Miracle-dz/UniFAR-FTUs huggingface dataset:
Type I Phosphatidylinositol Phosphate Kinase Beta Regulates Focal Adhesion Disassembly by Promoting (cid:1) 1 Integrin Endocytosis (cid:1)

Cell migration requires the regulated disassembly of focal adhesions, but the underlying mechanisms remain poorly deﬁned. We have previously shown that focal adhesion disassembly requires the dynamin 2- and clathrin-dependent endocytosis of ligand-activated (cid:1) 1 integrins. Here, we identify type I phosphatidylinositol phosphate kinase beta (PIPKI (cid:1) ), an enzyme that generates phosphatidylinositol-4,5-bisphosphate (PI4,5P 2 ), as a key regulator of this process. We found that knockdown of PIPKI (cid:1) by RNA interference blocks the internalization of active (cid:1) 1 integrins and impairs focal adhesion turnover and cell migration. These defects are caused by the failure to target the endocytic machinery, including clathrin adaptors and dynamin 2, to focal adhesion sites. As a consequence, depletion of PIPKI (cid:1) blocks clathrin assembly at adhesion plaques and prevents complex formation between dynamin 2 and focal adhesion kinase (FAK), a critical step in focal adhesion turnover. Together, our ﬁndings identify PIPKI (cid:1)
Transethnic genome-wide scan identifies novel Alzheimer disease loci

BACKGROUND— Genetic loci for Alzheimer disease (AD) have been identified in whites of European ancestry, but the genetic architecture of AD among other populations is less understood. METHODS— We conducted a transethnic genome-wide association study (GWAS) for late-onset AD in Stage 1 sample including whites of European Ancestry, African Americans, Japanese, and Israeli-Arabs assembled by the Alzheimer’s Disease Genetics Consortium (ADGC). Suggestive results from Stage 1 from novel loci were followed up using summarized results in the International Genomics Alzheimer’s Project (IGAP) GWAS dataset. RESULTS— Genome-wide significant (GWS) associations in SNP-based tests (P<5×10 −8 ) were identified for SNPs in PFDN1/HBEGF, USP6NL/ECHDC3, and BZRAP1-AS1, and for the interaction of the APOE ε 4 allele with NFIC SNP. We also obtained GWS evidence (P<2.7×10 −6 ) for gene-based association in the total sample with a novel locus, TPBG (P=1.8×10 −6 ). DISCUSSION— Our findings highlight the value of transethnic studies for identifying novel AD susceptibility loci.
Modeled reconstructions of the oceanic carbonate system for different histories of atmospheric carbon dioxide during the last 20 Ma

A box model was used to estimate oceanic carbonate system parameters (total dissolved inorganic carbon, alkalinity, CO2(aq), CO32−, HCO3−, and pH) in the surface and deep ocean over the past 20 Ma. Geological data were used to constrain boundary conditions, including the carbonate compensation depth (CCD) and seawater temperature, salinity, and ionic composition. In addition, ∼14,000 δ13C measurements of planktic and benthic foraminifera were compiled. Sensitivity tests were performed to evaluate potential errors arising from uncertainties in model boundary conditions. Values of surface water pH were modeled assuming four different histories of atmospheric CO2, and compared with proxy‐based estimates of pH. The system is underconstrained, and therefore multiple CO2 histories can be invoked to explain the same pH trend, depending on the assumptions made regarding ocean overturning and biological productivity. Despite this uncertainty, we conclude that if CO2 was strongly coupled to temperature and ice volume over the last 20 Ma, predicted values of surface ocean pH fit poorly with current proxy‐based pH reconstructions.
Quantitative imaging of rhizosphere pH and CO2 dynamics with planar optodes.

BACKGROUND AND AIMS Live imaging methods have become extremely important for the exploration of biological processes. In particular, non-invasive measurement techniques are key to unravelling organism-environment interactions in close-to-natural set-ups, e.g. in the highly heterogeneous and difficult-to-probe environment of plant roots: the rhizosphere. pH and CO2 concentration are the main drivers of rhizosphere processes. Being able to monitor these parameters at high spatio-temporal resolution is of utmost importance for relevant interpretation of the underlying processes, especially in the complex environment of non-sterile plant-soil systems. This study introduces the application of easy-to-use planar optode systems in different set-ups to quantify plant root-soil interactions. METHODS pH- and recently developed CO2-sensors were applied to rhizobox systems to investigate roots with different functional traits, highlighting the potential of these tools. Continuous and highly resolved real-time measurements were made of the pH dynamics around Triticum turgidum durum (durum wheat) roots, Cicer arietinum (chickpea) roots and nodules, and CO2 dynamics in the rhizosphere of Viminaria juncea. KEY RESULTS Wheat root tips acidified slightly, while their root hair zone alkalized their rhizosphere by more than 1 pH unit and the effect of irrigation on soil pH could be visualized as well. Chickpea roots and nodules acidified the surrounding soil during N2 fixation and showed diurnal changes in acidification activity. A growing root of V. juncea exhibited a large zone of influence (mm) on soil CO2 content and therefore on its biogeochemical surrounding, all contributing to the extreme complexity of the root-soil interactions. CONCLUSIONS This technique provides a unique tool for future root research applications and overcomes limitations of previous systems by creating quantitative maps without, for example, interpolation and time delays between single data points.
Results of a phase I pilot clinical trial examining the effect of plant-derived resveratrol and grape powder on Wnt pathway target gene expression in colonic mucosa and colon cancer

Context: Resveratrol exhibits colon cancer prevention activity in animal models; it is purported to have this activity in humans and inhibit a key signaling pathway involved in colon cancer initiation, the Wnt pathway, in vitro . Design: A phase I pilot study in patients with colon cancer was performed to evaluate the effects of a low dose of plant-derived resveratrol formulation and resveratrol-containing freeze-dried grape powder (GP) on Wnt signaling in the colon. Eight patients were enrolled and normal colonic mucosa and colon cancer tissue were evaluated by Wnt pathway-speciﬁ c microarray and quantitative real-time polymerase chain reaction (qRT-PCR) pre- and post-exposure to resveratrol/GP. Results: Based on the expression of a panel of Wnt target genes, resveratrol/GP did not inhibit the Wnt pathway in colon cancer but had signiﬁ cant (p (cid:2) 0.03) activity in inhibiting Wnt target gene expression in normal colonic mucosa. The greatest effect on Wnt target gene expression was seen following ingestion of 80 g of GP per day (p (cid:2) 0.001). These results were conﬁ rmed with qRT-PCR of cyclinD1 and axinII . The inhibitory effect of GP on Wnt signal throughput was conﬁ rmed in vitro with a normal colonic mucosa-derived cell line. Conclusions: These data suggest that GP, which contains low dosages of resveratrol in combination with other bioactive components, can inhibit the Wnt pathway in vivo and that this effect is conﬁ ned to the normal colonic mucosa. Further study of dietary supplementation with resveratrol-containing foods such as whole grapes or GP as a potential colon cancer preventive strategy is warranted.
The Asian 'Noodle Bowl': Is it Serious for Business

A lively debate is taking place over the impact of free trade agreements (FTAs) on East Asia's business between those who view the agreements as a harmful Asian "noodle bowl"â€”i.e., overlapping regional trade agreementsâ€”of trade deals and others who see net beneficial effects in terms of regional liberalization and a building block to multilateral liberalization. A lack of enterprise-level data has made it difficult to resolve the debate. Providing new evidence from surveys of 609 East Asian firms (in Japan, Singapore, Republic of Korea [hereafter Korea], Thailand, and Philippines), this paper seeks to address the critical question of whether the Asian noodle bowl of multiple overlapping FTAs is harmful to business activity, particularly for small- and medium-sized enterprises (SMEs). [ADBI WP NO 136]
Lidar observations of thermospheric Na layers up to 170 km with a descending tidal phase at Lijiang (26.7°N, 100.0°E), China

We report the first lidar observations of thermospheric Na layers up to 170 km at Lijiang (geomagnetic 21.6°N, 171.8°E), China, in March, April, and December 2012. The Na densities inside the layers are low, ranging from ~1 to ~6 cm−3 at altitudes of 130–170 km, about 3 orders of magnitude lower than the Na peak density in the mesopause region. All of these layers exhibit an apparent downward phase progression with a descending rate of 11–12 km/h or ~3 m/s, consistent with the vertical phase speed of semidiurnal tides around 140 km. We have identified at least 12 events from the total 37 nights of lidar observations with four shown in this report, giving an occurrence frequency of ~33% over Lijiang. These thermospheric layer events correspond to strong to moderate equatorial fountain effects, bolstering our hypothesis that the deposit of metallic ions from the equatorial region to low latitudes via the fountain effect provides the Na+ ions in the thermosphere over Lijiang. Adopting the theory by Chu et al. (2011) and the hypothesis by Tsuda et al. (2015), we further hypothesize that the thermospheric Na layers are formed through the neutralization of the tidal‐wind‐shear‐converged Na+ layers via direct electron‐Na+ recombination Na+ + e− → Na + hν. An envelope calculation using reasonable ion and electron densities shows good consistency with the observations.
Genetic studies of autoimmunity and retrovirus expression in crosses of New Zealand black mice I. Xenotropic virus

The relationship between expression of xenotropic virus and the development of autoimmunization was studied in the progeny of crosses between New Zealand Black (NZB) and SWR mice. The (F1 X SWR) and F2 progeny segregated into three phenotypes: high-virus, low-virus, and virus-negative; F1 and (F1 X NZB) progeny were always high-virus. Autoantibodies, immune deposit nephritis and lymphomas developed in the progeny of these crosses. The virological phenotype of the animal could be dissociated from the presence of either autoantibodies or nephritis. For example, mice that expressed titers of virus as high as the NZB parent failed to develop signs of autoimmunization, even up to 24 mo of age. By contrast, some (F1 X SWR) and F2 mice that expressed low titers of virus developed autoimmune disease. Furthermore, a proportion of virus-negative mice produced autoantibodies and were found to have typical immune deposit nephritis. No viral antigens could be detected in the renal lesions of such virus-negative animals. By contrast with the dissociation between expression of virus and occurrence of nephritis, the presence of antibodies to DNA correlated with the development of renal lesions. We conclude that the genes that determine the expression of infectious xenotropic virus in NZB mice segregate independently from those that are involved in the autoimmune disease of these animals.
Lane Detection in Complex Environment Using Grid-Based Morphology and Directional Edge-link Pairs

This paper presents a real-time lane detection method which can accurately find the lane-mark boundaries in complex road environment. Unlike many existing methods that pay much attention on the post-processing stage to fit lane-mark position among a great deal of outliers, the proposed method aims at removing those outliers as much as possible at feature extraction stage, so that the searching space at post-processing stage can be greatly reduced. To achieve this goal, a grid-based morphology operation is firstly used to generate the regions of interest (ROI) dynamically, in which a directional edge-linking algorithm with directional edge-gap closing is proposed to link edge-pixels into edge-links which lie in the valid directions, these directional edge-links are then grouped into pairs by checking the valid lane-mark width at certain height of the image. Finally, lane-mark colors are checked inside edge-link pairs in the YUV color space, and lane-mark types are estimated employing a Bayesian probability model. Experimental results show that the proposed method is effective in identifying lane-mark edges among heavy clutter edges in complex road environment, and the whole algorithm can achieve an accuracy rate around 92% at an average speed of 10ms/frame at the image size of .
Role of methane and biogenic volatile organic compound sources in late glacial and Holocene fluctuations of atmospheric methane concentrations

Recent analyses of ice core methane concentrations suggested that methane emissions from wetlands were the primary driver for prehistoric changes in atmospheric methane. However, these interpretations conflict as to the location of wetlands, magnitude of emissions, and the environmental controls on methane oxidation. The flux of other reactive trace gases to the atmosphere also controls apparent atmospheric methane concentrations because these compounds compete for the hydroxyl radical (OH), which is the primary atmospheric sink for methane. In a series of linked biosphere‐atmosphere chemistry‐climate modeling experiments, we simulate the methane and biogenic volatile organic compound emissions from the terrestrial biosphere from the Last Glacial Maximum (LGM) to the present. Using a state‐of‐the‐art chemistry‐climate model, we simulate the atmospheric concentrations of methane, OH, and other reactive trace gas species. Over the past 21,000 years, methane emissions from wetlands increased slightly to the end of the Pleistocene but then decreased again, reaching levels at the preindustrial Holocene that were similar to the LGM. Global wetland area decreased by 14% from LGM to the preindustrial time. Emissions of biogenic volatile organic compounds (BVOCs), however, nearly doubled over the same period of time. Atmospheric OH burdens and methane concentrations were affected by this major change in BVOC emissions, with methane lifetimes increasing by more than 2 years from LGM to the present. We simulate a change in methane concentration of ∼385 ppb, accounting for 88% of the ∼440 ppb increase in methane concentrations observed in ice cores. Thus glacial‐interglacial changes in atmospheric methane concentrations would have been modulated by BVOC emissions. In addition, the increase in atmospheric methane concentrations since the mid‐Holocene is partly caused in our results by the increases in anthropogenic methane emissions over this period. While the interplay between BVOC and wetland methane emissions since the LGM cannot explain the entire record of ice core methane concentrations, consideration of BVOC source dynamics is central to understanding ice core methane. Rapid changes in atmospheric methane concentrations, also observed in ice cores, require further study.
Risk assessment for optimal drought management of an integrated water resources system using a genetic algorithm

A decision support system (DSS) is developed and applied to assess the susceptibility of water supply systems to droughts, and to aid decision‐makers in determining optimal supply strategies. The DSS integrates three fundamental modules for water resources management: (1) a real time rainfall‐runoff forecasting model enhanced by Kalman filtering; (2) a water demand forecast model; and (3) a reservoir operation model. Simulation and optimization procedures for the reservoir operation model are based on risk analysis to evaluate the system performance and to derive the most appropriate supply strategy of minimum risk, for the designed operating conditions. The optimization technique, based on genetic algorithms, introduces two new and distinct features, with the aim of minimizing the risks of drought damage and improving the convergence of the model toward practical solutions. Firstly, risk‐based measures of system performance, termed reliability, resiliency and vulnerability, are combined into a global risk index, referred to as the drought risk index (DRI). The DRI, formulated as a weighted function of the risk measures, serves as the objective function to be minimized during the search for the optimal operation. Secondly, in the genetic algorithm search, each new generation of water supply solutions is created from solutions with risk levels clustered inside a defined ‘acceptable risk space’. In other words, the convergence of the algorithm is improved by retaining only those solutions with DRI values smaller than the maximum acceptable risk. As a case study, the DSS is applied to the water resources system in Fukuoka City, western Japan. The DSS is believed to be an efficient tool for the assessment of a sequence of water supply scenarios, leading to the improved utilization of existing water resources during drought. Copyright © 2002 John Wiley & Sons, Ltd.
Automatic diatom recognition on digital images

Diatoms are a large group of microscopic algae that grow as independent organisms or in small colonies and are characterized by a silica cell wall. They are widely used as ecosystem health and evolution tracers. One of the their most important characteristic is the fact that they vary their shape among different families and this makes possible its classification using pattern recognition techniques. In this paper, we describe a new process based on determining the invariant moments of the objects presented in a digital image to classify them according to the different families. We present a technique to segment the diatoms using a new thresholding technique, contour tracing and a recognition process. Finally, the results are presented.
Toward a generalization of the TOPMODEL concepts:Topographic indices of hydrological similarity

Preliminary studies of the application of TOPMODEL to the 36-ha Ringelbach catchment suggested that the original form of exponential transmissivity function leading to the In (a/tan β) topographic index and first-order hyperbolic base flow recession curve is not appropriate to this catchment. Two alternative forms of topographic index and soil-topographic index are developed based on parabolic and linear transmissivity functions, leading to the more frequently observed second-order hyperbolic and exponential recession curves, respectively. It is shown how these can be used in the same way as the original to relate catchment average water table depths to local water table depths so that patterns of saturation can be evaluated. Two companion [Ambroise et al., this issue; Freer et al., this issue] papers show how the new parabolic index is used in the prediction of Ringelbach discharges, and how the limitations of the model are reflected in the estimated predictive uncertainties using the Generalised Likelihood Uncertainty Estimation (GLUE) approach.
MODEL STUDIES ON MECHANICS OF JOINTED ROCK

A generalized physical model is tested triaxially in order to relate properties of the intact material and of the discontinuities to the strength and deformability of a jointed rock mass. The behavior of jointed models can be divided into three characteristic zones. At low confining stresses there is either sliding along preexisting joints or brittle failure through intact material and across joints with strength depending on the number of intersected joints. At intermediate confining stressed sliding or failure may occur again, but the failure mode changes from brittle to ductile. At high confining stresses no sliding and only ductile failure occurs. The three zones and the upper and lower bounds of strength are easily obtained by a few confined compression tests on the intact material, by sliding tests along joints, and by a direct tension test. If this characteristic behavior is valid for other materials, as seems likely because of the basically similar underlying mechanism, it may become possible to determine the behavior of a jointed rock mass by relatively simple experiments.
Segregation of subducted oceanic crust in the convecting mantle

Subducted oceanic crust, transformed into dense mineral assemblages at high pressure, may gravitationally segregate at the bottom of the convecting mantle, for example, the D″ layer. Here it could be stored for a long enough time to develop an “enriched” isotopic signature, before it is recycled in mantle plumes and hence control the geochemical character of hot-spot basalts. We study both the geodynamical and geochemical aspects of this hypothesis in two-dimensional numerical convection models, in which plate motion is imposed by a velocity boundary condition. About 250,000 tracer particles are used to identify the basalt fraction in the oceanic crustmantle system. High-, average-, and low-tracer densities indicate basalt or eclogite, peridotite, and harzburgite, respectively. The tracers are negatively buoyant to account for the density differences between the rock types. At surface divergence zones, crust formation is simulated by extracting tracers and transferring them into a thin layer at the surface. The tracers carry a certain amount of the relevant nuclides of the U-Pb and Sm-Nd systems, which are fractionated between the basalt tracers and a second species of residue tracers during crust formation. Using reasonable parameter values, we find that of the order of 1/6 of the subducted crust accumulates in pools at the bottom, which reside underneath thermal plumes. After 3.6 Ga, the [207Pb]/[204Pb], [206Pb]/[204Pb], and [143Nd]/[ 144Nd] ratios in various parts of the model cover the observed HIMU-MORB range. A systematic study of the influence of control parameters on the results indicates that the amount of segregation and the diversity of isotope ratios (1) increases strongly with Rρ, the ratio of chemical to thermal buoyancy; (2) decreases moderately with the Rayleigh number Ra, where Ra = 106 is the highest value that we employed; (3) increases strongly with the degree of temperature dependence of the viscosity; and (4) is not very sensitive to the partitioning between internal and bottom heating. The largest uncertainty in applying our model results to the Earth lies in the lack of accurate density data for conditions at the core-mantle boundary. We conclude that, if our density estimates are correct, segregation and reentrainment of subducted crust is of fundamental importance for the dynamics and chemistry of mantle plumes.
An effective Bayesian model for lithofacies estimation using geophysical data

A Bayesian model coupled with a fuzzy neural network (BFNN) is developed to enhance the use of geophysical data in lithofacies estimation. Prior estimates are inferred from borehole lithofacies measurements using indicator kriging, and posterior estimates are obtained by updating the prior using geophysical data. The novelty of this study lies in the use of the fuzzy neural network for the inference of the likelihood function. This allows spatial correlation of lithofacies as well as nonlinear cross correlation between lithofacies and geophysical attributes to be incorporated into lithofacies estimation. The effectiveness of BFNN is demonstrated using synthetic data emulating measurements at the Lawrence Livermore National Laboratory (LLNL) Site.