Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating Surface Reflectance from Images

Motivation: Physical surfaces such as metal, plastic, or paper have different optical qualities that lead to different characteristics in images. Information on the reflectance of a visual surface can be a valuable cue for inferring the properties or identity of a material. Such information is necessary to render a surface realistically in computer graphics and could also allow a vision algorithm to compensate for the effects of non-Lambertian reflectance in visual tasks such as motion estimation, stereo reconstruction, and object recognition. A complete specification of a surface involves the bidirectional reflectance distribution function (BDRF), which describes the proportion of light reflected from any given incident direction to any given view direction. It is a massive four-dimensional function, which can be carefully measured in the laboratory. Humans are sensitive to a small subset of surface properties, such as the color, gloss, or roughness, and they are able to infer these properties from single images taken in unknown, uncontrolled lighting.
SAPling: a Scan-Add-Print barcoding database system to label and track asexual organisms

SUMMARY We have developed a ‘Scan-Add-Print’ database system, SAPling, to track and monitor asexually reproducing organisms. Using barcodes to uniquely identify each animal, we can record information on the life of the individual in a computerized database containing its entire family tree. SAPling has enabled us to carry out large-scale population dynamics experiments with thousands of planarians and keep track of each individual. The database stores information such as family connections, birth date, division date and generation. We show that SAPling can be easily adapted to other asexually reproducing organisms and has a strong potential for use in large-scale and/or long-term population and senescence studies as well as studies of clonal diversity. The software is platform-independent, designed for reliability and ease of use, and provided open source from our webpage to allow project-specific customization.
Personality and alignment processes in dialogue: towards a lexically-based unified model

This thesis explores approaches to modelling individual differences in language use. The differences under consideration fall into two broad categories: Variation of the personality projected through language, and modelling of language alignment behaviour between dialogue partners. In a way, these two aspects oppose each other – language related to varying personalities should be recognisably different, while aligning speakers agree on common language during a dialogue. The central hypothesis is that such variation can be captured and produced with restricted computational means. Results from research on personality psychology and psycholinguistics are transformed into a series of lexically-based Affective Language Production Models (ALPMs) which are parameterisable for personality and alignment. The models are then explored by varying the parameters and observing the language they generate. ALPM-1 and ALPM-2 re-generate dialogues from existing utterances which are ranked and filtered according to manually selected linguistic and psycholinguistic features that were found to be related to personality. ALPM-3 is based on true overgeneration of paraphrases from semantic representations using the OPENCCG framework for Combinatory Categorial Grammar (CCG), in combination with corpus-based ranking and filtering by way of n-gram language models. Personality effects are achieved through language models built from the language of speakers of known personality. In ALPM-4, alignment is captured via a cache language model that remembers the previous utterance and thus influences the choice of the next. This model provides a unified treatment of personality and alignment processes in dialogue. In order to evaluate the ALPMs, dialogues between computer characters were generated and presented to human judges who were asked to assess the characters’ personality. In further internal simulations, cache language models were used to reproduce results of psycholinguistic priming studies. The experiments showed that the models are capable of producing natural language dialogue which exhibits human-like personality and alignment effects.
An update of the appraisal of the accuracy of thoracic discography as a diagnostic test for chronic spinal pain.

BACKGROUND Even though the prevalence of thoracic pain has been reported to be 13% of the general population and up to 22% of the population in interventional pain management settings, the role of thoracic discs as a cause of chronic thoracic and extrathoracic pain has not been well studied. The intervertebral discs, zygapophysial or facet joints, and other structures including the costovertebral and costotransverse joints have been identified as a source of thoracic pain. STUDY DESIGN A systematic review of provocation thoracic discography. OBJECTIVE To systematically assess and update the quality of clinical studies evaluating the diagnostic accuracy of provocation thoracic discography. METHODS A systematic review of the literature was performed to assess the diagnostic accuracy of thoracic discography with respect to chronic, function limiting, thoracic or extrathoracic pain. The available literature on thoracic discography was reviewed. A methodological quality assessment of included studies was performed using Quality Appraisal of Reliability Studies (QAREL). The level of evidence was classified as good, fair, and limited (or poor) based on the quality of evidence developed by the U.S. Preventive Services Task Force (USPSTF). Data sources included relevant literature identified through searches of PubMed and EMBASE from 1966 to June 2012, and manual searches of the bibliographies of known primary and review articles. RESULTS The evidence and clinical value of thoracic provocation discography is limited (poor) with a paucity of evidence, with only 2 studies meeting inclusion criteria. LIMITATIONS The limitation of this study continues to be the paucity of literature. CONCLUSION Based on the available evidence for this systematic review, due to limited evidence, thoracic provocation discography is rarely recommended for the diagnosis of discogenic pain in the thoracic spine, if conservative management has failed and facet joint pain has been excluded.
Collaborative perception for collision avoidance

The aim of this paper is to propose a collaborative perception system in order to avoid potential vehicle collisions. We present a basic system where vehicles ensure their own localization using a global positioning system with a Kalman filtering process. This information and the velocity data are broadcasted via a wireless network to its neighbours. Moreover, some of the vehicles are equipped with telemetric sensors, thus they can supply a direct perception of their surrounding environment and update the knowledge given by the network. If a potential collision is detected, the vehicles are brought under speed control. We analyse the results and the limits of this system. All results are validated via an extended perception simulator.
Distance magic graphs of high regularity

A distance magic labeling of a graph G with n vertices is such a bijection f from the vertex set of G to the set of integers {1, 2, . , n} that for every vertex in G the sum of labels of all adjacent vertices gives the same value k. A graph that allows such a labeling is a distance magic graph. There is an elegant construction of r-regular distance magic graphs with an even number of vertices for all feasible values of r. For graphs of odd order certain necessary and certain sufficient conditions are known for the existence of a distance magic labeling. In this paper we show that an (n−3)-regular distance magic graph with n vertices exists iff n ≡ 3 (mod 6) and that its structure is determined uniquely. Moreover, we simplify the constructions from a recent paper by Fronček into a single construction and provide another sufficient condition for the existence a distance magic graph with an odd number of vertices.
Contribution of conserved amino acids in mediating the interaction between EBNA2 and CBF1/RBPJk

The Epstein-Barr virus EBNA2 protein is a transcriptional activator that achieves promoter specificity through interaction with the cellular DNA-binding protein CBF1/RBPJk. Within the amino acid 252-to-425 EBNA2 domain that targets CBF1/RBPJk lie three amino acid clusters, conserved regions (CR) 5, 6, and 7, that are retained in the Epstein-Barr virus type A and type B and herpesvirus papio proteins. To further define the important features of the targeting domain, we constructed EBNA2 polypeptides containing deletions in the targeting domain and double or triple point mutations in the conserved motifs. The ability of these polypeptides and the type B and herpesvirus papio domains to interact with CBF1/RBPJk was examined by performing electrophoretic mobility shift assays and correlated with the effect of the mutations on EBNA2 transactivation. Both human type B EBNA2 and herpesvirus papio EBNA2 bound CBF1/RBPJk efficiently. Mutation of hydrophobic residues in CR6 severely impaired CBF1/RBPJk interaction and transactivation, while mutation of CR5 led to a moderate decrease in both activities. Mutation of CR7 had only a minor effect. Synthetic peptides corresponding to each of the conserved motifs were also used as competitors in an electrophoretic mobility shift assay. Only the peptide representing CR6 (amino acids 318 to 327), and not a version of this peptide mutated at the tryptophan residues at positions 323 and 324 (WW323,324), could compete for EBNA2 complex formation with CBF1/RBPJk. Overall, the data indicated that CR5 contributes to an optimal interaction, perhaps through stabilizing contacts, while CR6 forms a crucial interface with CBF1/RBPJk. The peptide competition data are consistent with direct contacts between WW323,324 and CBF1/RBPJk.
Associations of the fecal microbiome with urinary estrogens and estrogen metabolites in postmenopausal women.

CONTEXT The gut microbiota may influence the risk of breast cancer through effects on endogenous estrogens. OBJECTIVE The objective of the study was to investigate whether urinary estrogens and estrogen metabolites are associated with the diversity and composition of the fecal microbiome. DESIGN AND SETTING This was a cross-sectional study among women enrolled in Kaiser Permanente of Colorado. PARTICIPANTS A total of 60 women drawn from a random sample of healthy postmenopausal women (aged 55-69 y), without current or recent use of antibiotics or hormone therapy and no history of cancer or gastrointestinal disease participated in the study. OUTCOME MEASURES AND METHODS: Creatinine-standardized urinary estrogens (estrone and estradiol) and 13 hydroxylated estrogen metabolites were measured in spot urines by liquid chromatography-tandem mass spectrometry. The fecal microbiome was assessed using pyrosequencing of 16S rRNA amplicons. General linear models were used to test for associations of diversity and composition of the fecal microbiome with parent estrogen (estrone + estradiol), total estrogens, and estrogen metabolites and the ratio of estrogen metabolites to parent estrogen, which has been predictive of postmenopausal breast cancer risk in previous studies. RESULTS The ratio of metabolites to parents was directly associated with whole-tree phylogenetic diversity (R = 0.35, P = .01). Relative abundances of the order Clostridiales (R = 0.32, P = .02) and the genus Bacteroides (R = -0.30, P = .03) were also correlated with the ratio of metabolites to parents. Associations were independent of age, body mass index, and study design factors. CONCLUSIONS Our data suggest that women with a more diverse gut microbiome exhibit an elevated urinary ratio of hydroxylated estrogen metabolites to parent estrogen. Further research is warranted to confirm and relate these findings to clinical disease.
Hydrogen passivation of laser-induced defects for silicon solar cells

Hydrogen passivation of laser-induced defects is shown to be essential for the fabrication of laser doped solar cells. On first generation laser doped selective emitter solar cells where open circuit voltages are predominately limited by the full area back surface field, a 10 mV increase and 0.4 % increase in pseudo fill factor is observed through hydrogen passivation of defects generated during the laser doping process resulting in an efficiency gain of 0.35 % absolute. The passivation of such defects becomes of increasing importance when developing higher voltage devices, and can result in improvements on test structures up to 25 mV. On n-type PERT solar cells, an efficiency gain of 0.7 % absolute is demonstrated with increases in open circuit voltage and pseudo fill factor by applying a short low temperature hydrogenation process incorporating minority carrier injection using only hydrogen within the device. This process is also shown to improve the rear surface passivation increasing the short circuit current density from long wavelengths 0.2 mA/cm2 compared to that achieved using an Alneal process. Subsequently an average efficiency of 20.54 % is achieved.
Structural and Diffusional Effects of Hydrogen in TiNi

Hydrogen can be inadvertently added to Nitinol medical devices through electropolishing, caustic cleaning, or exposure to other acidic or basic solutions. Moderately high hydrogen concentrations can lead to embrittlement characterized by lowered ductility and changes in transformation behavior. The purpose of the present report is to discuss recent results on the effects of hydrogen in annealed TiNi. Samples are charged with hydrogen and analyzed with x-ray diffraction; these data indicate that even relatively small amounts of hydrogen can affect the crystal structure. Additions of up to 1000 wppm hydrogen increase the atomic volume by more than 2%, decrease peak intensity and broaden peak width. These observations are consistent with hydrogen-induced lattice strain. Peak splitting and additional diffraction peaks are observed with the absorption of 6000 wppm hydrogen, which indicates formation of a new phase. It is speculated that the new phase may be based on the B2 structure or may be stress-induced R-phase or martensite. This paper also discusses experiments and analysis on the removal of hydrogen from TiNi wire with 800 wppm through heat treatments at 400-800°C for 30-3000 seconds. Extensive experimental and analytical computations show that the activation energy of hydrogen diffusion under these conditions is approximately 125 kJ/mol.
A 1973-2008 Archive of Climate Surfaces for NW Maghreb

Climate archives are time series. They are used to assess temporal trends of a climate-dependent target variable, and to make climate atlases. A high-resolution gridded dataset with 1728 layers of monthly mean maximum, mean and mean minimum temperatures and precipitation for the NW Maghreb (28°N–37.3°N, 12°W–12°E, ~1-km resolution) from 1973 through 2008 is presented. The surfaces were spatially interpolated by ANUSPLIN, a thin-plate smoothing spline technique approved by the World Meteorological Organization (WMO), from georeferenced climate records drawn from the Global Surface Summary of the Day (GSOD) and the Global Historical Climatology Network-Monthly (GHCN-Monthly version 3) products. Absolute errors for surface temperatures are approximately 0.5 °C for mean and mean minimum temperatures, and peak up to 1.76 °C for mean maximum temperatures in summer months. For precipitation, the mean absolute error ranged from 1.2 to 2.5 mm, but very low summer precipitation caused relative errors of up to 40% in July. The archive successfully captures climate variations associated with large to medium geographic gradients. This includes the main aridity gradient which increases in the S and SE, as well as its breaking points, marked by the Atlas mountain range. It also conveys topographic effects linked to kilometric relief mesoforms.
Advances in Human Action Recognition: A Survey

Human action recognition has been an important topic in computer vision due to its many applications such as video surveillance, human machine interaction and video retrieval. One core problem behind these applications is automatically recognizing low-level actions and high-level activities of interest. The former is usually the basis for the latter. This survey gives an overview of the most recent advances in human action recognition during the past several years, following a well-formed taxonomy proposed by a previous survey [1]. From this state-of-the-art survey, researchers can view a panorama of progress in this area for future research.
Total and specific IgE in nasal polyps is related to local eosinophilic inflammation.

BACKGROUND Nasal polyps (NPs) are characterized by eosinophilic inflammation and often coexist with asthma. However, the role of atopy and IgE in NP pathogenesis is unclear. OBJECTIVE We sought to determine whether there is an association between total and specific IgE to a variety of allergens in polyp and nonpolyp tissue and markers of eosinophilic inflammation or skin test results. METHODS Homogenates were prepared from nasal tissue of 20 patients with NPs and 20 patients without NPs and analyzed for concentrations of IL-5, IL-4, eotaxin, leukotriene (LT) C4/D4/E4, sCD23, and histamine (ELISA). Eosinophil cationic protein (ECP), tryptase, and total and specific IgE for inhalant allergens and Staphylococcus aureus enterotoxins were measured (ImmunoCAP). RESULTS The concentrations of total IgE, IL-5, eotaxin, ECP, LTC4/D4/E4, and sCD23 were significantly higher in NP tissue compared with nonpolyp tissue. Total IgE was significantly correlated to IL-5, ECP, LTC4/D4/E4, and sCD23 and to the number of eosinophils in NPs. On the basis of the presence of specific IgE antibodies in tissue, 3 NP groups were defined. NP group 1 demonstrated no measurable specific IgE, and NP group 2 selected specific IgE. The third group demonstrated a multiclonal specific IgE, including IgE to S aureus enterotoxins, a high total IgE level, and a high prevalence of asthma. CONCLUSIONS These studies suggest that there is an association between increased levels of total IgE, specific IgE, and eosinophilic inflammation in NPs, which may be of relevance in the pathophysiology of nasal polyposis. Similarly, the presence of specific IgE to staphylococcal enterotoxins A and B also points to a possible role of bacterial superantigens.
A single high dose of vitamin C counteracts the acute negative effect on microcirculation induced by smoking a cigarette.

Cigarette smoking is associated with marked acute changes in microcirculation including reduced blood flow. We tested the hypothesis that the reduced blood flow velocity is due to the imbalance between prooxidants and antioxidants that occurs as a consequence of smoking and that it can be reduced by an antioxidant. The effect of smoking a single cigarette on nail-fold microcirculation was analyzed in 24 healthy subjects with varying smoking habits. Vital capillary microscopy was used and the blood cell flow velocity in the capillaries was evaluated before and 1-30 min after smoking. Smoking induced a marked decrease in microcirculatory blood flow in 23 of the 24 subjects (40-50% decrease 1-5 min after smoking). This change was reduced by more than 50% in the same subjects after intake of 2 g of vitamin C 2 h before smoking (P < 0.0001 by ANOVA test) with smokers responding similarly to nonsmokers in these experiments. Intake of 1 g of vitamin C had no significant effect on the smoking-induced changes in most of the subjects tested (n = 11). Pretreatment with aspirin had little or no effect on the response to smoking (n = 9). Our results show that treatment with a single high dose of vitamin C can reduce and in some individuals even completely abolish the negative acute effect on microcirculation induced by smoking a single cigarette. This effect of vitamin C is not likely to be mediated by the cyclooxygenase system.
Effect of Corn Residue Biochar on the Hydraulic Properties of Sandy Loam Soil

Biochar has an ability to alter the biological, chemical, and physical properties of soil due to its physicochemical properties such as surface area, porosity, nutrient retention ability, available nutrient contents, aromaticity, etc. The present study was designed to evaluate the impact of physical properties and application rate of biochar on the hydraulic properties of a sandy loam soil in the short term. Biochar was produced at 500 °C from dried corn residue (BC500). The BC500 was incorporated at the rates of 0, 2.5%, 5.0%, 7.5%, and 10% (w·w−1) into the sandy loam soil and filled up to a height of 4 cm, in cores having 5 cm diameter and height. Each treatment was performed in triplicate and equilibrated for 30 days. Then saturated hydraulic conductivity (Ksat), water holding capacity (WHC), and bulk density were determined in each sample after four days of saturation at room temperature in a water bath. The BC500 particle size distribution, pores, and surface functional groups were assessed. The Ksat exhibited a highly significant exponential reduction from 0% to 7.5% of BC500 application and approached an asymptote at 10% BC500. Bulk density showed a significant negative correlation to biochar application rate. The WHC and BC500 application rate illustrated a strong positive relationship. Biochar surface was free from hydrophobic functional groups. The addition of BC500 has a positive influence on soil hydraulic properties, primarily due to the increased soil porosity. The BC500 is composed of a microporous structure and hydrophilic surface that retain water in sandy textured soils. The application of BC500 would be a wise investment to maximize the water use efficiency in soils for agricultural production.
BioRuby: bioinformatics software for the Ruby programming language

Summary: The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. Availability: BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. Contact: katayama@bioruby.org
Cromaticity improvement in images with poor lighting using the Multiscale-Retinex MSR algorithm

An important factor when realizing image capture using electronic means (photographic or video camera), is the lighting source type present at the capture moment. If the lighting is deficient, the information present in the image is hidden for the Human Vision System (HVS), such that the color and detail characteristics introduce values with low luminance. As a solution for this lighting problem, the Multiscale-Retinex (MSR) algorithm is proposed, based on the understanding of how the HVS interprets and adapts the perception of colors. This solution can be used as a preprocessing stage to correct the lack of an adequate lighting source like the standard illuminant D65 (light source with similar characteristics to midday sunlight). The MSR algorithm increase the chromatic content of the image, this improves the objects visibility in the scene. The lack effects of lighting are minimized and its magnitude content evaluates the resulting chromaticity vector to characterize the MSR.