consistent with those screened in conventional 96-well plates. This novel, simple and robust single-cell trapping method has great potential in biological research at the single cell level.
Pyruvate secretion by oral streptococci modulates hydrogen peroxide dependent antagonism
Authors: Redanz Sylvio , Treerat Puthayalai , Mu Rong , Redanz Ulrike , Zou Zhengzhong , Koley Dipankar , Merritt Justin , Kreth Jens 
Published: January 2020

AbstractMany commensal oral streptococci generate H2O2 via pyruvate oxidase (SpxB) to inhibit the growth of competing bacteria like Streptococcus mutans, a major cariogenic species. In Streptococcus sanguinis SK36 (SK36) and Streptococcus gordonii DL1 (DL1), spxB expression and H2O2 release are subject to carbon catabolite repression by the catabolite control protein A (CcpA). Surprisingly, ccpA deletion mutants of SK36 and DL1 fail to inhibit S. mutans despite their production of otherwise inhibitory levels of H2O2. Using H2O2-deficient spxB deletion mutants of SK36 and DL1, it was subsequently discovered that both strains confer protection in trans to other bacteria when H2O2 is added exogenously. This protective effect depends on the direct detoxification of H2O2 by the release of pyruvate. The pyruvate dependent protective effect is also present in other spxB-encoding streptococci, such as the pneumococcus, but is missing from spxB-negative species like S. mutans. Targeted and transposon-based mutagenesis revealed Nox (putative H2O-forming NADH dehydrogenase) as an essential component required for pyruvate release and oxidative protection, while other genes such as sodA and dps play minor roles. Furthermore, pyruvate secretion is only detectable in aerobic growth conditions at biofilm-like cell densities and is responsive to CcpA-dependent catabolite control. This ability of spxB-encoding streptococci reveals a new facet of the competitive interactions between oral commensals and pathobionts and provides a mechanistic basis for the variable levels of inhibitory potential observed among H2O2-producing strains of commensal oral streptococci.
The concentration of tumor necrosis factor-α determines its protective or damaging effect on liver injury by regulating Yap activity
Authors: Zhao Shanmin , Jiang Jinghua , Jing Yingying , Liu Wenting , Yang Xue , Hou Xiaojuan , Gao Lu , Wei Lixin 
Published: January 2020

AbstractPrevious studies have shown that tumor necrosis factor (TNF)-α is a mediator of hepatotoxicity in liver injury. Moreover, TNF-α has also been reported to have a protective effect in liver regeneration, yet the function of TNF-α during liver injury remains controversial. Here, we report that the concentration of TNF-α determines its functions. High concentrations of TNF-α could aggravate LPS-induced liver injury. However, the TNF-α level was unchanged during APAP-induced liver injury, which exerted a protective effect. We expected that the concentration of TNF-α may affect its function. To test this hypothesis, TNF-α−/−rats or hepatocyte cells were treated with different concentrations of TNF-α. We found low TNF-α could reduce the levels of ALT and AST in the plasma of TNF-α−/−rats and promote the proliferation of hepatocyte cells. However, the levels of ALT and AST increased gradually with increasing TNF-α concentration after reaching the lowest value. Moreover, we showed that TNF-α affects the cell proliferation and cell death of hepatocytes by regulating Yap activity. Low TNF-α promoted Yap1 nuclear translocation, triggering the proliferation of hepatocytes. However, high TNF-α triggered the phosphorylation and inactivation of Yap1, preventing its nuclear import and consequently promoting cell death. Collectively, our findings provide novel evidence that the concentration of TNF-α is an important factor affecting its function in liver injury, which may provide a reference for the clinical treatment of liver injury.
Pursuit of reversible Zn electrochemistry: a time-honored challenge towards low-cost and green energy storage
Authors: Zhang Yaojian , Chen Zheng , Qiu Huayu , Yang Wuhai , Zhao Zhiming , Zhao Jingwen , Cui Guanglei 
Published: January 2020

AbstractThe world’s mounting demands for environmentally benign and efficient resource utilization have spurred investigations into intrinsically green and safe energy storage systems. As one of the most promising types of batteries, the Zn battery family, with a long research history in the human electrochemical power supply, has been revived and reevaluated in recent years. Although Zn anodes still lack mature and reliable solutions to support the satisfactory cyclability required for the current versatile applications, many new concepts with optimized Zn/Zn2+redox processes have inspired new hopes for rechargeable Zn batteries. In this review, we present a critical overview of the latest advances that could have a pivotal role in addressing the bottlenecks (e.g., nonuniform deposition, parasitic side reactions) encountered with Zn anodes, especially at the electrolyte-electrode interface. The focus is on research activities towards electrolyte modulation, artificial interphase engineering, and electrode structure design. Moreover, challenges and perspectives of rechargeable Zn batteries for further development in electrochemical energy storage applications are discussed. The reviewed surface/interface issues also provide lessons for the research of other multivalent battery chemistries with low-efficiency plating and stripping of the metal.
Ionophore constructed from non-covalent assembly of a G-quadruplex and liponucleoside transports K+-ion across biological membranes
Authors: Debnath Manish , Chakraborty Sandipan , Kumar Y. Pavan , Chaudhuri Ritapa , Jana Biman , Dash Jyotirmayee 
Published: January 2020

AbstractThe selective transport of ions across cell membranes, controlled by membrane proteins, is critical for a living organism. DNA-based systems have emerged as promising artificial ion transporters. However, the development of stable and selective artificial ion transporters remains a formidable task. We herein delineate the construction of an artificial ionophore using a telomeric DNA G-quadruplex (h-TELO) and a lipophilic guanosine (MG). MG stabilizes h-TELO by non-covalent interactions and, along with the lipophilic side chain, promotes the insertion of h-TELO within the hydrophobic lipid membrane. Fluorescence assays, electrophysiology measurements and molecular dynamics simulations reveal that MG/h-TELO preferentially transports K+-ions in a stimuli-responsive manner. The preferential K+-ion transport is presumably due to conformational changes of the ionophore in response to different ions. Moreover, the ionophore transports K+-ions across CHO and K-562 cell membranes. This study may serve as a design principle to generate selective DNA-based artificial transporters for therapeutic applications.
Genetically stable poliovirus vectors activate dendritic cells and prime antitumor CD8 T cell immunity
Authors: Mosaheb Mubeen M. , Dobrikova Elena Y. , Brown Michael C. , Yang Yuanfan , Cable Jana , Okada Hideho , Nair Smita K. , Bigner Darell D. , Ashley David M. , Gromeier Matthias 
Published: January 2020

AbstractViruses naturally engage innate immunity, induce antigen presentation, and mediate CD8 T cell priming against foreign antigens. Polioviruses can provide a context optimal for generating antigen-specific CD8 T cells, as they have natural tropism for dendritic cells, preeminent inducers of CD8 T cell immunity; elicit Th1-promoting inflammation; and lack interference with innate or adaptive immunity. However, notorious genetic instability and underlying neuropathogenicity has hampered poliovirus-based vector applications. Here we devised a strategy based on the polio:rhinovirus chimera PVSRIPO, devoid of viral neuropathogenicity after intracerebral inoculation in human subjects, for stable expression of exogenous antigens. PVSRIPO vectors infect, activate, and induce epitope presentation in DCs in vitro; they recruit and activate DCs with Th1-dominant cytokine profiles at the injection site in vivo. They efficiently prime tumor antigen-specific CD8 T cells in vivo, induce CD8 T cell migration to the tumor site, delay tumor growth and enhance survival in murine tumor models.
Paris Climate Agreement passes the cost-benefit test
Authors: Glanemann Nicole , Willner Sven N. , Levermann Anders 
Published: January 2020

AbstractThe Paris Climate Agreement aims to keep temperature rise well below 2 °C. This implies mitigation costs as well as avoided climate damages. Here we show that independent of the normative assumptions of inequality aversion and time preferences, the agreement constitutes the economically optimal policy pathway for the century. To this end we consistently incorporate a damage-cost curve reproducing the observed relation between temperature and economic growth into the integrated assessment model DICE. We thus provide an inter-temporally optimizing cost-benefit analysis of this century’s climate problem. We account for uncertainties regarding the damage curve, climate sensitivity, socioeconomic future, and mitigation costs. The resulting optimal temperature is robust as can be understood from the generic temperature-dependence of the mitigation costs and the level of damages inferred from the observed temperature-growth relationship. Our results show that the politically motivated Paris Climate Agreement also represents the economically favourable pathway, if carried out properly.
Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations
Authors: Lee David S. M. , Ghanem Louis R. , Barash Yoseph 
Published: January 2020

AbstractG-quadruplex (G4) sequences are abundant in untranslated regions (UTRs) of human messenger RNAs, but their functional importance remains unclear. By integrating multiple sources of genetic and genomic data, we show that putative G-quadruplex forming sequences (pG4) in 5’ and 3’ UTRs are selectively constrained, and enriched for cis-eQTLs and RNA-binding protein (RBP) interactions. Using over 15,000 whole-genome sequences, we find that negative selection acting on central guanines of UTR pG4s is comparable to that of missense variation in protein-coding sequences. At multiple GWAS-implicated SNPs within pG4 UTR sequences, we find robust allelic imbalance in gene expression across diverse tissue contexts in GTEx, suggesting that variants affecting G-quadruplex formation within UTRs may also contribute to phenotypic variation. Our results establish UTR G4s as important cis-regulatory elements and point to a link between disruption of UTR pG4 and disease.
Spin Hall effect in prototype Rashba ferroelectrics GeTe and SnTe
Authors: Wang Haihang , Gopal Priya , Picozzi Silvia , Curtarolo Stefano , Buongiorno Nardelli Marco , Sławińska Jagoda 
Published: January 2020

AbstractFerroelectric Rashba semiconductors (FERSCs) have recently emerged as a promising class of spintronics materials. The peculiar coupling between spin and polar degrees of freedom responsible for several exceptional properties, including ferroelectric switching of Rashba spin texture, suggests that the electron’s spin could be controlled by using only electric fields. In this regard, recent experimental studies revealing charge-to-spin interconversion phenomena in two prototypical FERSCs, GeTe and SnTe, appear extremely relevant. Here, by employing density functional theory calculations, we investigate spin Hall effect (SHE) in these materials and show that it can be large either in ferroelectric or paraelectric structure. We further explore the compatibility between doping required for the practical realization of SHE in semiconductors and polar distortions which determine Rashba-related phenomena in FERSCs, but which could be suppressed by free charge carriers. Based on the analysis of the lone pairs which drive ferroelectricity in these materials, we have found that the polar displacements in GeTe can be sustained up to a critical hole concentration of over ~1021/cm3, while the tiny distortions in SnTe vanish at a minimal level of doping. Finally, we have estimated spin Hall angles for doped structures and demonstrated that the spin Hall effect could be indeed achieved in a polar phase. We believe that the confirmation of spin Hall effect, Rashba spin textures and ferroelectricity coexisting in one material will be helpful for design of novel all-in-one spintronics devices operating without magnetic fields.
Land use and cover maps for Mato Grosso State in Brazil from 2001 to 2017
Authors: Simoes Rolf , Picoli Michelle C. A. , Camara Gilberto , Maciel Adeline , Santos Lorena , Andrade Pedro R. , Sánchez Alber , Ferreira Karine , Carvalho Alexandre 
Published: January 2020

AbstractThis paper presents a dataset of yearly land use and land cover classification maps for Mato Grosso State, Brazil, from 2001 to 2017. Mato Grosso is one of the world’s fast moving agricultural frontiers. To ensure multi-year compatibility, the work uses MODIS sensor analysis-ready products and an innovative method that applies machine learning techniques to classify satellite image time series. The maps provide information about crop and pasture expansion over natural vegetation, as well as spatially explicit estimates of increases in agricultural productivity and trade-offs between crop and pasture expansion. Therefore, the dataset provides new and relevant information to understand the impact of environmental policies on the expansion of tropical agriculture in Brazil. Using such results, researchers can make informed assessments of the interplay between production and protection within Amazon, Cerrado, and Pantanal biomes.
Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data
Authors: Kumar Sunil , Lun Xiao-Kang , Bodenmiller Bernd , Rodríguez Martínez María , Koeppl Heinz 
Published: January 2020

AbstractInferring cell-signaling networks from high-throughput data is a challenging problem in systems biology. Recent advances in cytometric technology enable us to measure the abundance of a large number of proteins at the single-cell level across time. Traditional network reconstruction approaches usually consider each time point separately, resulting thus in inferred networks that strongly vary across time. To account for the possibly time-invariant physical couplings within the signaling network, we extend the traditional graphical lasso with an additional regularizer that penalizes network variations over time. ROC evaluation of the method on in silico data showed higher reconstruction accuracy than standard graphical lasso. We also tested our approach on single-cell mass cytometry data of IFNγ-stimulated THP1 cells with 26 phospho-proteins simultaneously measured. Our approach recapitulated known signaling relationships, such as connection within the JAK/STAT pathway, and was further validated in characterizing perturbed signaling network with PI3K, MEK1/2 and AMPK inhibitors.