Miracle-dz/UniFAR-FTUs huggingface dataset:
Macroscopic Percolation Model of Immiscible Displacement: Effects of Buoyancy and Spatial Structure

Percolation theory, commonly used to study quasi-static immiscible displacement at the microscopic scale, is here extended to simulations of gravity-stable drainage and imbibition in three-dimensional porous media with spatially correlated macroscopic properties. The result of this extension is a macroscopic percolation on a regular lattice of sites, where lattice sites represent regions in a porous medium characterized by different macroscopic properties (e.g., absolute permeability, capillary pressure, and relative permeability curves). These properties are assigned to lattice sites by virtue of parametrizations in terms of local permeability. We present a general formulation of macroscopic percolation that accounts for gravitational effects, which can be important in large-scale immiscible displacements with nonzero density difference. In such cases, we find that the local saturation distribution is markedly different from the distribution of saturation under conditions of negligible buoyancy. Displacements with nonzero density difference proceed with the formation of a transition zone of length inversely proportional to a macroscopic Bond number which characterizes the relative importance of capillary and buoyancy forces at the macroscopic scale. Several important features of percolation at the microscopic scale are also manifested at the macroscopic scale. These include the effects of lattice dimensionality and spatial correlation on the macroscopic percolation threshold and accessibility characteristics. In the absence of buoyancy forces, the large-scale capillary pressure and relative permeability behavior of a heterogeneous system is dictated mainly by the structure of the permeability field and can be explained in terms of macroscopic accessibility. Spatial correlation of permeability is found to have pronounced effects on the large-scale drainage relative permeability curves.
Tracking 3D free form object in video sequence

In this paper we describe an original method for the 3D free form object tracking in monocular vision. The main contribution of this article is the use of the skeleton of an object in order to recognize, locate and track this object in real time. Indeed, the use of this kind of representation made it possible to avoid difficulties related to the absence of prominent elements in free form objects (which makes the matching process easier). The skeleton is a lower dimension representation of the object, it is homotopic and it has a graph structure. This allowed us to use powerful tools of the graph theory in order to perform matching between scene objects and models (recognition step). Thereafter, we used skeleton extremities as interest points for the tracking. Keywords: Tracking, 3D free form object, Skeletonization, Graph matching.
ABySS-Explorer: Visualizing Genome Sequence Assemblies

One bottleneck in large-scale genome sequencing projects is reconstructing the full genome sequence from the short subsequences produced by current technologies. The final stages of the genome assembly process inevitably require manual inspection of data inconsistencies and could be greatly aided by visualization. This paper presents our design decisions in translating key data features identified through discussions with analysts into a concise visual encoding. Current visualization tools in this domain focus on local sequence errors making high-level inspection of the assembly difficult if not impossible. We present a novel interactive graph display, ABySS-Explorer, that emphasizes the global assembly structure while also integrating salient data features such as sequence length. Our tool replaces manual and in some cases pen-and-paper based analysis tasks, and we discuss how user feedback was incorporated into iterative design refinements. Finally, we touch on applications of this representation not initially considered in our design phase, suggesting the generality of this encoding for DNA sequence data.
Application of the eddy-covariance method under the canopy at a boreal forest site in central Sweden

The eddy-covariance (EC) method was applied at 1.5 m height, for the period 2007-2010 at Norunda, central Sweden, for calculating energy (sensible and latent heat) and carbon dioxide (CO2) fluxes. The aim of this study was to assess the applicability of EC method above the forest floor. In 2007 an open-path EC system was used and in 2008, 2009 and 2010 a closed-path system was used. The energy and CO2 fluxes showed a clear annual pattern, with maximum values occurring in the summer season or at the beginning of September. The values of the sensible heat (H) flux were low, below 10 Wm-2, while the latent heat (LE) flux had annual daily average maximum values of 48 Wm-2 (2007), 18 Wm-2 (2008) and 27 Wm-2 (2009 and 2010). The mean annual CO2 flux values were 2.5 µmol m-2s-1 (2007 and 2008), 3 µmol m-2s-1 in 2009 and 2.8 µmol m-2s-1 in 2010. The fluxes measured in 2009 and 2010 were on average higher than the ones measured in 2008, a possible consequence of the forest thinning operation, which allowed more net radiation to reach the ground and caused an increase in turbulence above the forest floor. LE and CO2 fluxes measured with the open-path system had the biggest values and the largest variability under the entire study periods. The summer daily patterns of the energy fluxes showed higher LE than H throughout the entire 24 hours cycle. Daily summertime H flux was positive during 2009 and 2010, however a decrease was observed during afternoon, when the flux became negative. CO2 flux was very variable in time in 2007 and during nights, a consequence of both the use of an open-path system and the data selection turbulence criterion, linked to the standard deviation of the vertical wind velocity. A mid-day minimum was observed for the summer CO2 flux in 2009 and 2010, caused by photosynthesis inside the footprint area of the EC system. A comparison of EC and soil chamber data showed that CO2 fluxes measured by both methods followed in general the same patterns; however there was a discrepancy between the recorded values. On average, the EC fluxes accounted for 39 to 52% of the soil chamber fluxes. These results are consistent to other studies. In order to have a complete understanding of the applicability of the EC method above the forest floor at Norunda, further studies are necessary in order to analyze the energy balance closure, the spectral corrections for the raw EC data and the treatment of CO2 flux under very low turbulent conditions.
Cascading Behavior in Large Blog Graphs

How do blogs cite and influence each other? How do such links evolve? Does the popularity of old blog posts drop exponentially with time? These are some of the questions that we address in this work. Our goal is to build a model that generates realistic cascades, so that it can help us with link prediction and outlier detection. Blogs (weblogs) have become an important medium of information because of their timely publication, ease of use, and wide availability. In fact, they often make headlines, by discussing and discovering evidence about political events and facts. Often blogs link to one another, creating a publicly available record of how information and influence spreads through an underlying social network. Aggregating links from several blog posts creates a directed graph which we analyze to discover the patterns of information propagation in blogspace, and thereby understand the underlying social network. Not only are blogs interesting on their own merit, but our analysis also sheds light on how rumors, viruses, and ideas propagate over social and computer networks. Here we report some surprising findings of the blog linking and information propagation structure, after we analyzed one of the largest available datasets, with 45,000 blogs and ~ 2.2 million blog-postings. Our analysis also sheds light on how rumors, viruses, and ideas propagate over social and computer networks. We also present a simple model that mimics the spread of information on the blogosphere, and produces information cascades very similar to those found in real life.
Improved Differential Evolution on Optimizing 2-Level Ant Clustering Using of Variation

Ant based Clustering (ANT) is a very powerful tool for automatic detection of relevant clusters. The extended version of ANT, two-level Ant based Clustering (2LANT) was introduced for improving ANT clustering in explorative manner. However, structural methods for efficiently confirming the competent optimization of 2LANT initialization are lacking. Due to the important advantages over other optimization algorithms belonging to differential evolution (DE) approach, this paper investigates the utilization of the original DE as well as the variations, here called VarDE1 and VarDE2 as tools for optimizing the initial cluster weights of 2LANT. Such investigated approaches are respectively so called DE+2LANT, VarDE1+2LANT and VarDE2+2LANT. With respect to the different choices of mutation process, both variant DEs would get better accuracy than the original one. More elitism on mutation process is involved with VarDE2+2LANT rather than with VarDE1+2LANT; whilst the most random mutation is applied by DE+2LANT. 10fold cross validation experiments are taken on real-world and artificial data sets with an identified number of clusters. Within the scope of this paper, the investigation results point out the better clustering performance of the variant DEs, VarDE2+2LANT over the related approaches. 
ESTIMATION OF IN-SITU SHEAR STRENGTH PARAMETERS OF WEATHERED GRANITIC (MASADO) SLOPES USING LIGHTWEIGHT DYNAMIC CONE PENETROMETER

ABSTRACT A major problem in the geotechnical approach to the stability of natural slopes is that there is usually little information on the in-situ geotechnical conditions, because of the extreme difficulty associated with ground investigations of steep slopes covered with vegetation. In this study, a lightweight dynamic cone penetration test (LWDCPT) has been introduced for a geotechnical survey of natural weathered granitic (Masado) slopes. Based on a series of direct shear tests, the internal friction angle and the apparent cohesion of reconstituted Masado soil were found to be fairly closely related to the void ratio and the degree of saturation in the soil. From the laboratory calibration tests, an equation was created to relate the dynamic cone resistance (qd) and the void ratio of reconstituted Masado under different degrees of saturation. Equations were developed to calculate the internal friction angle and the apparent cohesion from the value of qd for Masado at a known degree of saturation. LWDCPT and direct shear tests were carried out on undisturbed samples taken from a natural Masado slope. The estimated internal friction angle and the apparent cohesion calculated with the value of qd in the LWDCPTs agreed fairly well with those of tests on the undisturbed samples obtained in laboratory shear tests.
Lo stock di capitale nelle regioni italiane

In questo lavoro si descrive la costruzione di una base di dati dello stock di capitale, sia privato che pubblico, nelle regioni italiane. Il capitale privato e’ calcolato utilizzando come riferimento una ripartizione regionale dello stock aggregato per l’anno 1981. Le stime per gli altri anni, dal 1970 al 1991, si ottengono ripartendo le variazioni dello stock aggregato in base all’andamento degli investimenti regionali. Il capitale pubblico e’ calcolato con la tecnica dell’inventario permanente. L’investimento pubblico aggregato e’ ripartito per regione e per tipologia di bene utilizzando i dati contenuti nella pubblicazione annuale dell’ISTAT "Opere Pubbliche". Si ottengono cosi’ delle stime del capitale pubblico regionale per gli anni dal 1970 al 1991.
Sociodemographic and clinical factors associated with the preference between NNRTIs and PIs for the initial treatment of HIV infection: Perfil-es study

ABSTRACT The Perfil-es study demonstrated that, while non-nucleoside reverse transcriptase inhibitor (NNRTI)-based initial antiretroviral therapy (ART) is more frequently used in human immunodeficiency virus (HIV)-infected naïve patients, ritonavir-boosted protease inhibitors (PI/r)-based regimens are the preferred option in patients with advanced infectious stages or high baseline viral load. The present analysis focused on the second phase of the Perfil-es study, where sociodemographic and clinical data were retrospectively collected from patients starting NNRTI- or PI/r-based regimens in order to identify factors that could influence the choice of initial ART. Patients’ characteristics were compared by both bivariate and multivariate analyses. A total of 642 patients were evaluated. The main transmission group was men who have sex with men (MSM) (48%), and 24% of patients were coinfected with hepatitis B or C. Patients with cardiovascular risk accounted for 56%, and 15% had a neuropsychiatric history. Anxiolytics (29%), antidepressants (18%) and methadone (18%) were the most frequent concomitant medications. The use of PI/r-based regimens was more frequent in older patients, childbearing potential women patients coinfected with hepatitis B or C, and those with cardiovascular risk and a neuropsychiatric history. The presence of a neuropsychiatric disorder (OR: 1.912; CI 95%: 1.146–3.191; p < .05) and the use of concomitant medication (OR: 1.736; CI 95%: 1.204–2.502; p < .01) were identified as independent factors associated with the selection of PI/r-based regimens. MSM sexual conduct was the only independent factor related to the selection of NNRTI-based ART (OR: 0.699; CI 95%: 0.504–0.970; p < .05). Neither the physicians’ characteristics nor the geographical area where HIV patients were attended influenced the choice of ART. In conclusion, patients’ comorbidity, pregnancy potential and lifestyle seem to influence the choice of ART. Neuropsychiatric comorbidity and concomitant medication, mainly related to this condition, appear to be associated with the use of PI/r-based initial ART while MSM seem more likely to receive NNRTI-based regimens in Spain.
Enigma variations for peptides and their transporters in higher plants.

BACKGROUND Two families of proteins that transport small peptides, the oligopeptide transporters (OPTs) and the peptide transporters (PTRs), have been recognized in eukaryotes. Higher plants contain a far greater number of genes for these transporters than do other eukaryotes. This may be indicative of the relative importance of (oligo)peptides and their transport to plant growth and metabolism. RECENT PROGRESS Recent studies are now allowing us to assign functions to these transporters and are starting to identify their in-planta substrates, revealing unexpected and important contributions of the transporters to plant growth and developmental processes. This Botanical Briefing appraises recent findings that PTRs and OPTs have key roles to play in the control of plant cell growth and development. Evidence is presented that some of these transporters have functions outside that of nitrogen nutrition and that these carriers can also surprise us with their totally unexpected choice of substrates.
A new formalism for the quantification of tissue perfusion by the destruction-replenishment method in contrast ultrasound imaging

A new formalism is presented for the destruction-replenishment perfusion quantification approach at low mechanical index. On the basis of physical considerations, best-fit methods should be applied using perfusion functions with S-shape characteristics. These functions are first described for the case of a geometry with a single flow velocity, then extended to the case of vascular beds with blood vessels having multiple flow velocity values and directions. The principles guiding the analysis are, on one hand, a linearization of video echo signals to overcome the log-compression of the imaging instrument, and, on the other hand, the spatial distribution of the transmit-receive ultrasound beam in the elevation direction. An in vitro model also is described; it was used to confirm experimentally the validity of the approach using a commercial contrast agent. The approach was implemented in the form of a computer program, taking as input a sequence of contrast-specific images, as well as parameters related to the ultrasound imaging equipment used. The generated output is either flow-parameter values computed in regions-of-interest, or parametric flow-images (e.g., mean velocity, mean transit time, mean flow, flow variance, or skewness). This approach thus establishes a base for extracting information about the morphology of vascular beds in vivo, and could allow absolute quantification provided that appropriate instrument calibration is implemented.
Depth Weighted Modified Hausdorff Distance for Range Face Recognition

The definition of Hausdorff distance is a measure of the correspondence of two point sets. In this paper, we propose a novel implementation of a person verification system based on depth-weighted Hausdorff distance (DWHD) using the surface curvatures of the human face. This new method incorporates the depth information and curvatures of local facial features. The weighting function used in this paper is based on depth values, which have differential properties of a face according to the people, so that the distance of this extracted edge maps will be emphasized. Experimental results based on combination of the maximum, minimum, and Gaussian curvature according to threshold values show that DWHD achieves recognition rate of 92.8%, 97.6% and 92.8% of the cases for 5 ranked candidates, respectively, and the proposed method of combined recognition rate for each curvature shows the best.
Work efficient higher-order vectorisation

Existing approaches to higher-order vectorisation, also known as flattening nested data parallelism, do not preserve the asymptotic work complexity of the source program. Straightforward examples, such as sparse matrix-vector multiplication, can suffer a severe blow-up in both time and space, which limits the practicality of this method. We discuss why this problem arises, identify the mis-handling of index space transforms as the root cause, and present a solution using a refined representation of nested arrays. We have implemented this solution in Data Parallel Haskell (DPH) and present benchmarks showing that realistic programs, which used to suffer the blow-up, now have the correct asymptotic work complexity. In some cases, the asymptotic complexity of the vectorised program is even better than the original.
Median Filtered Image Quality Enhancement and Anti-Forensics via Variational Deconvolution

Median filtering enjoys its popularity as a widely adopted image denoising and smoothing tool. It is also used by anti-forensic researchers in helping disguise traces of other image processing operations, e.g., image resampling and JPEG compression. This paper proposes an image variational deconvolution framework for both quality enhancement and anti-forensics of median filtered (MF) images. The proposed optimization-based framework consists of a convolution term, a fidelity term with respect to the MF image, and a prior term. The first term is for the approximation of the median filtering process, using a convolution kernel. The second fidelity term keeps the processed image to some extent still close to the MF image, retaining some denoising or other image processing artifact hiding effects. Using the generalized Gaussian as the distribution model, the last image prior term regularizes the pixel value derivative of the obtained image so that its distribution resembles the original one. Our method can serve as an MF image quality enhancement technique, whose efficacy is validated by experiments conducted on MF images which have been previously “salt & pepper” noised. Using another parameter setting and with an additional pixel value perturbation procedure, the proposed method outperforms the state-of-the-art median filtering anti-forensics, with a better forensic undetectability against existing detectors as well as a higher visual quality of the processed image. Furthermore, the feasibility of concealing image resampling traces and JPEG blocking artifacts is demonstrated by experiments, using the proposed median filtering anti-forensic method.
A Prototype WRF-Based Ensemble Data Assimilation System for Dynamically Downscaling Satellite Precipitation Observations

Abstract In the near future, the Global Precipitation Measurement (GPM) mission will provide precipitation observations with unprecedented accuracy and spatial/temporal coverage of the globe. For hydrological applications, the satellite observations need to be downscaled to the required finer-resolution precipitation fields. This paper explores a dynamic downscaling method using ensemble data assimilation techniques and cloud-resolving models. A prototype ensemble data assimilation system using the Weather Research and Forecasting Model (WRF) has been developed. A high-resolution regional WRF with multiple nesting grids is used to provide the first-guess and ensemble forecasts. An ensemble assimilation algorithm based on the maximum likelihood ensemble filter (MLEF) is used to perform the analysis. The forward observation operators from NOAA–NCEP’s gridpoint statistical interpolation (GSI) are incorporated for using NOAA–NCEP operational datastream, including conventional data and clear-sky satellite obse.
A pre-Hispanic chiefdom in Barinas, Venezuela : excavations at Gaván-complex sites

7 Acknowledgments. 1
Pruning policies for two-tiered inverted index with correctness guarantee

The Web search engines maintain large-scale inverted indexes which are queried thousands of times per second by users eager for information. In order to cope with the vast amounts of query loads, search engines prune their index to keep documents that are likely to be returned as top results, and use this pruned index to compute the first batches of results. While this approach can improve performance by reducing the size of the index, if we compute the top results only from the pruned index we may notice a significant degradation in the result quality: if a document should be in the top results but was not included in the pruned index, it will be placed behind the results computed from the pruned index. Given the fierce competition in the online search market, this phenomenon is clearly undesirable. In this paper, we study how we can avoid any degradation of result quality due to the pruning-based performance optimization, while still realizing most of its benefit. Our contribution is a number of modifications in the pruning techniques for creating the pruned index and a new result computation algorithm that guarantees that the top-matching pages are always placed at the top search results, even though we are computing the first batch from the pruned index most of the time. We also show how to determine the optimal size of a pruned index and we experimentally evaluate our algorithms on a collection of 130 million Web pages.
Probing deep weathering in the Shale Hills Critical Zone Observatory, Pennsylvania (USA): the hypothesis of nested chemical reaction fronts in the subsurface

Weathering is both an acid‐base and a redox reaction in which rocks are titrated by meteoric carbon dioxide (CO2) and oxygen (O2). In general, the depths of these weathering reactions are unknown. To determine such depths, cuttings of Rose Hill shale were investigated from one borehole from the ridge and four boreholes from the valley at the Susquehanna Shale Hills Observatory (SSHO). Pyrite concentrations are insignificant to depths of 23 m under the ridge and 8–9 m under the valley. Likewise, carbonate concentrations are insignificant to 22 and 2 m, respectively. In addition, a 5–6 m‐thick fractured layer directly beneath the land surface shows evidence for loss of illite, chlorite, and feldspar. Under the valley, secondary carbonates may have precipited.