Miracle-dz/UniFAR-FTUs huggingface dataset:
Skybox as Info Billboard

In this paper we propose a new way of information mapping to the upper part of the virtual skybox. This mapping brings improvement to the existing virtual world’s projects with providing relevant information instead of a static or animated skybox. Information that is used in our approach is visualized in a chronological correspondence. We explain basic terms as well as previous similar projects. Application of the Ajax3D technology is described as a powerful method to provide the connection between database and X3D scene. Moreover, except the visible order also solution for the user interaction is provided. Implementation is shown in the SkyBoard application, that can be found in the page http://www.dzana. sk/projects/bakalarka/index.html. It is possible to use this method for educational or informative purposes.
Perceptions and social valuations of landscape. Objectives and methodology for citizen participation in landscape policies

Abstract Since the approval of the European Landscape Convention, social perception has been accepted as one of landscape’s defining components and, therefore, any strategy for its planning, protection or management has to be in possession of knowledge produced by citizen participation procedures. The Convention did not formally state what these procedures are and no methodology has been agreed upon for guaranteeing their inclusion in landscape analysis and praxis. This article puts forward a methodological proposal to this end that has been designed, tested and put into practice in the compiling of the Landscape Catalogue of the Province of Seville (Andalusia, Spain). Arguments put forward to support the methodological choices made are evaluated with the aim that this proposal might be of use for other initiatives to create a theoretical and practical corpus for social participation in landscape policies.
Combining DMN and the Knowledge Base Paradigm for Flexible Decision Enactment

Representing business rules and the rules governing businesses is in itself a challenging task. Supporting the enactment of the represented rules poses even greater challenges. We present a novel approach to enact decisions represented using the Decision Model and Notation standard. The IDP knowledge base system is used as an inference engine for DMN decision models. The different forms of inference provided by the knowledge base system allow for flexible decision enactment. Our approach additionally allows for decision enactment by automatically generating an interactive graphical interface from the specification of the decisions.
Preliminary Phytochemical Screening and Antispasmodic Activity of Artemisia macrocephala Jacquem

The current work describes the antispasmodic action of Artemisia macrocephala, which is achieved via blocking of the calcium channels. This explains its traditional use as an antispasmodic.The crude methanolic extract of A. macrocephala was studied for possible relaxant effect(s) on spontaneous rabbits′ jejunum preparations. Analytical-grade chemicals were used in the experimental protocols. A. macrocephala gave positive tests for flavonoids, saponins, glycosides, alkaloids, and terpenes. A. macrocephala caused relaxation of spontaneous rabbits′ jejunum preparations (n=6) at a dose of 10.0 mg/mL (EC 50 = 6.95 ± 0.20 mg/mL; 95% CI: 6.2 to 7.5). Contractions induced by 80 mM potassium chloride (KCl) were also relaxed by the A. macrocephala at dose of 10.0 mg/mL. Attempting to find an explanation for the possible mode of action, we found that, A. macrocephala at concentration of 1.0 mg/mL produced rightward shift in the calcium chloride curves, with EC 50 value of −1.65 ± 0.02 log [Ca ++ ] M vs control with EC 50 value of −2.44 ± 0.043 for calcium chloride curves. At a concentration of 1.0 mg/mL it could produce 52.4% of the control response at log [Ca ++ ] M = −1.6. Similarly, verapamil at a concentration of 0.1 μM produced a rightward shift, with EC 50 value of −1.74 ± 0.026 log [Ca ++ ] M (95% CI: -1.66 to -1.82; n=6) vs control with EC 50 value of −2.45 ± 0.05 log [Ca ++ ] M (95% CI: - 2.23 to -2.91; n=6). The right shift of the EC 50 values is justification for the folkloric use of A. macrocephala as an antispasmodic, suggesting that the possible mode of action is through calcium channel blockade.
Cohesion , Genome Stability , and Carcinogenesis Replication Slippage : Implications for Sister Chromatid Damage and Suppresses Spontaneous Sister Chromatid BRCA 1 Regulates RAD 51 Function in Response to DNA

The breast/ovarian cancer susceptibility proteins BRCA1 and BRCA2 maintain genome stability, at least in part, through a functional role in DNA damage repair. They both colocalize with RAD51 at sites of DNA damage/replication and activate RAD51-mediated homologous recombination repair of DNA double-strand breaks (DSB). Whereas BRCA2 interacts directly with and regulates RAD51, the role of BRCA1 in this process is unclear. However, BRCA1 may regulate RAD51 in response to DNA damage or through its ability to interact with and regulate MRE11/RAD50/NBS1 (MRN) during the processing of DSBs into single-strand DNA (ssDNA) ends, prerequisite substrates for RAD51, or both. To test these hypotheses, we measured the effect of BRCA1 on the competition between RAD51-mediated homologous recombination (gene conversion and crossover) versus RAD51-independent homologous recombination [single-strand annealing (SSA)] for ssDNA at a site-specific chromosomal DSB within a DNA repeat, a substrate for both homologous recombination pathways. Expression of wild-type BRCA1 in BRCA1-deficient human recombination reporter cell lines promoted both gene conversion and SSA but greatly enhanced gene conversion. In addition, BRCA1 also suppressed both spontaneous gene conversion and deletion events, which can arise from either crossover or sister chromatid replication slippage (SCRS), a RAD51-independent process. BRCA1 does not seem to block crossover. From these results, we conclude that (a) BRCA1 regulates RAD51 function in response to the type of DNA damage and (b) BRCA1 suppresses SCRS, suggesting a role for this protein in sister chromatid cohesion/alignment. Loss of such control in response to estrogen-induced DNA damage after BRCA1 inactivation may be a key initial event that triggers genome instability and carcinogenesis. (Cancer Res 2005; 65(24): 11384-91)
Spatial and Temporal Patterns in Macrofaunal Diversity Components Relative to Sea Floor Landscape Structure

We examined temporal changes in macrofaunal α- and β-diversity over several spatial scales (within patches, among patches, across landscapes and across regions) in Long Island Sound on the northeast USA coast. Regional ε-diversity was estimated at 144 taxa, however γ-diversity fluctuated over time as did α- and β-diversity components. Based on additive partitioning, patch- and region-scale β-diversity components generally had the highest contributions to γ-diversity; lower percentages were found at within-patch and landscape scales. Multiplicative diversity partitioning indicated highest species turnover at within- and among patch scales. For all partition results, within-patch and patch-scale β-diversity increased sharply when hypoxia impacted benthic communities. Spatial variation in diversity components can be attributed to the collection of different patch types at varying spatial scales and their associated habitats across the benthic landscapes, as well as gradients in depth and other estuarine-scale characteristics. Temporal variation in diversity components across spatial scales may be related to seasonal changes in habitat heterogeneity, species population dynamics, and seasonal disturbances. Rare species were significant and temporally consistent components of macrofaunal diversity patterns over different spatial scales. Our findings agree with other marine and terrestrial studies that show diversity components vary significantly over different spatial scales and the importance of habitat/landscape heterogeneity in supporting diversity. However, our results indicate that the relative contributions of scale-specific β-diversity components can also change significantly over time. Thus, studies of diversity patterns across patches and landscapes based on data collected at one time, or assembled into a single data set from different times, may not capture the full suite of diversity patterns that occur over varying spatial scales and any time-specific determinants of those patterns. Many factors that shape and maintain sedimentary communities vary temporally, and appear to play an important role in determining and maintaining macrofaunal diversity over different spatial scales.
The stellar mass ratio of GK Persei

We study the absorption lines present in the spectra of the long-period cataclysmic variable GK Per during its quiescent state, which are associated with the secondary star. By comparing quiescent data with outburst spectra we infer that the donor star appears identical during the two states and the inner face of the secondary star is not noticeably irradiated by flux from the accreting regions. We obtain new values for the radial velocity semi-amplitude of the secondary star, KK ? 120:5 ^ 0:7 kms21, a projected rotational velocity, VK sin i ? 61:5 ^ 11:8 kms21; and consequently a measurement of the stellar mass ratio of GK Per, q ? MK/MWD ? 0:55 ^ 0:21. The inferred white dwarf radial velocities are greater than those measured traditionally using the wings of Doppler-broadened emission lines suspected to originate in an accretion disc, highlighting the unsuitability of emission lines for mass determinations in cataclysmic variables. We determine mass limits for both components in the binary, MK $ 0:48 ^ 0:32M( and MWD $ 0:87 ^ 0:24M(.
Enhancing spot noise visualizations of 2d and 3d vector fields

Spot noise is a simple and effective algorithm to visualize vector fields. Originally proposed for visualizing two-dimensional flows or flows on surfaces, it is also easily extendible to three dimensions. However, images resulting from a straightforward extension of spot noise to 3D are rather cluttered and confusing, they do not show the underlying flow too well and are also missing any indication of flow orientation. The latter is also an inherent drawback of two-dimensional spot noise. In this paper we outline several strategies to improve visualizations of both twoand three-dimensional vector fields with spot noise. These include orientation indication by anisotropic spots, sorted spots and depth cueing for better depth perception, and colour coding strategies.
Recent Advances in Finite Element Applications in Artificial Lumbar Disc Replacement

As a new choice for the treatment of degenerative lumbar disease, artificial lumbar disc replacement has been widely used in clinical surgery. The finite element is a very effective method to predict and simulate the surgery effect. The purpose of this paper is to review the applications of finite element in artificial lumbar disc replacement, such as design of artificial lumbar disc prosthesis, risk and effect evaluation of artificial lumbar disc replacement, and assessment of operation methods. Lastly, we discuss the future development of finite element method applied in this field, including personalized design of the prosthesis, postoperative behavior guide, and artificial lumbar disc replacement combined with fusion surgery. In conclusion, as an invaluable complement to biomechanical experiments and clinical studies, the finite element method makes important contributions to our understanding of biomechanics of intervertebral disc, and plays an important role in the field of artificial lumbar disc replacement.
I Transactivator Expression in Mice Deficient for Nlrc 5 / Class Cutting Edge : Impaired MHC Class

MHC class I and class II are crucial for the adaptive immune system. Although regulation of MHC class II expression by CIITA has long been recognized, the mechanism of MHC class I transactivation has been largely unknown until the recent discovery of NLRC5/ class I transactivator. In this study, we show using Nlrc5-deficient mice that NLRC5 is required for both constitutive and inducible MHC class I expression. Loss of Nlrc5 resulted in severe reduction in the expression of MHC class I and related genes such as b 2-micro-globulin, Tap1, or Lmp2, but did not affect MHC class II levels. IFN-g stimulation could not overcome the impaired MHC class I expression in Nlrc5-deficient cells. Upon infection with Listeria monocyogenes, Nlrc5-deficient mice displayed impaired CD8 + T cell activation, accompanied with increased bacterial loads. These findings illustrate critical roles of NLRC5/class I trans-activator in MHC class I gene regulation and host defense by CD8 + T cell responses. M ajor histocompatibility complex class I and class II molecules play key roles in the activation of the adaptive immune system. MHC class I molecules present peptide Ags of intracellular origin such as tumor or viral Ags to CD8 + T cells, whereas MHC class II molecules present peptide Ags of extracellular sources to CD4 + T cells (1). The expression of both constitutive and inducible MHC class II requires the master transcriptional coactivator CIITA (2). Although CIITA itself lacks a DNA binding domain, CIITA can activate the promoters of MHC class II genes by engaging in a nucleoprotein complex called the MHC enhanceosome (3, 4), together with promoter-resident transcription factors, including the trimeric regulatory factor X protein complex, CREB/activating transcription factor 1 family members, and the NF-Y protein (5, 6). CIITA can also trans-activate MHC class I genes at least in vitro (7, 8), although both bare lymphocyte syndrome patients with mutations in the CIITA gene and CIITA-deficient mice retain intact MHC class I expression, indicating that there is another mechanism for the activation of MHC class I in vivo (2, 9–12). The recent discovery of a transactivator specific for MHC class I genes, NLRC5, identified a new addition to the regulators of MHC genes (13, 14). Both NLRC5 and CIITA belong to the NLR or nucleotide binding domain (NBD), leucine-rich repeat family of proteins, and phylogenetically they are most closely related to each other (13, 15). NLRC5, or class I transactivator (CITA), …
Complete genome sequence of Thalassolituus oleivorans R6-15, an obligate hydrocarbonoclastic marine bacterium from the Arctic Ocean

Strain R6-15 belongs to the genus Thalassolituus, in the family Oceanospirillaceae of Gammaproteobacteria. Representatives of this genus are known to be the obligate hydrocarbonoclastic marine bacteria. Thalassolituus oleivorans R6-15 is of special interest due to its dominance in the crude oil-degrading consortia enriched from the surface seawater of the Arctic Ocean. Here we describe the complete genome sequence and annotation of this strain, together with its phenotypic characteristics. The genome with size of 3,764,053 bp comprises one chromosome without any plasmids, and contains 3,372 protein-coding and 61 RNA genes, including 12 rRNA genes.
Health-Related Lifestyle Factors and Sexual Functioning and Behavior in Older Adults

ABSTRACT This study explored associations between health-related lifestyle factors and sexual functioning and behavior in 6,916 adults aged 50 and over. Results showed that an active lifestyle was associated with a higher sex drive, more sexual activity, and lower levels of sexual dysfunction (with stronger associations among men). Poor sleep was associated with less sexual activity, higher levels of sexual dissatisfaction, and higher levels of sexual dysfunction. A healthier diet and a higher alcohol intake were associated with more sexual activity and a higher sex drive. Taken together, these findings demonstrate that health-related lifestyle factors are important for sexual functioning and behavior in older adulthood.
Progressive loss of PAX6, TBR2, NEUROD and TBR1 mRNA gradients correlates with translocation of EMX2 to the cortical plate during human cortical development

The transcription factors Emx2 and Pax6 are expressed in the proliferating zones of the developing rodent neocortex, and gradients of expression interact in specifying caudal and rostral identities. Pax6 is also involved in corticoneurogenesis, being expressed by radial glial progenitors that give rise to cells that also sequentially express Tbr2, NeuroD and Tbr1, genes temporally downstream of Pax6. In this study, using in situ hybridization, we analysed the expression of EMX2, PAX6, TBR2, NEUROD and TBR1 mRNA in the developing human cortex between 8 and 12 postconceptional weeks (PCW). EMX2 mRNA was expressed in the ventricular (VZ) and subventricular zones (SVZ), but also in the cortical plate, unlike in the rodent. However, gradients of expression were similar to that of the rodent at all ages studied. PAX6 mRNA expression was limited to the VZ and SVZ. At 8 PCW, PAX6 was highly expressed rostrally but less so caudally, as has been seen in the rodent, however this gradient disappeared early in corticogenesis, by 9 PCW. There was less restricted compartment‐specific expression of TBR2, NEUROD and TBR1 mRNA than in the rodent, where the gradients of expression were similar to that of PAX6 prior to 9 PCW. The gradient disappeared for TBR2 by 10 PCW, and for NEUROD and TBR1 by 12 PCW. These data support recent reports that EMX2 but not PAX6 is more directly involved in arealization, highlighting that analysis of human development allows better spatio‐temporal resolution than studies in rodents.
Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers

We examined the downriver patterns of variation in taxonomic diversity of the Mississippi River bacterioplankton microbiome along 1,300 river kilometers, or approximately one third the total length of the river. The study section included portions of the Upper, Middle, and Lower Mississippi River, confluences with five tributaries draining distinct sub-basins, river cities, and extended stretches without major inputs to the Mississippi. The composition and proportional abundance of dominant bacterial phyla was distinct for free-living and particle-associated cells, and constant along the entire reach, except for a substantial but transient disturbance near the city of Memphis, Tennessee. At a finer scale of taxonomic resolution (operational taxonomic units, OTUs), however, there were notable patterns in downriver variation in bacterial community alpha diversity (richness within a site) and beta diversity (variation in composition among sites). There was a strong and steady increase downriver in alpha diversity of OTUs on suspended particles, suggesting an increase in particle niche heterogeneity, and/or particle colonization. Relatively large shifts in beta diversity of free-living and particle-associated communities occurred following major tributary confluences and transiently at Memphis, while in long stretches between these points diversity typically varied more gradually. We conclude that the Mississippi River possesses a bacterioplankton microbiome distinct in diversity from other large river microbiomes in the Mississippi River Basin, that at major river confluences or urban point sources its OTU diversity may shift abruptly and substantially, presumably by immigration of distinct external microbiomes, but that where environmental conditions are more stable along the downriver gradient, microbiome diversity tends to vary gradually, presumably by a process of successional change in community composition.
Nested effects models for high-dimensional phenotyping screens

MOTIVATION In high-dimensional phenotyping screens, a large number of cellular features is observed after perturbing genes by knockouts or RNA interference. Comprehensive analysis of perturbation effects is one of the most powerful techniques for attributing functions to genes, but not much work has been done so far to adapt statistical and computational methodology to the specific needs of large-scale and high-dimensional phenotyping screens. RESULTS We introduce and compare probabilistic methods to efficiently infer a genetic hierarchy from the nested structure of observed perturbation effects. These hierarchies elucidate the structures of signaling pathways and regulatory networks. Our methods achieve two goals: (1) they reveal clusters of genes with highly similar phenotypic profiles, and (2) they order (clusters of) genes according to subset relationships between phenotypes. We evaluate our algorithms in the controlled setting of simulation studies and show their practical use in two experimental scenarios: (1) a data set investigating the response to microbial challenge in Drosophila melanogaster, and (2) a compendium of expression profiles of Saccharomyces cerevisiae knockout strains. We show that our methods identify biologically justified genetic hierarchies of perturbation effects. AVAILABILITY The software used in our analysis is freely available in the R package 'nem' from www.bioconductor. org.
Changes in the airway lumen and surrounding parenchyma in chronic obstructive pulmonary disease

Background The purpose of this study was to examine changes in the airway lumen and parenchyma in relation to lung function in patients with chronic obstructive pulmonary disease (COPD) compared with controls. Methods We studied 70 patients with COPD and 15 normal subjects. Using reconstructed computed tomography (CT) images, we traced the bronchial trees and reconstructed 3 cm circle images around the airways exactly perpendicular to the airway axis at the peripheral, middle, and central zones of the bronchi. We measured the number of airways and vessels, the airway inner diameter, and the area of emphysema in the circles, and analyzed the relationship of these image parameters to lung function. Results Reduced airway numbers and increased upper lobe emphysema were observed even in early spirometric stages in patients with COPD compared with controls. Other findings included decreased airway inner diameter in advanced spirometric stages. The numbers of peripheral zone bronchi, the extent of the middle zone emphysematous area, and the mean airway inner diameter of the airways were the best predictors of spirometric parameters. A portion of the airways in patients with COPD showed a loss of airway patency at middle or central zone bronchi predominantly in the late spirometric stages. Lumen-obliterated bronchial trees could be traced into emphysematous areas showing air trapping. Conclusion Compared with controls, our CT observations in patients with COPD showed that airway lumen and lung parenchyma changes along airways differed by spirometric stage, and these changes were associated with decreased lung function. A portion of CT-identified emphysema in patients with COPD appeared to be due to lumen-obliterated airways in the bronchial tree.