Miracle-dz/UniFAR-FTUs huggingface dataset:
QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice

The QlicRice database is designed to host publicly accessible, abiotic stress responsive quantitative trait loci (QTLs) in rice (Oryza sativa) and their corresponding sequenced gene loci. It provides a platform for the data mining of abiotic stress responsive QTLs, as well as browsing and annotating associated traits, their location on a sequenced genome, mapped expressed sequence tags (ESTs) and tissue and growth stage-specific expressions on the whole genome. Information on QTLs related to abiotic stresses and their corresponding loci from a genomic perspective has not yet been integrated on an accessible, user-friendly platform. QlicRice offers client-responsive architecture to retrieve meaningful biological information—integrated and named ‘Qlic Search’—embedded in a query phrase autocomplete feature, coupled with multiple search options that include trait names, genes and QTL IDs. A comprehensive physical and genetic map and vital statistics have been provided in a graphical manner for deciphering the position of QTLs on different chromosomes. A convenient and intuitive user interface have been designed to help users retrieve associations to agronomically important QTLs on abiotic stress response in rice. Database URL: http://nabg.iasri. res.in:8080/qlic-rice/.
Phase relations in the system Ag 2 S-Cu 2 S-PbS-Bi 2 S 3

The formation of sulfbismuthides and the extents of solid solutions in the system Ag 2 S-Cu 2 S-PbS-Bi 2 S 3 were studied at 500 degrees C using sealed and evacuated capsule methods. Liquid is present in the Cu 2 S-rich region of both the systems Ag 2 S-Cu 2 S-PbS and Cu 2 S-PbS-Bi 2 S 3 . In the system Ag 2 S-Cu 2 S-Bi 2 S 3 two new phases, Ag 2 Bi 4 S 7 and AgCu 5 Bi 6 S 12 , were found. Ag 2 Bi 4 S 7 was identified to be a benjaminite-type phase.Nine solid solutions were recognized in the system Ag 2 S-Cu 2 S-PbS-Bi 2 S 3 . Among the four extensive series, the pavonite solid solution can be expressed as Ag (sub 1-(x+y)) Cu (sub y+(n+1)z) Pb (sub 2x (super -) ) Bi (sub 3-(x+z) ) S 5 with 0 < x < 0.36, 0 < y < 0.36, 0 < z < 0.53 and n [asymp] 2, the benjaminite solid solution as Ag (sub 3.43-(x+y)) Cu (sub y+(n+1)z) Pb 2x Bi (sub 6.85-(x+z)) S 12 with 0 < x < 1.53, 0 < y < 0.55, 0 < z < 1.41, and n [asymp] 2, the Cu 3 Bi 5 S 9 solid solution as Ag y Cu (sub 3-(x+y)+(n+1)z) Pb 2x Bi (sub 5-(x+z)) S 9 with 0 < x < 0.56, 0 < y < 0.70, -0.21 < z < 0.16, and n [asymp] 2, and the CuBi 3 S 5 solid solution as Ag y Cu (sub 1-(x+y)+(n+1)z) Pb 2x Bi (sub 3-(x+z)) S 5 with 0 < x < 0.09, 0 < y < 0.12, 0 < z < 0.08, and n [asymp] 2. In each of the formulas, x, y, z, and n represent substitutions between Ag (or Cu) + Bi and 2Pb, Ag and Cu, and Bi and Cu, and interstitial addition of Cu, respectively. The lillianite solid solution extends from Pb (sub 2.8) Bi (sub 2.1) S 6 to Ag (sub 0.68) Cu (sub 0.20) Pb (sub 1.56) Bi (sub 2.67) S 6 , whereas the range of the heyrovskyite solid solution is limited to the range between Pb (sub 5.4) Bi (sub 2.4) S 9 and Ag (sub 0.76) Cu (sub 1.31) Pb (sub 3.18) Bi (sub 3.18) S 9 . In the AgBiS 2 solid solution, the amount of Cu varies inversely with the amount of Pb and the solid solution decreases in range with increasing PbS content. The wittichenite solid solution has a range from Cu 3 BiS 3 to Cu (sub 2.5) Ag (sub 0.5) BiS 3 and does not accommodate any detectable amount of PbS. The bismuthinite-aikinite solid solution is restricted to the system Cu 2 S-PbS-Bi 2 S 3 .
Geophysical variables as predictors of megabenthos assemblages from the northern Great Barrier Reef, Australia

The question as to whether geophysical data from habitats can be used to predict the occurrence of benthic biodiversity is becoming more important with the increase in Marine Protected Areas as tools for marine conservation. To help answer this question and to better understand the relationship between sediment, geomorphology and benthos, we conducted a multibeam sonar survey over two areas in the northern Great Barrier Reef - Gulf of Papua region. Multivariate statistical analyses (cluster, multi-dimensional scaling and BIO-ENV procedure) of the physical and biological datasets from both areas, determined that the geophysical variables, slope and gravel percentage, were the best predictors for megabenthos assemblage patterns. In conjunction with Geographic Information System (GIS) models of the geomorphology and bathymetry, these geophysical variables were used to derive the spatial boundaries of benthic habitats for each study area. We applied a hierarchical method of benthic habitat mapping to the Secondary Biotope and Biological Facies levels at the site (<10 km) scale. The combination of substrate type, sedimentary dynamics and physical processes related to near-seabed currents appear to be a dominant control on the benthic communities in the northern Great Barrier Reef - Gulf of Papua region. These results add confidence to the use of geophysical data from seabed habitats, such as geology, sediment and morphology, as predictors for benthos distribution and thus provide a basis for marine reserve selection.
Noise-Driven Anisotropic Diffusion Filtering of MRI

A new filtering method to remove Rician noise from magnetic resonance images is presented. This filter relies on a robust estimation of the standard deviation of the noise and combines local linear minimum mean square error filters and partial differential equations for MRI, as the speckle reducing anisotropic diffusion did for ultrasound images. The parameters of the filter are automatically chosen from the estimated noise. This property improves the convergence rate of the diffusion while preserving contours, leading to more robust and intuitive filtering. The partial derivative equation of the filter is extended to a new matrix diffusion filter which allows a coherent diffusion based on the local structure of the image and on the corresponding oriented local standard deviations. This new filter combines volumetric, planar, and linear components of the local image structure. The numerical scheme is explained and visual and quantitative results on simulated and real data sets are presented. In the experiments, the new filter leads to the best results.
Conditional gene recombination by adenovirus‐driven Cre in the mouse uterus

Cre‐mediated conditional gene targeting has been shown to be successful in many cell and tissue types. However, gene recombination in the uterus with heterogeneous cell types by Cre activation is not yet well established. Using recombinant adenoviruses expressing a functional Cre (ADV‐Cre) and ROSA26 reporter mice, we show here that ADV‐Cre infused intraluminally in a small volume (10 μl) conditionally excises the loxP site, resulting in lacZ expression in uterine luminal epithelial cells without significantly affecting pregnancy. In contrast, a similar intraluminal infusion of ADV‐Cre in a larger volume (50 μl) damages the normal architecture and integrity of the luminal epithelium, inducing gene recombination in the underneath stromal cells, with disruption of pregnancy. Further, decidualizing stromal cells at the implantation sites can be targeted by ADV‐Cre after intravenous administration on days 5–6. This route of administration also elicits Cre activity in other tissues, including the liver, spleen, ovary, and, more remarkably, in the adrenal cortex. These findings demonstrate the feasibility of achieving conditional expression or deletion of specific genes in uterine cells at desired times and physiological states. genesis 44:51–56, 2006. © 2006 Wiley‐Liss, Inc.
A Flow Adhesion Assay to Study Leucocyte Recruitment to Human Hepatic Sinusoidal Endothelium Under Conditions of Shear Stress

Leucocyte infiltration into human liver tissue is a common process in all adult inflammatory liver diseases. Chronic infiltration can drive the development of fibrosis and progression to cirrhosis. Understanding the molecular mechanisms that mediate leucocyte recruitment to the liver could identify important therapeutic targets for liver disease. The key interaction during leucocyte recruitment is that of inflammatory cells with endothelium under conditions of shear stress. Recruitment to the liver occurs within the low shear channels of the hepatic sinusoids which are lined by hepatic sinusoidal endothelial cells (HSEC). The conditions within the hepatic sinusoids can be recapitulated by perfusing leucocytes through channels lined by human HSEC monolayers at specific flow rates. In these conditions leucocytes undergo a brief tethering step followed by activation and firm adhesion, followed by a crawling step and subsequent transmigration across the endothelial layer. Using phase contrast microscopy, each step of this 'adhesion cascade' can be visualized and recorded followed by offline analysis. Endothelial cells or leucocytes can be pretreated with inhibitors to determine the role of specific molecules during this process.
Self-service bike sharing systems: simulation, repositioning, pricing

Self-service bike sharing systems experience often imbalance problems: in some stations there is a lack of bikes while in others there are too many bikes, leaving no empty rack for a user willing to park his bike. Imbalance problems can be partially settled by the actions of vehicles moving bikes during the night in order to prepare the forthcoming day. We speak then of static regulation, since bikes can be assumed to be not moving. These problems can also be partially countered by actions of the vehicles during the day. This is dynamic regulation and forms the topic of our present work. We build a precise theoretical framework for studying this dynamic problem and discuss the kind of impact vehicles moving bikes can have on the system. We prove moreover the inherent hardness of the dynamic regulation problem and present some ways to circumvent it by the use of heuristics. A pricing technique, not involving vehicles, is also proposed. An open-source and versatile simulator is also briefly described and used to compare the aforementioned methods.
Lower-Stratospheric Radiative Damping and Polar-Night Jet Oscillation Events

AbstractThe effect of stratospheric radiative damping time scales on stratospheric variability and on stratosphere–troposphere coupling is investigated in a simplified global circulation model by modifying the vertical profile of radiative damping in the stratosphere while holding it fixed in the troposphere. Perpetual-January conditions are imposed, with sinusoidal topography of zonal wavenumber 1 or 2.The depth and duration of the simulated sudden stratospheric warmings closely track the lower-stratospheric radiative time scales. Simulations with the most realistic profiles of radiative damping exhibit extended time-scale recoveries analogous to polar-night jet oscillation (PJO) events, which are observed to follow sufficiently deep stratospheric warmings. These events are characterized by weak lower-stratospheric winds and enhanced stability near the tropopause, which persist for up to 3 months following the initial warming. They are obtained with both wave-1 and wave-2 topography. Planetary-scale Elia.
Kernel and shell based applications integrity assurance

The verification of the authenticity of software by an executing host has become a vital security issue in recent years with the original postulation and subsequent evolution of computer viruses. The CASS (Computer Architecture for Secure Systems) project addresses this issue by incorporating integrity checking at the operating system level. This paper describes three prototype implementations of the architecture, two of these at the kernel level targetting UNIX SVR4.2 and the Mach 3.0 microkernel, with the third-for reasons of generality-involving the implementation of a specialised shell which is then portable across UNIX-style platforms in general. The paper focusses on a description of the former, viz. the kernel-based implementations, and examines the design and implementation issues which had to be addressed in achieving kernel-based integrity checking of executables for the two platforms.
Inhibitory Effects of d-Amino Acids on Staphylococcus aureus Biofilm Development

ABSTRACT Biofilms are communities of cells held together by a self-produced extracellular matrix typically consisting of protein, exopolysaccharide, and often DNA. A natural signal for biofilm disassembly in Bacillus subtilis is certain d-amino acids, which are incorporated into the peptidoglycan and trigger the release of the protein component of the matrix. d-Amino acids also prevent biofilm formation by the related Gram-positive bacterium Staphylococcus aureus. Here we employed fluorescence microscopy and confocal laser scanning microscopy to investigate how d-amino acids prevent biofilm formation by S. aureus. We report that biofilm formation takes place in two stages, initial attachment to surfaces, resulting in small foci, and the subsequent growth of the foci into large aggregates. d-Amino acids did not prevent the initial surface attachment of cells but blocked the subsequent growth of the foci into larger assemblies of cells. Using protein- and polysaccharide-specific stains, we have shown that d-amino acids inhibited the accumulation of the protein component of the matrix but had little effect on exopolysaccharide production and localization within the biofilm. We conclude that d-amino acids act in an analogous manner to prevent biofilm development in B. subtilis and S. aureus. Finally, to investigate the potential utility of d-amino acids in preventing device-related infections, we have shown that surfaces impregnated with d-amino acids were effective in preventing biofilm growth.
GLUCURONIDATION OF 7-ETHYL-10-HYDROXYCAMPTOTHECIN ( SN-38 ) , AN ACTIVE METABOLITE OF IRINOTECAN ( CPT-11 ) , BY HUMAN UGT 1 A 1 VARIANTS

7-Ethyl-10-hydroxycamptothecin (SN-38), an active metabolite of antitumor agent irinotecan (CPT-11), is conjugated and detoxified to SN-38-glucuronide by UDP-glucuronosyltransferase (UGT) 1A1. Genetic polymorphisms in UGT1A1 are thought to contribute to severe diarrhea and/or leukopenia caused by CPT-11. In this regard, it has been reported that polymorphisms in the promoter region could affect the CPT-11 pharmacokinetics and interindividual variation of toxicity. However, little information is available on the influence of UGT1A1 polymorphisms in the coding region on the SN-38 glucuronidation activity. In the present study, wild-type (WT) and three variant (G71R, P229Q, and Y486D) cDNAs of human UGT1A1s were transiently expressed in COS-1 cells, and the kinetic parameters of these UGT1A1s were determined for SN-38 glucuronidation. A partially reduced UGT1A1 protein expression was observed in COS-1 cells for G71R and Y486D. WT UGT1A1 catalyzed SN-38 glucuronidation with an apparent Km value of 11.5 M, whereas those of G71R, P229Q, and Y486D were 14.0, 18.0, and 63.5 M, respectively. The SN-38 glucuronidation efficiency ratio (Vmax/Km) normalized for the level of expression was 1.4, 0.66 (47% of WT), 0.73 (52%), and 0.07 (5%) l/min/mg of protein for WT, G71R, P229Q, and Y486D, respectively. Thus, the SN-38 glucuronidation activity of Y486D was drastically reduced, whereas the reduction in the G71R and P229Q activities was fractional. The decreased SN-38 glucuronidation efficiency ratio of G71R and P229Q could be critical in combination with other polymorphisms
Metabolic products of soluble epoxide hydrolase are essential for monocyte chemotaxis to MCP-1 in vitro and in vivo

Monocyte chemoattractant protein-1 (MCP-1)-induced monocyte chemotaxis is a major event in inflammatory disease. Our prior studies have demonstrated that MCP-1-dependent chemotaxis requires release of arachidonic acid (AA) by activated cytosolic phospholipase A2 (cPLA2). Here we investigated the involvement of AA metabolites in chemotaxis. Neither cyclooxygenase nor lipoxygenase pathways were required, whereas pharmacologic inhibitors of both the cytochrome-P450 (CYP) and the soluble epoxide hydrolase (sEH) pathways blocked monocyte chemotaxis to MCP-1. To verify specificity, we demonstrated that the CYP and sEH products epoxyeiscosatrienoic acids (EETs) and dihydroxyeicosatrienoic acids (DHETs), respectively, restored chemotaxis in the presence of the inhibitors, indicating that sEH-derived products are essential for MCP-1-driven chemotaxis. Importantly, DHETs also rescued chemotaxis in cPLA2-deficient monocytes and monocytes with blocked Erk1/2 activity, because Erk controls cPLA2 activation. The in vitro findings regarding the involvement of CYP/sEH pathways were further validated in vivo using two complementary approaches measuring MCP-1-dependent chemotaxis in mice. These observations reveal the importance of sEH in MCP-1-regulated monocyte chemotaxis and may explain the observed therapeutic value of sEH inhibitors in treatment of inflammatory diseases, cardiovascular diseases, pain, and even carcinogenesis. Their effectiveness, often attributed to increasing EET levels, is probably influenced by the impairment of DHET formation and inhibition of chemotaxis.
A Pacific hydrographic section at 88°W: Water-property distribution

Full-depth conductivity-temperature-depth (CTD)/hydrographic measurements with high horizontal and vertical resolution were made in February-April 1993 along a line lying at a nominal longitude of 88°W and extending from southern Chile (54°S) to Guatemala (14°N). It crossed five major deep basins (Southeast Pacific, Chile, Peru, Panama, and Guatemala basins) east of the East Pacific Rise. Vertical sections of potential temperature, salinity, potential density, oxygen, silica, phosphate, nitrate, and nitrite are presented to illustrate the structure of the entire water column. Some features of interest found in the sections are described, and an attempt is made to interpret them in terms of the isopycnal property distributions associated with the large-scale ocean circulation. These features include: various near-surface waters observed in the tropical and subtropical regions and the fronts that mark the boundaries of these waters; the possible importance of salt fingering to the downward salt transfer from the high-salinity subtropical water; a shallow thermostad (pycnostad) developed at 16°–18.5°C in the subtropical water; low-salinity surface water in the subantarctic zone west of southern Chile; large domains of extremely low oxygen in the subpycnocline layer on both sides of the equator and a secondary nitrite maximum associated with a nitrate minimum in these low-oxygen domains; high-salinity, low-oxygen, high-nutrient subpycnocline water that is carried poleward along the eastern boundary by the Peru-Chile Undercurrent; the Subantarctic Mode and Antarctic Intermediate waters; middepth isopycnal property extrema observed at the crest of the Sala y Gomez Ridge; influences of the North Pacific and the North Atlantic upon deep waters along the section; and the characteristics and sources of the bottom waters in the five deep basins along the section.
Gaze Cues Influence the Allocation of Attention in Natural Scene Viewing

In two experiments we examined whether the allocation of attention in natural scene viewing is influenced by the gaze cues (head and eye direction) of an individual appearing in the scene. Each experiment employed a variant of the flicker paradigm in which alternating versions of a scene and a modified version of that scene were separated by a brief blank field. In Experiment 1, participants were able to detect the change made to the scene sooner when an individual appearing in the scene was gazing at the changing object than when the individual was absent, gazing straight ahead, or gazing at a nonchanging object. In addition, participants’ ability to detect change deteriorated linearly as the changing object was located progressively further from the line of regard of the gazer. Experiment 2 replicated this change detection advantage of gaze-cued objects in a modified procedure using more critical scenes, a forced-choice change/no-change decision, and accuracy as the dependent variable. These findings establish that in the perception of static natural scenes and in a change detection task, attention is preferentially allocated to objects that are the target of another's social attention.
Security on over the top tv services

The widespread availability of high bandwidth Internet access on fixed and mobile networks, in conjunction with the availability of mobile devices powerful enough to play streamed high quality video, has created the demand for services that deliver television and video content over the Internet to television sets, personal computers and mobile devices. This demand has lead to the appearance of over-the-top TV and video service providers that deliver video over the Internet, using networks not operated by them. Video delivery in an open environment, like the Internet, requires operators to implement security mechanisms to protect their valuable content from illicit access and distribution. In this thesis, we investigate security properties needed to securely deliver OTT video services. In order to assess the security mechanisms employed to enforce authentication, authorization, digital rights management and geographical restrictions, we survey three prominent OTT service providers. Due to their size and choice of technologies, we selected Netflix, Hulu and Comcast. We studied the interactions between the client applications and the providers’ servers by inspecting the traffic of messages exchanged. For each of the security mechanisms analyzed, experiments were designed to find flaws and test their effectiveness. The most important of the identified security issues are related to the handling and transmission of HTTP cookies when using web browser-based clients. These vulnerabilities are common to all surveyed providers and can be exploited by adversaries to steal authentication cookies and impersonate the customer, allowing illicit access to video assets and private information of the customer. A cookie stealing and session hijacking attack is described and mitigation strategies are presented for OTT service providers, users and wireless network access point administrators. These consist in the use of SSL to protect authentication tokens, the use HTTPS only or VPN services, and the use of WPA2 to protect wireless networks, respectively. An interesting result, observed with the analyzed mobile client for Android devices, is that it uses SSL to protect the transmission of HTTP cookies used for authentication. Thus, it is not vulnerable to the described attack.
Application of a Macroscale Hydrologic Model to Estimate Streamflow across Southeast Australia

AbstractReliable predictions of water availability and streamflow characteristics, and the impact of climate and land use change on water availability, are central to water resources planning and management. This paper assesses the application of the widely used macroscale hydrologic model, the three-layer Variable Infiltration Capacity model (VIC-3L), to estimate daily streamflow in 191 unregulated catchments across southeast Australia and evaluates the regionalization of model parameters to predict streamflow in ungauged catchments. The parameter values in the VIC-3L model are estimated using three methods: default values, optimized values based on model calibration, and regionalized values based on spatial proximity method. The modeled streamflows from VIC-3L are assessed against the observed streamflows from the catchments. The authors discuss the model performance based on different parameter estimation methods and the effects of rainfall regimes on streamflow prediction. Also the implication of usin.