bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermal, Moisture, and Solute Transport Responses Effects on Unsaturated Soil Hydraulic Parameters Estimation
Authors: Lemoubou Ernest Léontin , Tagne Kamdem Hervé Thierry , Bogning Jean Roger , Zefack Tonnang Edouard Henri 
Published: December 2019

AbstractThis paper studies the estimation of unsaturated soil parameters based on thermal, moisture, and solute characteristics, which are important factors that affect productivity and the environment. The objective of this investigation was to determine optimal hydraulic parameters in unsaturated soil. The soil thermal, moisture, and solute transport processes are approached using one‐dimensional isothermal models characterized with nonlinear permeability effects, sorption, and reaction that generally cause considerable experimental and numerical difficulties. The spectral element method is presented for space discretization while the time scheme is constructed along the fully implicit approach with the modified Picard iterative procedure. The iterative Levenberg‐Marquardt optimization algorithm is adopted for the inverse process. The reliability and performance of the studied model is conducted using refinement indicators based on error, residual, and variance analyses, which allow drawing more representative uncertainty of model parameters estimation. Good agreement with the nonlinear optimization of soil hydraulic parameters estimated and true values is obtained. The estimated responses from respective shape curves show relatively small variability. A consideration of ionic diffusional and average temperature effects was revealed, indicating that the change of one of these factors might not necessarily improve parameter identification responses. For soil moisture content ranges between 0.04 and 0.5 cm3 cm−3, average temperature input from 20 to 40 ° C as well as when the ionic molecular diffusion coefficient is greater than 10 cm2 hr−1, a rough representation of moisture, thermal, and hydrochemical characteristics might be sufficient to estimate soil hydraulic parameters.
Hydrological Spaces of Long‐Term Catchment Water Balance
Authors: Daly Edoardo , Calabrese Salvatore , Yin Jun , Porporato Amilcare 
Published: December 2019

AbstractLand and water management often relies upon relationships describing the catchment‐scale water balance using only a few parameters. The classic Budyko and Turc frameworks are examples of these relationships applicable to large catchments, where the effect of climatic variables on the water balance overshadows that of catchment characteristics, including the catchment ability to store water to supply evapotranspiration. To account for the latter in the list of variables driving evapotranspiration, here we introduce a new framework that includes Budyko and Turc as particular cases. The four variables in this framework are combined to form dimensionless groups, the choice of which leads to the definition of hydrological spaces highlighting different features of the long‐term hydrological partitioning. In addition to the Budyko and Turc spaces, suitable for water‐ and energy‐limited catchments, respectively, a new space ensues; this is especially apt to describe catchments where evapotranspiration is mainly controlled by catchment characteristics. An existing stochastic model for the soil water balance is used to specify the relationship between the variables in these different hydrological spaces. This framework, successfully tested here against about 400 catchments in the continental United States, provides a concise yet realistic description of long‐term catchment‐scale water balance and overcomes some limitations of current models for the estimation of long‐term evapotranspiration and runoff in ungauged catchments.
Stochastic Analysis of the Soil Water Content Standard Deviation‐Mean Value Relationships: On the Physical Significance of the Critical Mean Soil Water Content
Authors: Russo David 
Published: December 2019

AbstractThe spatial heterogeneity in the soil hydraulic properties was considered here as the main cause of the spatial variability in soil water content, θ. The aim of the study was (i) to identify the critical mean soil water content, Θcr, below which the standard deviation of the soil water content, σθ, can only diminish, and (ii) to provide a mathematical tool capable of linking Θcr to inherent soil hydraulic properties. The relationships between σθ and the mean value of θ, Θ, were analyzed by a first‐order analysis, based on a stochastic continuum presentation of steady‐state flow in 3‐D, spatially hetrogeneous, unsaturated soils, using the Gardner‐Russo model to describe the constitutive relations locally. Novel results of the study suggested that the mean pressure head, H, associated with Θcr, Hcr = H (Θcr), is an inflection point of the mean soil water capacity function, C(H) = dΘ/dH. Results of numerical simulations of flow in 3‐D, spatially heterogeneous, unsaturated soils, using the van Genuchten (1980, https://doi.org/10.2136/sssaj1980.03615995004400050002x) model to describe the constitutive relations locally, suggested that the results of the first‐order analysis might be applicable to more realistic situations, involving transient, nonmonotonous flows and more complicated descriptions of the local constitutive relations.
Intracellular sensing of viral genomes and viral evasion
Authors: Lee Hyun-Cheol , Chathuranga Kiramage , Lee Jong-Soo 
Published: December 2019

AbstractDuring viral infection, virus-derived cytosolic nucleic acids are recognized by host intracellular specific sensors. The efficacy of this recognition system is crucial for triggering innate host defenses, which then stimulate more specific adaptive immune responses against the virus. Recent studies show that signal transduction pathways activated by sensing proteins are positively or negatively regulated by many modulators to maintain host immune homeostasis. However, viruses have evolved several strategies to counteract/evade host immune reactions. These systems involve viral proteins that interact with host sensor proteins and prevent them from detecting the viral genome or from initiating immune signaling. In this review, we discuss key regulators of cytosolic sensor proteins and viral proteins based on experimental evidence.
Monkeys mutant for PKD1 recapitulate human autosomal dominant polycystic kidney disease
Authors: Tsukiyama Tomoyuki , Kobayashi Kenichi , Nakaya Masataka , Iwatani Chizuru , Seita Yasunari , Tsuchiya Hideaki , Matsushita Jun , Kitajima Kahoru , Kawamoto Ikuo , Nakagawa Takahiro , Fukuda Koji , Iwakiri Teppei , Izumi Hiroyuki , Itagaki Iori , Kume Shinji , Maegawa Hiroshi , Nishinakamura Ryuichi , Nishio Saori , Nakamura Shinichiro , Kawauchi Akihiro , Ema Masatsugu 
Published: December 2019

AbstractAutosomal dominant polycystic kidney disease (ADPKD) caused by PKD1 mutations is one of the most common hereditary disorders. However, the key pathological processes underlying cyst development and exacerbation in pre-symptomatic stages remain unknown, because rodent models do not recapitulate critical disease phenotypes, including disease onset in heterozygotes. Here, using CRISPR/Cas9, we generate ADPKD models with PKD1 mutations in cynomolgus monkeys. As in humans and mice, near-complete PKD1 depletion induces severe cyst formation mainly in collecting ducts. Importantly, unlike in mice, PKD1 heterozygote monkeys exhibit cyst formation perinatally in distal tubules, possibly reflecting the initial pathology in humans. Many monkeys in these models survive after cyst formation, and cysts progress with age. Furthermore, we succeed in generating selective heterozygous mutations using allele-specific targeting. We propose that our models elucidate the onset and progression of ADPKD, which will serve as a critical basis for establishing new therapeutic strategies, including drug treatments.
Normalization governs attentional modulation within human visual cortex
Authors: Bloem Ilona M. , Ling Sam 
Published: December 2019

AbstractAlthough attention is known to increase the gain of visuocortical responses, its underlying neural computations remain unclear. Here, we use fMRI to test the hypothesis that a neural population’s ability to be modulated by attention is dependent on divisive normalization. To do so, we leverage the feature-tuned properties of normalization and find that visuocortical responses to stimuli sharing features normalize each other more strongly. Comparing these normalization measures to measures of attentional modulation, we demonstrate that subpopulations which exhibit stronger normalization also exhibit larger attentional benefits. In a converging experiment, we reveal that attentional benefits are greatest when a subpopulation is forced into a state of stronger normalization. Taken together, these results suggest that the degree to which a subpopulation exhibits normalization plays a role in dictating its potential for attentional benefits.
Giant single molecule chemistry events observed from a tetrachloroaurate(III) embedded Mycobacterium smegmatis porin A nanopore
Authors: Cao Jiao , Jia Wendong , Zhang Jinyue , Xu Xiumei , Yan Shuanghong , Wang Yuqin , Zhang Panke , Chen Hong-Yuan , Huang Shuo 
Published: December 2019

AbstractBiological nanopores are capable of resolving small analytes down to a monoatomic ion. In this research, tetrachloroaurate(III), a polyatomic ion, is discovered to bind to the methionine residue (M113) of a wild-type α-hemolysin by reversible Au(III)-thioether coordination. However, the cylindrical pore geometry of α-hemolysin generates shallow ionic binding events (~5–6 pA) and may have introduced other undesired interactions. Inspired by nanopore sequencing, a Mycobacterium smegmatis porin A (MspA) nanopore, which possesses a conical pore geometry, is mutated to bind tetrachloroaurate(III). Subsequently, further amplified blockage events (up to ~55 pA) are observed, which report the largest single ion binding event from a nanopore measurement. By taking the embedded Au(III) as an atomic bridge, the MspA nanopore is enabled to discriminate between different biothiols from single molecule readouts. These phenomena suggest that MspA is advantageous for single molecule chemistry investigations and has applications as a hybrid biological nanopore with atomic adaptors.
Palladium-bearing intermetallic electride as an efficient and stable catalyst for Suzuki cross-coupling reactions
Authors: Ye Tian-Nan , Lu Yangfan , Xiao Zewen , Li Jiang , Nakao Takuya , Abe Hitoshi , Niwa Yasuhiro , Kitano Masaaki , Tada Tomofumi , Hosono Hideo 
Published: December 2019

AbstractSuzuki cross-coupling reactions catalyzed by palladium are powerful tools for the synthesis of functional organic compounds. Excellent catalytic activity and stability require negatively charged Pd species and the avoidance of metal leaching or clustering in a heterogeneous system. Here we report a Pd-based electride material, Y3Pd2, in which active Pd atoms are incorporated in a lattice together with Y. As evidenced from detailed characterization and density functional theory (DFT) calculations, Y3Pd2 realizes negatively charged Pd species, a low work function and a high carrier density, which are expected to be beneficial for the efficient Suzuki coupling reaction of activated aryl halides with various coupling partners under mild conditions. The catalytic activity of Y3Pd2 is ten times higher than that of pure Pd and the activation energy is lower by nearly 35%. The Y3Pd2 intermetallic electride catalyst also exhibited extremely good catalytic stability during long-term coupling reactions.
Probable basal allosauroid from the early Middle Jurassic Cañadón Asfalto Formation of Argentina highlights phylogenetic uncertainty in tetanuran theropod dinosaurs
Authors: Rauhut Oliver W. M. , Pol Diego 
Published: December 2019

AbstractTetanurae, the most successful clade of theropod dinosaurs, including modern birds, split into three major clades early in their evolutionary history: Megalosauroidea, Coelurosauria, and Allosauroidea. The oldest tetanurans occur in the earliest Middle Jurassic, but the early fossil record of the clade is still poor. Here we report one of the oldest known and most complete pre-Late Jurassic tetanuran, the probable allosauroid Asfaltovenator vialidadi gen. et sp. nov., which has an unusual character combination, uniting features currently considered to be apomorphic of different tetanuran lineages. A phylogenetic analysis resulted in a monophyletic Carnosauria (Allosauroidea + Megalosauroidea), and the inclusion of the new taxon significantly changes topology within carnosaurs. The analysis shows concentrated homoplasy in proximal nodes at the base of Tetanurae, and a temporal peak at the Pliensbachian-Toarcian extinction event, recently identified as a potential driver of tetanuran radiation. These results highlight the complex morphological evolution in the early radiation of tetanuran theropods, in which convergences and parallelisms were extremely common. This pattern seems to be a common feature in rapid radiation events of major clades of vertebrates and might explain the common difficulties to unravel phylogenetic relationships of important lineages at the base of major clades.
The green peach aphid gut contains host plant microRNAs identified by comprehensive annotation of Brassica oleracea small RNA data
Authors: Thompson Max C. , Feng Honglin , Wuchty Stefan , Wilson Alex C. C. 
Published: December 2019

AbstractLike all organisms, aphids, plant sap-sucking insects that house a bacterial endosymbiont called Buchnera, are members of a species interaction network. Ecological interactions across such networks can result in phenotypic change in network members mediated by molecular signals, like microRNAs. Here, we interrogated small RNA data from the aphid, Myzus persicae, to determine the source of reads that did not map to the aphid or Buchnera genomes. Our analysis revealed that the pattern was largely explained by reads that mapped to the host plant, Brassica oleracea, and a facultative symbiont, Regiella. To start elucidating the function of plant small RNA in aphid gut, we annotated 213 unique B. oleracea miRNAs; 32/213 were present in aphid gut as mature and star miRNAs. Next, we predicted targets in the B. oleracea and M. persicae genomes for these 32 plant miRNAs. We found that plant targets were enriched for genes associated with transcription, while the distribution of targets in the aphid genome was similar to the functional distribution of all genes in the aphid genome. We discuss the potential of plant miRNAs to regulate aphid gene expression and the mechanisms involved in processing, export and uptake of plant miRNAs by aphids.
Biomechanical investigation of extragraft bone formation influences on the operated motion segment after anterior cervical spinal discectomy and fusion
Authors: Park Won Man , Jin Yong Jun 
Published: December 2019

AbstractAlthough the clinical importance of extragraft bone formation (ExGBF) and bridging (ExGBB) has been reported, few studies have investigated the biomechanical influences of ExGBF on the motion segment. In this study, ExGBF was simulated at the C5-C6 motion segment after anterior cervical discectomy and fusion using a developed finite element model and a sequential bone-remodelling algorithm in flexion and extension. The computer simulation results showed that extragraft bone was primarily formed in the extension motion and grew to form ExGBB. A stepwise decrease in the intersegmental rotation angle, maximum von Mises stress and strain energy density on the trabecular bone with ExGBF were predicted in extension. When ExGBB was formed in the trabecular bone region, the intersegmental rotation angle slightly decreased with additional bone formation. However, the stress and strain energy density on the trabecular bone region decreased until ExGBB reached the peripheral cortical margin. The results offer a rationale supporting the hypothesis that mechanical stimuli influence ExGBF. ExGBF was helpful in increasing the stability of the motion segment and decreasing the fracture risk of trabecular bones, even in cases in which ExGBB was not formed. ExGBB can be classified as either soft or hard bridging based on a biomechanical point of view.
Improving the odds of drug development success through human genomics: modelling study
Authors: Hingorani Aroon D. , Kuan Valerie , Finan Chris , Kruger Felix A. , Gaulton Anna , Chopade Sandesh , Sofat Reecha , MacAllister Raymond J. , Overington John P. , Hemingway Harry , Denaxas Spiros , Prieto David , Casas Juan Pablo 
Published: December 2019

AbstractLack of efficacy in the intended disease indication is the major cause of clinical phase drug development failure. Explanations could include the poor external validity of pre-clinical (cell, tissue, and animal) models of human disease and the high false discovery rate (FDR) in preclinical science. FDR is related to the proportion of true relationships available for discovery (γ), and the type 1 (false-positive) and type 2 (false negative) error rates of the experiments designed to uncover them. We estimated the FDR in preclinical science, its effect on drug development success rates, and improvements expected from use of human genomics rather than preclinical studies as the primary source of evidence for drug target identification. Calculations were based on a sample space defined by all human diseases – the ‘disease-ome’ – represented as columns; and all protein coding genes – ‘the protein-coding genome’– represented as rows, producing a matrix of unique gene- (or protein-) disease pairings. We parameterised the space based on 10,000 diseases, 20,000 protein-coding genes, 100 causal genes per disease and 4000 genes encoding druggable targets, examining the effect of varying the parameters and a range of underlying assumptions, on the inferences drawn. We estimated γ, defined mathematical relationships between preclinical FDR and drug development success rates, and estimated improvements in success rates based on human genomics (rather than orthodox preclinical studies). Around one in every 200 protein-disease pairings was estimated to be causal (γ = 0.005) giving an FDR in preclinical research of 92.6%, which likely makes a major contribution to the reported drug development failure rate of 96%. Observed success rate was only slightly greater than expected for a random pick from the sample space. Values for γ back-calculated from reported preclinical and clinical drug development success rates were also close to the a priori estimates. Substituting genome wide (or druggable genome wide) association studies for preclinical studies as the major information source for drug target identification was estimated to reverse the probability of late stage failure because of the more stringent type 1 error rate employed and the ability to interrogate every potential druggable target in the same experiment. Genetic studies conducted at much larger scale, with greater resolution of disease end-points, e.g. by connecting genomics and electronic health record data within healthcare systems has the potential to produce radical improvement in drug development success rate.
Host phylogeny, diet, and habitat differentiate the gut microbiomes of Darwin’s finches on Santa Cruz Island
Authors: Loo Wesley T. , García-Loor Jefferson , Dudaniec Rachael Y. , Kleindorfer Sonia , Cavanaugh Colleen M. 
Published: December 2019

AbstractDarwin’s finches are an iconic example of an adaptive radiation with well-characterized evolutionary history, dietary preferences, and biogeography, offering an unparalleled opportunity to disentangle effects of evolutionary history on host microbiome from other factors like diet and habitat. Here, we characterize the gut microbiome in Darwin’s finches, comparing nine species that occupy diverse ecological niches on Santa Cruz island. The finch phylogeny showed moderate congruence with the microbiome, which was comprised mostly of the bacterial phyla Firmicutes, Actinobacteria, and Proteobacteria. Diet, as measured with stable isotope values and foraging observations, also correlated with microbiome differentiation. Additionally, each gut microbial community could easily be classified by the habitat of origin independent of host species. Altogether, these findings are consistent with a model of microbiome assembly in which environmental filtering via diet and habitat are primary determinants of the bacterial taxa present with lesser influence from the evolutionary history between finch species.
Fingerprints of slingshot non-sequential double ionization on two-electron probability distributions
Authors: Katsoulis G. P. , Emmanouilidou A. 
Published: December 2019

AbstractWe study double ionization of He driven by near-single-cycle laser pulses at low intensities at 400 nm. Using a three-dimensional semiclassical model, we identify the pathways that prevail non-sequential double ionization (NSDI). We focus mostly on the delayed pathway, where one electron ionizes with a time-delay after recollision. We have recently shown that the mechanism that prevails the delayed pathway depends on intensity. For low intensities slingshot-NSDI is the dominant mechanism. Here, we identify the differences in two-electron probability distributions of the prevailing NSDI pathways. This allows us to identify properties of the two-electron escape and thus gain significant insight into slingshot-NSDI. Interestingly, we find that an observable fingerpint of slingshot-NSDI is the two electrons escaping with large and roughly equal energies.
Association of circulating miR-20a, miR-27a, and miR-126 with non-alcoholic fatty liver disease in general population
Authors: Ando Yoshitaka , Yamazaki Mirai , Yamada Hiroya , Munetsuna Eiji , Fujii Ryosuke , Mizuno Genki , Ichino Naohiro , Osakabe Keisuke , Sugimoto Keiko , Ishikawa Hiroaki , Ohashi Koji , Teradaira Ryoji , Ohta Yoshiji , Hamajima Nobuyuki , Hashimoto Shuji , Suzuki Koji 
Published: December 2019

AbstractNon-alcoholic fatty liver disease (NAFLD) is closely associated with obesity, metabolic syndrome, and type II diabetes mellitus. Recently, circulating microRNAs (miRNAs) have been proposed as useful disease biomarkers. We examined whether circulating miRNAs, such as miR-20a, miR-27a, and miR-126, were useful biomarkers for NAFLD. We conducted a cross-sectional analysis of 527 subjects aged 39 years or older who had undergone a health examination in the Yakumo Study. Of the residents, 92 were diagnosed with NAFLD using a registered medical sonographer. Serum miR-20a, miR-27a and miR-126 levels were measured by quantitative real-time PCR. We then calculated the odds ratios for serum miRNA level changes according to the severity of NAFLD using normal liver status as the reference group. Serum levels of miR-20a and 27a, but not miR-126, were significantly lower in NAFLD subjects than normal subjects. Serum miR-20a and miR-27a levels were significantly lower in both male and female severe NAFLD subjects. Logistic regression analysis showed a significant relationship between low circulating miR-20a and 27a levels and severe NAFLD. Down-regulated circulating miR-20a and 27a levels were significantly associated with severe NAFLD in the general population. Circulating miR-20a and miR-27a may be useful biomarkers for severe NAFLD.