bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parameter Sensitivity Analysis for Computationally Intensive Spatially Distributed Dynamical Environmental Systems Models
Authors: Huo Xueli , Gupta Hoshin , Niu Guo‐Yue , Gong Wei , Duan Qingyun 
Published: August 2019

AbstractDynamical environmental systems models are highly parameterized, having large numbers of parameters whose values are uncertain. For spatially distributed continental‐scale applications, such models must be run for very large numbers of grid locations. To calibrate such models, it is useful to be able to perform parameter screening, via sensitivity analysis, to identify the most important parameters. However, since this typically requires the models to be run for a large number of sampled parameter combinations, the computational burden can be huge. To make such an investigation computationally feasible, we propose a novel approach to combining spatial sampling with parameter sampling and test it for the Noah‐MP land surface model applied across the continental United States, focusing on gross primary production and flux of latent heat simulations for two vegetation types. Our approach uses (a) progressive Latin hypercube sampling to sample at four grid levels and four parameter levels, (b) a recently developed grouping‐based sensitivity analysis approach that ranks parameters by importance group rather than individually, and (c) a measure of robustness to grid and parameter sampling variability. The results show that a relatively small grid sample size (i.e., 5% of the total grids) and small parameter sample size (i.e., 5 times the number of parameters) are sufficient to identify the most important parameters, with very high robustness to grid sampling variability and a medium level of robustness to parameter sampling variability. The results ensure a dramatic reduction in computational costs for such studies.
Unified Linear Stability Analysis for Thermal Convections in Spherical Shells Under Different Boundary Conditions and Heating Modes
Authors: Yu Hongzheng , Wang Shimin 
Published: August 2019

AbstractLayered interior structure of most planets may be well approximated by spherical shells. An important subject for analyzing planet thermal structure and evolution is to determine the transitional condition from heat conduction dominated mechanism to thermal convection dominated mechanism inside a spherical shell, which can be accomplished through linear stability analysis. In this paper, we propose an analytical solution in terms of Frobenius series to the linear stability analysis that systematically unifies various boundary conditions, heating modes, and shell geometries characterized by inner‐out radius ratio. The analysis is eventually reduced to solving the critical Rayleigh number together with its corresponding spherical harmonic degree from a vanishing determinant of sixth order, and formulas for calculating the elements of the determinant are explicitly provided. The obtained high‐accuracy results clearly show that thermal instability depends strongly on the constraining strength posed by the boundary conditions, heating modes, and shell geometry. The critical Rayleigh number generally decreases with increasing internal heating fraction and inner‐out radius ratio, as well as with switches from fixed to free‐slip or from isothermal to constant heat flux in boundary conditions, whereas remarkable exceptional cases do exist. A thorough analysis is provided to fully explain the general trends and exceptional cases, which uncovers the complicated interplay between shell geometry, heating modes, and boundary conditions, and thus substantially improves our understanding of the underlying physics for thermal convections in spherical shells. Flow streamlines and perturbation temperature distributions for some typical cases of axisymmetric thermal convections are presented as well.
Phaeodaria: An Important Carrier of Particulate Organic Carbon in the Mesopelagic Twilight Zone of the North Pacific Ocean
Authors: Ikenoue Takahito , Kimoto Katsunori , Okazaki Yusuke , Sato Miyako , Honda Makio C. , Takahashi Kozo , Harada Naomi , Fujiki Tetsuichi 
Published: August 2019

AbstractPhaeodaria, which comprise one group of large, single‐celled eukaryotic zooplankton, have been largely ignored by past marine biological studies because Phaeodaria and their delicate skeletons are liable to collapse. As a result, collection and quantification of specimens are difficult, and seasonal changes of phaeodarian abundance have not been thoroughly studied. The transport of biogenic elements by sinking phaeodarians has been estimated for only a few representative species. Sinking particles >1 mm in size and swimmers have traditionally been excluded when estimating sinking particle fluxes. The focus of this study is the large number of phaeodarians among the >1‐mm sinking particles collected in the western North Pacific from June 2014 to July 2015. Careful sorting by microscopic examination and chemical analyses revealed that phaeodarians accounted for up to about 10% of the organic carbon in all sinking particles and accounted for a mean of 33% of the organic carbon in the >1‐mm sinking particles. The high‐standing stocks of phaeodarians at depths of 150–1,000 m in the mesopelagic twilight zone suggested that particles sinking from the euphotic zone as aggregates and fecal pellets can be efficiently exported to the deep sea by the ballasting effect of large phaeodarian particles rich in organic carbon.
Thermohaline Evolution of the Western Mediterranean Deep Waters Since 2005: Diffusive Stages and Interannual Renewal Injections
Authors: Piñeiro S. , González‐Pola C. , Fernández‐Díaz J. M. , Balbin R. 
Published: August 2019

AbstractA large production of anomalous dense water in the northwestern Mediterranean Sea during winter 2005 led to a widespread abrupt shift in Western Mediterranean deep waters characteristics. This new configuration, the so‐called Western Mediterranean Transition (WMT), involved a complex thermohaline structure that was tracked over time through a deep hydrographic station located NE of Minorca Island, sampled 37 times between 2004 and 2017. In this study, the thermohaline evolution of the WMT signal is analyzed in detail. Using a 1‐D diffusion model sensitive to double‐diffusive mixing phenomena, the contribution to the heat and salt budgets of the deep Western Mediterranean in terms of ventilation and diffusive transference from the intermediate layers above is disentangled. Results show distinct stages in the evolution of the deep waters, driven by background diffusion and intermittent injections of new waters. The progression of a multilayered structure in the deep ocean is well represented through existing parameterizations of salt fingering and diffusive layering processes and makes it possible to infer an independent estimate of regional background diffusivity consistent with current knowledge. Overall, the deep layers of the Western Mediterranean underwent substantial warming (0.059 °C) and salt increase (0.021) between 2004 and 2017, mostly dominated by injections of dense waters in the 2005–2006 and 2011–2013 periods. Thus, within the WMT period, heat uptake rate in the deep Western Mediterranean was substantially higher than that of the intermediate levels in the global ocean.
Persistent depressive symptoms, HPA-axis hyperactivity, and inflammation: the role of cognitive-affective and somatic symptoms
Authors: Iob Eleonora , Kirschbaum Clemens , Steptoe Andrew 
Published: August 2019

AbstractHypothalamic-pituitary-adrenal (HPA)-axis hyperactivity and inflammation are thought to be prominent in the aetiology of depression. Although meta-analyses have confirmed this relationship, there is considerable variability in the effect sizes across studies. This could be attributed to a differential role of such biological systems in somatic versus cognitive-affective depressive symptoms which remains largely unexplored. Furthermore, most longitudinal research to date has focused on transient rather than persistent depressive symptoms. In the current study, we investigated the associations of hair cortisol and plasma C-reactive protein (CRP) with the longitudinal persistence and dimensions (cognitive-affective versus somatic) of depressive symptoms over a 14-year period using Trait‐State‐Occasion (TSO) structural equation modelling. The data came from a large sample of older adults from the English Longitudinal Study of Ageing. Depressive symptoms were assessed from wave 1 (2002–03) to wave 8 (2016–17). Hair cortisol (N = 4761) and plasma CRP (N = 5784) were measured in wave 6 (2012–13). Covariates included demographic, socioeconomic, lifestyle, chronic disease, and medication data. Our results revealed that higher cortisol and CRP levels were significantly associated with persistent depressive symptoms across the study period. Notably, both biomarkers exhibited stronger relationships with somatic than with cognitive-affective symptoms. The associations with somatic symptoms were also independent of relevant confounding factors. In contrast, their associations with cognitive-affective symptoms were weak after adjustment for all covariates. These distinct associations reveal the importance of considering symptom-specific effects in future studies on pathophysiological mechanisms. Ultimately, this will have the potential to advance the search for biomarkers of depression and facilitate more targeted treatments.
Divergent engagements between adeno-associated viruses with their cellular receptor AAVR
Authors: Zhang Ran , Xu Guangxue , Cao Lin , Sun Zixian , He Yong , Cui Mengtian , Sun Yuna , Li Shentao , Li Huapeng , Qin Lan , Hu Mingxu , Yuan Zhengjia , Rao Zipei , Ding Wei , Rao Zihe , Lou Zhiyong 
Published: August 2019

AbstractAdeno-associated virus (AAV) receptor (AAVR) is an essential receptor for the entry of multiple AAV serotypes with divergent rules; however, the mechanism remains unclear. Here, we determine the structures of the AAV1-AAVR and AAV5-AAVR complexes, revealing the molecular details by which PKD1 recognizes AAV5 and PKD2 is solely engaged with AAV1. PKD2 lies on the plateau region of the AAV1 capsid. However, the AAV5-AAVR interface is strikingly different, in which PKD1 is bound at the opposite side of the spike of the AAV5 capsid than the PKD2-interacting region of AAV1. Residues in strands F/G and the CD loop of PKD1 interact directly with AAV5, whereas residues in strands B/C/E and the BC loop of PKD2 make contact with AAV1. These findings further the understanding of the distinct mechanisms by which AAVR recognizes various AAV serotypes and provide an example of a single receptor engaging multiple viral serotypes with divergent rules.
Cytoplasmic DAXX drives SQSTM1/p62 phase condensation to activate Nrf2-mediated stress response
Authors: Yang Yi , Willis Thea L. , Button Robert W. , Strang Conor J. , Fu Yuhua , Wen Xue , Grayson Portia R. C. , Evans Tracey , Sipthorpe Rebecca J. , Roberts Sheridan L. , Hu Bing , Zhang Jianke , Lu Boxun , Luo Shouqing 
Published: August 2019

AbstractAutophagy cargo recognition and clearance are essential for intracellular protein quality control. SQSTM1/p62 sequesters intracellular aberrant proteins and mediates cargo delivery for their selective autophagic degradation. The formation of p62 non-membrane-bound liquid compartments is critical for its function as a cargo receptor. The regulation of p62 phase separation/condensation has yet been poorly characterised. Using an unbiased yeast two-hybrid screening and complementary approaches, we found that DAXX physically interacts with p62. Cytoplasmic DAXX promotes p62 puncta formation. We further elucidate that DAXX drives p62 liquid phase condensation by inducing p62 oligomerisation. This effect promotes p62 recruitment of Keap1 and subsequent Nrf2-mediated stress response. The present study suggests a mechanism of p62 phase condensation by a protein interaction, and indicates that DAXX regulates redox homoeostasis, providing a mechanistic insight into the prosurvival function of DAXX.
Structural basis for lamin assembly at the molecular level
Authors: Ahn Jinsook , Jo Inseong , Kang So-mi , Hong Seokho , Kim Suhyeon , Jeong Soyeon , Kim Yong-Hak , Park Bum-Joon , Ha Nam-Chul 
Published: August 2019

AbstractNuclear structure and function are governed by lamins, which are intermediate filaments that mostly consist of α-helices. Different lamin assembly models have been proposed based on low resolution and fragmented structures. However, their assembly mechanisms are still poorly understood at the molecular level. Here, we present the crystal structure of a long human lamin fragment at 3.2 Å resolution that allows the visualization of the features of the full-length protein. The structure shows an anti-parallel arrangement of the two coiled-coil dimers, which is important for the assembly process. We further discover an interaction between the lamin dimers by using chemical cross-linking and mass spectrometry analysis. Based on these two interactions, we propose a molecular mechanism for lamin assembly that is in agreement with a recent model representing the native state and could explain pathological mutations. Our findings also provide the molecular basis for assembly mechanisms of other intermediate filaments.
Three-dimensional solitary waves with electrically tunable direction of propagation in nematics
Authors: Li Bing-Xiang , Xiao Rui-Lin , Paladugu Sathyanarayana , Shiyanovskii Sergij V. , Lavrentovich Oleg D. 
Published: August 2019

AbstractProduction of stable multidimensional solitary waves is a grand challenge in modern science. Steering their propagation is an even harder problem. Here we demonstrate three-dimensional solitary waves in a nematic, trajectories of which can be steered by the electric field in a plane perpendicular to the field. The steering does not modify the properties of the background that remains uniform. These localized waves, called director bullets, are topologically unprotected multidimensional solitons of (3 + 2)D type that show fore-aft and right-left asymmetry with respect to the background molecular director; the symmetry is controlled by the field. Besides adding a whole dimension to the propagation direction and enabling controlled steering, the solitons can lead to applications such as targeted delivery of information and micro-cargo.
Molecular basis of PIP2-dependent regulation of the Ca2+-activated chloride channel TMEM16A
Authors: Le Son C. , Jia Zhiguang , Chen Jianhan , Yang Huanghe 
Published: August 2019

AbstractThe calcium-activated chloride channel (CaCC) TMEM16A plays crucial roles in regulating neuronal excitability, smooth muscle contraction, fluid secretion and gut motility. While opening of TMEM16A requires binding of intracellular Ca2+, prolonged Ca2+-dependent activation results in channel desensitization or rundown, the mechanism of which is unclear. Here we show that phosphatidylinositol (4,5)-bisphosphate (PIP2) regulates TMEM16A channel activation and desensitization via binding to a putative binding site at the cytosolic interface of transmembrane segments (TMs) 3–5. We further demonstrate that the ion-conducting pore of TMEM16A is constituted of two functionally distinct modules: a Ca2+-binding module formed by TMs 6–8 and a PIP2-binding regulatory module formed by TMs 3–5, which mediate channel activation and desensitization, respectively. PIP2dissociation from the regulatory module results in ion-conducting pore collapse and subsequent channel desensitization. Our findings thus provide key insights into the mechanistic understanding of TMEM16 channel gating and lipid-dependent regulation.
Repeated semen exposure decreases cervicovaginal SIVmac251 infection in rhesus macaques
Authors: Abdulhaqq Shaheed A. , Martinez Melween , Kang Guobin , Rodriguez Idia V. , Nichols Stephanie M. , Beaumont David , Joseph Jocelin , Azzoni Livio , Yin Xiangfan , Wise Megan , Weiner David , Liu Qin , Foulkes Andrea , Münch Jan , Kirchhoff Frank , Coutifaris Christos , Tomaras Georgia D. , Sariol Carlos , Marx Preston A. , Li Qingsheng , Kraiselburd Edmundo N. , Montaner Luis J. 
Published: August 2019

AbstractSemen is the vehicle for virion dissemination in the female reproductive tract (FRT) in male-to-female HIV transmission. Recent data suggests that higher frequency semen exposure is associated with activation of anti-HIV mechanisms in HIV negative sex workers. Here, we use a non-human primate (NHP) model to show that repeated vaginal exposure to semen significantly reduces subsequent infection by repeated low-dose vaginal SIVmac251 challenge. Repeated semen exposures result in lower CCR5 expression in circulating CD4+ T-cells, as well as higher expression of Mx1 (in correlation with IFNε expression) and FoxP3 in the cervicovaginal mucosa, and increased infiltration of CD4+ T-cells. Establishing in vivo evidence of competing effects of semen on transmission impacts our basic understanding of what factors may determine HIV infectivity in humans. Our results clearly indicate that repeated semen exposure can profoundly modulate the FRT microenvironment, paradoxically promoting host resistance against HIV acquisition.
Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica
Authors: Martinez-Alonso Emma , Pena-Perez Sonia , Serrano Sandra , Garcia-Lopez Eva , Alcazar Alberto , Cid Cristina 
Published: August 2019

AbstractGlaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of these microbial populations, the type of metabolism and the biogeochemical cycles. Three ecosystems can be differentiated in glaciers: supraglacial, subglacial and englacial ecosystems. Firstly, the supraglacial ecosystem, sunlit and oxygenated, is predominantly populated by photoautotrophic microorganisms. Secondly, the subglacial ecosystem contains a majority of chemoautotrophs that are fed on the mineral salts of the rocks and basal soil. Lastly, the englacial ecosystem is the least studied and the one that contains the smallest number of microorganisms. However, these unknown englacial microorganisms establish a food web and appear to have an active metabolism. In order to study their metabolic potentials, samples of englacial ice were taken from an Antarctic glacier. Microorganisms were analyzed by a polyphasic approach that combines a set of -omic techniques: 16S rRNA sequencing, culturomics and metaproteomics. This combination provides key information about diversity and functions of microbial populations, especially in rare habitats. Several whole essential proteins and enzymes related to metabolism and energy production, recombination and translation were found that demonstrate the existence of cellular activity at subzero temperatures. In this way it is shown that the englacial microorganisms are not quiescent, but that they maintain an active metabolism and play an important role in the glacial microbial community.
Long-term Management Effects and Temperature Sensitivity of Soil Organic Carbon in Grassland and Agricultural Soils
Authors: Ghimire Rajan , Bista Prakriti , Machado Stephen 
Published: August 2019

AbstractSoil organic carbon (SOC) is integral to soil health and agroecosystem resilience. Despite much research, understanding of temperature sensitivity of SOC under long-term agricultural management is very limited. The main objective of this study was to evaluate SOC and nitrogen (N) dynamics under grasslands and winter wheat (Triticum aestivum L)-based crop rotations in the inland Pacific Northwest (IPNW), USA, and measure SOC mineralization under ambient and elevated incubation temperatures. Soil samples were collected from 0–10 and 10–20 cm depths from an undisturbed grassland (GP), winter wheat-pea (Pisum sativum L) rotations under conventional tillage (WP-CT) and no-tillage (WP-NT), and winter wheat-fallow rotation under conventional tillage (WF-CT) and analyzed for SOC and N pools. Soil samples were incubated at 20 °C and 30 °C for 10 weeks, and SOC mineralization rates were estimated using the first order kinetic model. The GP had the greatest amounts of SOC, total N (TN), and microbial biomass carbon (MBC) and WP rotations had higher inorganic N content than other treatments. The SOC mineralization at elevated incubation temperature was 72–177% more than at the ambient temperature, and the greatest effect was observed in GP. The SOC storage under a given management did not have consistent effects on soil carbon (C) and N mineralization under elevated temperature. However, soil disturbance under WP-CT and WF-CT accelerated SOC mineralization leading to soil C loss. Reducing tillage, integrating legumes into crop rotations, and growing perennial grasses could minimize SOC loss and have the potential to improve soil health and agroecosystem resilience under projected climate warming.
BTLA suppress acute rejection via regulating TCR downstream signals and cytokines production in kidney transplantation and prolonged allografts survival
Authors: Zhang Jiayi , Zhang Hengcheng , Wang Zijie , Yang Haiwei , Chen Hao , Cheng Hong , Zhou Jiajun , Zheng Ming , Tan Ruoyun , Gu Min 
Published: August 2019

AbstractAcute rejection is a major risk for renal transplant failure. During this adverse process, activated T cells are considered the main effectors. Recently, B and T lymphocyte attenuator (BTLA), a member of the CD28 family receptor, was reported to be a novel inhibitory regulator of T cell activation in heart and pancreatic allograft rejection. Due to the similarity of acute rejection pathways among different organs, we hypothesized that BTLA might play a role in acute rejection of kidney transplant. In renal transplant patients, we observed that BTLA expression was significantly decreased in peripheral CD3+ T lymphocytes of biopsy-proven acute rejection (BPAR) recipients compared with control patients with stable transplanted kidney functions. Remarkably, overexpression of BTLA in the rat model was found to significantly inhibit the process of acute rejection, regulate the postoperative immune status, and prolong allograft survival. BTLA overexpression significantly suppressed IL-2 and IFN-γ production and increased IL-4 and IL-10 production both in vivo and in vitro. Moreover, vital factors in T-cell signaling pathways, including mitogen-associated protein kinases (MAPK), nuclear factor-kappa B (NF-κB) and nuclear factor of activated T cells (NFAT), were also significantly repressed by BTLA overexpression. Therefore, BTLA can suppress acute rejection and regulate allogeneic responses of kidney transplant by regulating TCR downstream signals and inflammatory cytokines production to improve allografts outcomes.