Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational medicinal chemistry applications to target Asian-prevalent strain of hepatitis C virus

Hepatitis C Virus (HCV), affecting millions of people worldwide, is the leading cause of liver disorder, cirrhosis, and hepatocellular carcinoma. HCV is genetically diverse having eight genotypes and several subtypes predominant in different regions of the globe. The HCV NS3/4A protease is a primary therapeutic target for HCV with various FDA-approved antivirals and several clinical developments. However, available protease inhibitors (PIs) have lower potency against HCV genotype 3 (GT3), prevalent in South Asia. In this study, the incumbent computational tools were utilized to understand and explore interactions of the HCV GT3 receptor with the potential inhibitors after the virtual screening of one million compounds retrieved from the ZINC database. The molecular dynamics, pharmacological studies, and experimental studies uncovered the potential PIs as ZINC000224449889, ZINC000224374291, and ZINC000224374456 and the derivative of ZINC000224374456 from the ZINC library. The study revealed that these top-hit compounds exhibited good binding and better pharmacokinetics properties that might be considered the most promising compound against HCV GT3 protease. Viability test, on primary healthy Human Gingival Fibroblasts (HGFs) and cancerous AGS cell line, was also carried out to assess their safety profile after administration. In addition, Surface Plasmon Resonance (SPR) was also performed for the determination of affinity and kinetics of synthesized compounds with target proteins.
Nueva Especie de Tortuga Terrestre Gigante del Género Chelonoidis Fitzinger, 1835 (Cryptodira: Testudinidae), del Miembro Inferior de la Formación Toropí/ Yupoí (Pleistoceno Tardío/ Lujanense), Bella Vista, Corrientes, Argentina

Abstract. NEW SPECIES OF GIANT TORTOISE OF THE GENUS CHELONOIDIS FITZINGER, 1835 (CRYPTODIRA: TESTUDINIDAE), FROM THE LOWER MEMBER OF THE TOROPÍ/ YUPOÍ FORMATION (LATE PLEISTOCENE/ LUJANIAN), BELLA VISTA, CORRIENTES, ARGENTINA. A new species of giant tortoise from the upper section of the lower member of Toropí/ Yupoí Formation (late Pleistocene, 58–22 ka) is described. The holotype of this new species was recovered at Arroyo Toropí (10 km south from Bella Vista city, Corrientes Province, Argentina). The presence of pectoral scales in the plastron narrower in midline and antero-posteriorly expanded towards the marginal scutes, allow us to assign this tortoise to the genus Chelonoidis Fitzinger. The non parallel lateral margins, the peripheral bones lobed in the bridge, the elliptical depression on both sides of peripheral bones III, and a sub- rhomboidal entoplastron proximally broadening, with distal projections covering the pectoral scales, allow us to recognize a new species, Chelonoidis lutzae sp. nov. The strict consensus tree of the phylogenetic analysis of Chelonoidis shows a polytomy among Ch. lutzae sp. nov., ? Ch. gallardoi (Rovereto), ? Ch. australis (Moreno), and the extant and extinct species assigned to carbonaria and chilensis groups. The carbonaria group includes Ch. denticulata (Linnaeus) and another clade formed by Ch. carbonaria (Spix) and Ch. hesterna (Auffenberg). The chilensis group, includes two subclades, one composed by Ch. chilensis (Gray), Ch. petersi (Freiberg) and Ch. nigra (Quoy and Gaimard), and another formed by YPFBPAL 0932 and Ch. gringorum (Simpson). Using the “pruned tree” option of TNT an “extinct giant continental tortoise” clade (Ch. lutzae sp. nov. and ? Ch. australis) is recovered, clearly differentiated from the giant Galápagos tortoises.
GPU ray-traced collision detection for cloth simulation

We propose a method to perform collision detection with cloths with ray-tracing. Our method is able to perform collision detection between cloths and volumetric objects (rigid or deformable) as well as collision detection between cloths (including auto-collision). Our method casts rays between objects to perform collision detection, and an inversion-handling algorithm is introduced to correct errors introduced by discrete simulations. GPU computing is used to improve the performances. Our implementation handles scenes containing deformable objects at an interactive frame-rate, with collision detection lasting a few milliseconds.
Application of copper slag in geomagnetic archaeointensity research

[1] Paleointensity and archaeointensity studies since the 1950s have produced numerous geomagnetic intensity data for the last seven millennia. As a consequence of different experiments and materials, there is a complex and internally inconsistent picture of the geomagnetic field behavior. In this study we present data using a recently developed experimental design on a heretofore unexploited recording medium: copper slag deposits. Our results, based on hundreds of specimens from various archaeometallurgical sites of the Southern Levant, demonstrate the applicability of copper slag material for archaeointensity studies. In addition to frequently exhibiting good experimental behavior, slag has further advantages such as dense multilayer deposits and in cases embedded charcoals, which open the door to data sets with excellent age control and resolution. The data presented here augment the high quality database from the Middle East and support previously observed periods of rapid change of the intensity of the geomagnetic field.
Pre-employment examinations for preventing occupational injury and disease in workers.

BACKGROUND Many employers and other stakeholders believe that health examinations of job applicants prevent occupational diseases and sickness absence. OBJECTIVES To evaluate the effectiveness of pre-employment examinations of job applicants in preventing occupational injury, disease and sickness absence compared to no intervention or alternative interventions. SEARCH STRATEGY We searched CENTRAL (The Cochrane Library), MEDLINE, EMBASE, CINAHL, PsycINFO and PEDro (to December 2009) not restricted by date, language or publication type. SELECTION CRITERIA We included randomised controlled trials (RCTs), controlled before-after studies (CBA), and interrupted time-series (ITS) of health examinations to prevent occupational diseases and injuries in job applicants. DATA COLLECTION AND ANALYSIS Four review authors (NM, ML, JV, ES) independently selected studies, extracted data, and determined study quality. The studies were too heterogeneous for statistical pooling of results. MAIN RESULTS We included two RCTs, five CBA studies and two ITS. Seven studies with 5872 participants evaluated the screening process of pre-employment examinations and two studies with 2164 participants evaluated the measures to mitigate the risks found following the screening process.Of those studies that evaluated the screening process, one study found that a general examination did not reduce sick leave (Mean Difference -0.1 95% CI -0.5 to 0.3) but another study found that a more task focused examination did (MD -36 95% CI -68.3 to -3.8). One study found that incorporation of a bronchial challenge test decreased occupational asthma (trend change -2.6 95% CI -3.6 to -1.5). Three studies that included functional capacity evaluation found contradictory effects on injury rates and number of medical visits. The rates of rejecting job applicants varied from 2% to 35%. Neither of the two studies that evaluated risk mitigation found an increased injury rate after training or work accommodations had been implemented.We rated the evidence for all outcomes as very low quality. AUTHORS' CONCLUSIONS There is very low quality evidence that pre-employment examinations that are specific to certain jobs or health problems could reduce occupational disease, injury, or sickness absence. This supports the current policy to restrict pre-employment examinations to job-specific examinations. More studies are needed that take into account the harms of rejecting job applicants.
Seed Reserves of Desert Soils

Soil and litter samples were collected from the playa, playa fringe and bajada zones of the Jornada Validation Site. These samples were analyzed for their seed content, special attention being paid to spatial distribution. At the time of sampling, there was little litter on the soil surface, and the litter contained only a small proportion of the total seeds present.
Interactive 3D-visualization of a Solar Particle Event for Public Outreach

This report presents the work of our Master ́s thesis carried out remotely at the Community Coordinated Modeling Center at the National Aeronautics and Space Administration (NASA) Goddard Space Flight Center. In collaboration with the American Museum of Natural History (AMNH), Linköping University and Predictive Science Inc. The report presents and evaluates an implementation of an interactive 3D visualization of a Solar Particle Event in OpenSpace, an open source astrovisualization software. Data from a model developed by Predictive Science Inc. was used to implement the visualization. The visualization is done by visualizing fluxes of particles as points and utilizing a volumetric data set by applying 2D textures to geometrical shapes. The goal of these visualizations is to help describe the effect of space weather phenomena to the general public. The research conducted is focused on how to visualize a big Solar Particle Event to emphasize or showcase different aspects, such as the radiation exposure close to Earth. The result of the work is an interactive real-time visualization of a Solar Particle Event designed for public outreach. The project culminated in two live streamed events with AMNH, in collaboration with NASA and Predictive Science Inc.
Mechanical and electrical response due to fluid-pressure equilibration following an earthquake

[1] The mechanical and electrical response in a uniform porous crust are determined following a shear dislocation (earthquake) on an internal slip surface. A uniform crust is studied because many exact analytical relations hold between the various response fields in this case. The initial stress field that is created immediately following the earthquake subsequently relaxes through time as the fluid pressure equilibrates by fluid flow. Maps of the electric field generated due to the fluid flow (electrokinetic coupling) are presented. Using conservative estimates of the various parameters involved, electric fields significantly larger than the diurnal (magnetotelluric) fields are generated. Quantitative results for how various components of the stress tensor change due to the fluid equilibration are also presented. The Coulomb stress can easily change by 100% (and more) in the months following an earthquake due to the fluid-pressure equilibration.
World Reference Base for Soil Resources

In 1998, the International Union of Soil Sciences (IUSS) officially adopted the world reference base for soil resources (WRB) as the Union's system for soil correlation. The structure, concepts, and definitions of the WRB are strongly influenced by the FAO-UNESCO legend of the soil map of the world (1-2). At the time of itsinception, the WRB proposed 30 "Soil Reference Groups" accommodating more than 200 ("second level") soil units. WRB (3-5) was endorsed by the IUSS in 1998 and provides an opportunity to create and refine a common and global language for soil classification. WRB aims to serve as a framework through which ongoing soil classification throughout the world can be harmonized. The ultimate objective is to reach international agreement on the major soil groups to be recognized at a global scale as well as on the criteria and methodology to be applied for defining and separating them. Such an agreement is needed to facilitate the exchange of information and experience, to provide a common scientific language, to strengthen the applications of soil science, and to enhance the communication with other disciplines and make the major soil names into household names
Model predictive control of wind turbines using uncertain LIDAR measurements

The problem of Model predictive control (MPC) of wind turbines using uncertain LIDAR (LIght Detection And Ranging) measurements is considered. A nonlinear dynamical model of the wind turbine is obtained. We linearize the obtained nonlinear model for different operating points, which are determined by the effective wind speed on the rotor disc. We take the wind speed as a scheduling variable. The wind speed is measurable ahead of the turbine using LIDARs, therefore, the scheduling variable is known for the entire prediction horizon. By taking the advantage of having future values of the scheduling variable, we simplify state prediction for the MPC. Consequently, the control problem of the nonlinear system is simplified into a quadratic programming. We consider uncertainty in the wind propagation time, which is the traveling time of wind from the LIDAR measurement point to the rotor. An algorithm based on wind speed estimation and measurements from the LIDAR is devised to find an estimate of the delay and compensate for it before it is used in the controller. Comparisons between the MPC with error compensation, the MPC without error compensation and an MPC with re-linearization at each sample point based on wind speed estimation are given. It is shown that with appropriate signal processing techniques, LIDAR measurements improve the performance of the wind turbine controller.
An inhibitor of proteasome b 2 sites sensitizes myeloma cells to immunoproteasome inhibitors

block b 5c and b 5i sites. We report here that pharmacologically relevant concentrations of b 5i-speci ﬁ c inhibitor ONX-0914 show cytotoxicity in MM cell lines similar to that of car ﬁ lzomib and bortezomib. In addition, increasing immunoproteasome expression by interferon-g increases sensitivity to ONX-0914 but not to car ﬁ lzomib. LU-102, an inhibitor of b 2 sites, dramatically sensitizes MM cell lines and primary cells to ONX-0914. ONX-0914 synergizes with all FDA-approved proteasome inhibitors in MM in vitro and in vivo. Thus, immunoproteasome inhibitors, currently in clinical trials for the treatment of autoimmune diseases, should also be considered for the treatment of MM.
An aerosol optical thickness retrieval algorithm for Meteosat Second Generation (MSG) data over land: applications to the Mediterranean area

The Spinning Enhanced Visible and Infra Red Imager (SEVIRI) radiometer, on board on Meteosat Second Generation (MSG) geostationary satellite, collects, each 15 minutes, images of the underneath part of the globe in 12 spectral bands with a spatial resolution of 3 km. In this work the Aerosol Optical Thickness (AOT) retrieval over land using SEVIRI data is presented. AOT at 0.55 μm is estimated minimizing the difference between measured and computed radiances in the visible channel centered at 0.6 μm by means Look-Up Tables (LUT) obtained using 6S radiative ransfer code. The 0.6 μm surface reflectance has been computed using different procedures based on SEVIRI channels 3 and 4 centered respectively around 1.6 and 3.9 µm. For the 0.6 μm surface reflectance retrieval using the 1.6 μm procedure, the measurements of five automatic sun-photometers of the Aerosols Robotic Network (AERONET) located in the Mediterranean area (Avignon, Laegeren, Modena, Rome and Lecce) has been used. The procedures show encouraging results in case of 1.6 μm procedure retrieval and the inadequacy of 3.9 μm procedure. An AOT map of the Po Valley (Italy), obtained from an MSG image taken during a typical winter polluted day, is shown in the paper and compared with MODIS retrieval.
Low-Frequency Modulation of Turbulent Diapycnal Mixing by Anticyclonic Eddies Inferred from the HOT Time Series

Profiles of potential density obtained from CTD measurements during the Hawaii Ocean Time series (HOT)programin thevicinityoftheislandofOahu,Hawaii,areusedtoevaluatelow-frequencyvariabilityof turbulent kinetic dissipation rates based on a finescale parameterization method. A distinct seasonal cycle, as well asan increasingtrendofdissipationrates, is foundin the upper300‐600 m. Thetrendis mainlydueto the much weaker diapycnal mixing in the first four years of the record, that is, 1988‐92. In the upper 300‐600 m, enhanced diapycnal mixing is found under anticyclonic eddies with the mean dissipation rate about 53% larger than that under eddy-free conditions. The modulation of dissipation rates by anticyclonic eddies becomes more evident with increasing eddy strength. The role of cyclonic eddies in modulating diapycnal mixing is almost negligible compared with that of anticyclonic eddies. The mean dissipation rate under cyclonic eddies is comparable to that under eddy-free conditions with a difference of less than 10%. Seasonality of the dissipation rates is partly modulated by the seasonal variation of anticyclonic eddies.
Synthesis of ureas in the bio-alternative solvent Cyrene

Cyrene as a bio-alternative solvent: a highly efficient, waste minimizing protocol for the synthesis of ureas from isocyanates and secondary amines in the bio-available solvent Cyrene is reported. This method eliminated the use of toxic solvents, such as DMF, and established a simple work-up procedure for removal of the Cyrene, which led to a 28-fold increase in molar efficiency versus industrial standard protocols.
Future southern African summer rainfall variability related to a southwest Indian Ocean dipole in HadCM3

Southern Africa is subject to strong interannual summer rainfall extremes associated with modes of climate variability. Interaction between these modes and the climate change signal make improving understanding of their future operation and links with southern African rainfall a priority. This paper examines future southern African summer rainfall variability related to a meridional dipole mode of southwest Indian Ocean SST variability (the SWIOD) in coupled climate model HadCM3. The SWIOD is central to southern African rainfall in a 1000‐year control simulation, and remains so during the twenty‐first century under two different CO2 forcing scenarios: SRES A2 and B1. Future rainfall variability connected with this mode is found to be sensitive to the emissions pathway, particularly in the second half of the century. Flooding episodes with anomalies near 4 mm day−1 in already wet regions and which are unprecedented in a 1000 year control run are simulated under A2 SRES forcing.
Estructura de los Andes Nordpatagónicos en los cordones Piltriquitrón y Serrucho y en el valle de El Bolsón (41º 30´ - 42 º 00´ S), Río Negro

Structure of the North Patagonian Andes in the Piltriquitron and Serrucho ranges and in the El Bolson valley (41o30´-42o00´S), Rio Negro province. The Cenozoic structure of the North Patagonian Andes of Argentina (41o- 42o S) is characterised by an E-verging imbricated fold and thrust belt with some important back-thrusts. The western sector (west of 71o 15´ W) exhibits back-thrust systems that interact with the E-verging thrusts conforming triangular areas. There are two important back-thrust systems that have deformed both the Piltriquitron (2,284 m) and Serrucho ranges (2,120 m). The first is composed of three W-verging thrusts with belts of intense deformation; the second system consists of at least two N-trending faults that form the great western scarp of the mountain range. As a consequence of the interaction with the E-verging thrusts, the Paleogene deposits of the El Bolson valley have been deformed into a large N-trending drag-syncline. From a stratigraphical point of view, the back-thrust systems expose igneous and metamorphic rocks of the pre-Mesozoic basement. Their cartographic pattern suggests that both are branches of the Ventana - Catedral thrust, a main structure that is the boundary between the western and the eastern sectors of the fold and thrust belt. It is proposed that the surface structure might represent a subsurface thick-skinned triangular zone, whose location is related to the Cenozoic tectonic inversion of normal faults formed during Mesozoic extensional regime, which controlled the palaeogeographic distribution of the Jurassic volcano-sedimentary deposits.
UvA-DARE (

Clustering technology has found numerous applications in mining textual data. It was shown to enhance the performance of retrieval systems in various different ways, such as identifying different query aspects in search result diversiﬁcation, improving smoothing in the context of language modeling, matching queries with documents in a latent topic space in ad-hoc retrieval, summarizing documents etc. The vast majority of clustering methods have been developed under the assumption of a static corpus of long (and hence textually rich) documents. Little attention has been given to streaming corpora of short text, which is the predominant type of data in Web 2.0 applications, such as social media, forums, and blogs. In this paper, we consider the problem of dynamically clustering a streaming corpus of short documents. The short length of documents makes the inference of the latent topic distribution challenging, while the temporal dynamics of streams allow topic distributions to change over time. To tackle these two challenges we propose a new dynamic clustering topic model - DCT - that enables tracking the time-varying distributions of topics over documents and words over topics. DCT models temporal dynamics by a short-term or long-term dependency model over sequential data, and overcomes the difﬁculty of handling short text by assigning a single topic to each short document and using the distributions inferred at a certain point in time as priors for the next inference, allowing the aggregation of information. At the same time, taking a Bayesian approach allows evidence obtained from new streaming documents to change the topic distribution. Our experimental results demonstrate that the proposed clustering algorithm outperforms state-of-the-art dynamic and non-dynamic clustering topic models in terms of perplexity and when integrated in a cluster-based query likelihood model it also outperforms state-of-the-art models in terms of retrieval quality.
Evaluation of the instrumental and relocated epicentres of Iranian earthquakes

Summary. Comparison of the instrumentally located and relocated epicentres (ISS, BCIS, USGS, Nabavi (IGS), Nowroozi, etc.) of Iranian earthquakes with the macroseismic epicentres of the largest magnitude and best studied earth- quakes, reveals deficiencies in the deteimination of the earthquake epicentres. The errors of determination appear to be random rather than consistent and are substantially larger than those quoted by the various agencies or individuals. This suggests that the incompatibility of seismicity and tectonic structures revealed by seismotectonic maps is at least partly due to location errors.