Miracle-dz/UniFAR-FTUs huggingface dataset:
Strictly Level-Decreasing Logic Programs

We study strictly level-decreasing logic programs (sld-programs) as defined earlier by the present authors. It will be seen that sld-programs, unlike most other classes of logic programs, have both a highly intuitive declarative semantics, given as a unique supported model, and are computationally adequate in the sense that every partial recursive function can be represented by some sld-program P. Allowing for a safe use of cuts, an interpreter based on SLDNF-resolution, as implemented for example in standard Prolog systems, is shown to be sound and complete with respect to this class of programs. Furthermore, we study connections between topological dynamics and logic programming which are suggested by our approach to the declarative semantics of sld-programs.
Anterior segment imaging: ultrasound biomicroscopy and anterior segment optical coherence tomography

Purpose of review Recent advances in ocular imaging have included high-resolution techniques for visualizing the anterior segment and angle structures. This review will describe the two main anterior segment imaging modalities and summarize their applications, strengths and weaknesses. Recent findings Ultrasound biomicroscopy and more recently anterior segment optical coherence tomography are imaging modalities that can be used to obtain two-dimensional images of the angle and surrounding structures. Ultrasound biomicroscopy has the advantage of being able to illustrate the ciliary body and therefore give clinicians information on nonpupil block mechanisms of primary angle closure and also diagnose other abnormalities such as cyclodialysis clefts. Anterior segment optical coherence tomography is a noncontact and rapid method of imaging the angle and anterior segment that has great potential in the diagnosis and follow-up of patients with angle closure. This article will discuss these and other applications and compare and contrast the two technologies. Summary Rapid advances in anterior segment imaging are enlightening clinicians and researchers to the importance in making the diagnosis of primary angle closure, trying to establish underlying causal mechanisms, and evaluating treatments. Although they do not replace conventional angle and anterior segment examination, they hold great potential for the future.
Wnt16 Is Associated with Age-Related Bone Loss and Estrogen Withdrawal in Murine Bone

Genome Wide Association Studies suggest that Wnt16 is an important contributor to the mechanisms controlling bone mineral density, cortical thickness, bone strength and ultimately fracture risk. Wnt16 acts on osteoblasts and osteoclasts and, in cortical bone, is predominantly derived from osteoblasts. This led us to hypothesize that low bone mass would be associated with low levels of Wnt16 expression and that Wnt16 expression would be increased by anabolic factors, including mechanical loading. We therefore investigated Wnt16 expression in the context of ageing, mechanical loading and unloading, estrogen deficiency and replacement, and estrogen receptor α (ERα) depletion. Quantitative real time PCR showed that Wnt16 mRNA expression was lower in cortical bone and marrow of aged compared to young female mice. Neither increased nor decreased (by disuse) mechanical loading altered Wnt16 expression in young female mice, although Wnt16 expression was decreased following ovariectomy. Both 17β-estradiol and the Selective Estrogen Receptor Modulator Tamoxifen increased Wnt16 expression relative to ovariectomy. Wnt16 and ERβ expression were increased in female ERα-/- mice when compared to Wild Type. We also addressed potential effects of gender on Wnt16 expression and while the expression was lower in the cortical bone of aged males as in females, it was higher in male bone marrow of aged mice compared to young. In the kidney, which we used as a non-bone reference tissue, Wnt16 expression was unaffected by age in either males or females. In summary, age, and its associated bone loss, is associated with low levels of Wnt16 expression whereas bone loss associated with disuse has no effect on Wnt16 expression. In the artificially loaded mouse tibia we observed no loading-related up-regulation of Wnt16 expression but provide evidence that its expression is influenced by estrogen receptor signaling. These findings suggest that while Wnt16 is not an obligatory contributor to regulation of bone mass per se, it potentially plays a role in influencing pathways associated with regulation of bone mass during ageing and estrogen withdrawal.
Human longevity and common variations in the LMNA gene: a meta‐analysis

A mutation in the LMNA gene is responsible for the most dramatic form of premature aging, Hutchinson–Gilford progeria syndrome (HGPS). Several recent studies have suggested that protein products of this gene might have a role in normal physiological cellular senescence. To explore further LMNA’s possible role in normal aging, we genotyped 16 SNPs over a span of 75.4 kb of the LMNA gene on a sample of long‐lived individuals (LLI) (US Caucasians with age ≥ 95 years, N = 873) and genetically matched younger controls (N = 443). We tested all common nonredundant haplotypes (frequency ≥ 0.05) based on subgroups of these 16 SNPs for association with longevity. The most significant haplotype, based on four SNPs, remained significant after adjustment for multiple testing (OR = 1.56, P = 2.5 × 10−5, multiple‐testing‐adjusted P = 0.0045). To attempt to replicate these results, we genotyped 3619 subjects from four independent samples of LLI and control subjects from (i) the New England Centenarian Study (NECS) (N = 738), (ii) the Southern Italian Centenarian Study (SICS) (N = 905), (iii) France (N = 1103), and (iv) the Einstein Ashkenazi Longevity Study (N = 702). We replicated the association with the most significant haplotype from our initial analysis in the NECS sample (OR = 1.60, P = 0.0023), but not in the other three samples (P > 0.15). In a meta‐analysis combining all five samples, the best haplotype remained significantly associated with longevity after adjustment for multiple testing in the initial and follow‐up samples (OR = 1.18, P = 7.5 × 10−4, multiple‐testing‐adjusted P = 0.037). These results suggest that LMNA variants may play a role in human lifespan.
Two groups of human herpesvirus 6 identified by sequence analyses of laboratory strains and variants from Hodgkin's lymphoma and bone marrow transplant patients.

Fifteen human herpesvirus 6 (HHV-6) strain variants were analysed by PCR amplifications, restriction enzyme site polymorphism and sequence analyses. Three DNA regions were chosen for study: a fragment of a variable glycoprotein gene (210 bp), the conserved glycoprotein H (gH) gene complete with intergenic sequences (2381 bp) and the 5' intergenic region with the N-terminal coding sequence of gH up to a polymorphic BamHI site (427 bp). Infected cell DNA from five laboratory reference strains including GS, U1102, AJ, Z29 and KF were examined together with DNA from peripheral blood lymphocytes infected with HHV-6 reactivated from blood and/or marrow from five bone marrow transplant (BMT) patients. Separate blood and marrow isolates were obtained from four BMT patients. In addition, HHV-6 sequences were examined directly from one of six Hodgkin's lymphomas and six B cell proliferations which contained HHV-6 DNA as detected by PCR amplification. The results show two groups of very closely related but heterogeneous strains which correlate with previous groupings by antigenic and restriction site differences. These are variant A strains (including laboratory strains GS, U1102 and AJ) and variant B strains (including laboratory strains Z29 and KF, the Hodgkin's lymphoma strain, and the nine BMT patient isolates). Variations between the groups were 4 to 6% in nucleotide sequence and 5 to 8.5% in amino acid sequence. Within each group maximum heterogeneity was observed in different genes. Variant A strains differed by 2.0% in the variable glycoprotein gene sequence whereas variant B strains were identical in this region; conversely, variant B strains differed by 2 to 3% in the gH N-terminal and intergenic sequences whereas variant A strains differed there by less than 0.2%. There was evidence for sequence drift independent of selection: relationships between the groups were shown by analyses of amino acid sequence, coding nucleotide sequence as well as intergenic sequence, and the B variant-specific BamHI site in the gH gene was due to a non-coding nucleotide substitution. There was little evidence for in vivo or in vitro variation: the gH nucleotide sequence from the uncultured lymphoma strain (first variant B gH gene identified) was almost identical to the gH sequence from four BMT isolates, and matched BMT isolates from blood and marrow were identical or with a single nucleotide substitution. (ABSTRACT TRUNCATED AT 400 WORDS)
Molecular analysis of neurovirulent strains of Sindbis virus that evolve during persistent infection of scid mice

To understand the role of tissue-specific adaptation and antibody-induced selectional pressures in the evolution of neurovirulent viruses, we analyzed three strains of Sindbis virus isolated from the brains of persistently infected scid mice and four strains of Sindbis virus isolated from the brains of scid mice with viral reactivation following immune serum treatment. For each viral isolate, we tested neurovirulence in weanling BALB/c mice and sequenced regions of the E2 and E1 envelope glycoprotein genes that are known to contain important determinants of Sindbis virus neurovirulence. One strain isolated from a persistently infected scid mouse and two strains isolated from scid mice with viral reactivation were neurovirulent, resulting in mortality in 80 to 100% of weanling BALB/c mice. All three neurovirulent strains contained an A-->U change at nucleotide 8795, which predicts a Gln-->His substitution at E2 amino acid position 55. No nucleotide changes were detected in the other sequenced regions of the E2 and E1 envelope glycoprotein genes or in the avirulent isolates. Our findings indicate that tissue-specific adaptations, rather than antibody-induced selectional pressures, are a critical determinant of the evolution of neurovirulent strains of Sindbis virus and provide evidence that E2 His-55 is an important neuroadaptive mutation that confers neurovirulence properties on Sindbis virus.
Mathematical analysis of a size structured tree-grass competition model for savanna ecosystems

Several continuous-time tree-grass competition models have been developed to study conditions of long-lasting coexistence of trees and grass in savanna ecosystems according to environmental parameters such as climate or fire regime. In those models, fire intensity is a fixed parameter while the relationship between woody plant size and fire-sensitivity is not systematically considered. In this paper, we propose a mathematical model for the tree-grass interaction that takes into account both fire intensity and size-dependent sensitivity. The fire intensity is modeled by an increasing function of grass biomass and fire return time is a function of climate. We carry out a qualitative analysis that highlights ecological thresholds that summarize the dynamics of the system. Finally, we develop a non-standard numerical scheme and present some simulations to illustrate our analytical results.
Modeling and experimental validation of buckling dielectric elastomer actuators

Buckling dielectric elastomer actuators are a special type of electromechanical transducers that exploit electro-elastic instability phenomena to generate large out-of-plane axial-symmetric deformations of circular membranes made of non-conductive rubbery material. In this paper a simplified explicit analytical model and a general monolithic finite element model are described for the coupled electromechanical analysis and simulation of buckling dielectric elastomer membranes which undergo large electrically induced displacements. Experimental data are also reported which validate the developed models.
EFTUD2 Is a Novel Innate Immune Regulator Restricting Hepatitis C Virus Infection through the RIG-I/MDA5 Pathway

ABSTRACT The elongation factor Tu GTP binding domain-containing protein 2 (EFTUD2) was identified as an anti-hepatitis C virus (HCV) host factor in our recent genome-wide small interfering RNA (siRNA) screen. In this study, we sought to further determine EFTUD2's role in HCV infection and investigate the interaction between EFTUD2 and other regulators involved in HCV innate immune (RIG-I, MDA5, TBK1, and IRF3) and JAK-STAT1 pathways. We found that HCV infection decreased the expression of EFTUD2 and the viral RNA sensors RIG-I and MDA5 in HCV-infected Huh7 and Huh7.5. 1 cells and in liver tissue from in HCV-infected patients, suggesting that HCV infection downregulated EFTUD2 expression to circumvent the innate immune response. EFTUD2 inhibited HCV infection by inducing expression of the interferon (IFN)-stimulated genes (ISGs) in Huh7 cells. However, its impact on HCV infection was absent in both RIG-I knockdown Huh7 cells and RIG-I-defective Huh7.5. 1 cells, indicating that the antiviral effect of EFTUD2 is dependent on RIG-I. Furthermore, EFTUD2 upregulated the expression of the RIG-I-like receptors (RLRs) RIG-I and MDA5 to enhance the innate immune response by gene splicing. Functional experiments revealed that EFTUD2-induced expression of ISGs was mediated through interaction of the EFTUD2 downstream regulators RIG-I, MDA5, TBK1, and IRF3. Interestingly, the EFTUD2-induced antiviral effect was independent of the classical IFN-induced JAK-STAT pathway. Our data demonstrate that EFTUD2 restricts HCV infection mainly through an RIG-I/MDA5-mediated, JAK-STAT-independent pathway, thereby revealing the participation of EFTUD2 as a novel innate immune regulator and suggesting a potentially targetable antiviral pathway. IMPORTANCE Innate immunity is the first line defense against HCV and determines the outcome of HCV infection. Based on a recent high-throughput whole-genome siRNA library screen revealing a network of host factors mediating antiviral effects against HCV, we identified EFTUD2 as a novel innate immune regulator against HCV in the infectious HCV cell culture model and confirmed that its expression in HCV-infected liver tissue is inversely related to HCV infection. Furthermore, we determined that EFTUD2 exerts its antiviral activity mainly through governing its downstream regulators RIG-I and MDA5 by gene splicing to activate IRF3 and induce classical ISG expression independent of the JAT-STAT signaling pathway. This study broadens our understanding of the HCV innate immune response and provides a possible new antiviral strategy targeting this novel regulator of the innate response.
Age related changes in striatal resting state functional connectivity in autism

Characterizing the nature of developmental change is critical to understanding the mechanisms that are impaired in complex neurodevelopment disorders such as autism spectrum disorder (ASD) and, pragmatically, may allow us to pinpoint periods of plasticity when interventions are particularly useful. Although aberrant brain development has long been theorized as a characteristic feature of ASD, the neural substrates have been difficult to characterize, in part due to a lack of developmental data and to performance confounds. To address these issues, we examined the development of intrinsic functional connectivity, with resting state fMRI from late childhood to early adulthood (8–36 years), using a seed based functional connectivity method with the striatal regions. Overall, we found that both groups show decreases in cortico-striatal circuits over age. However, when controlling for age, ASD participants showed increased connectivity with parietal cortex and decreased connectivity with prefrontal cortex relative to typically developed (TD) participants. In addition, ASD participants showed aberrant age-related connectivity with anterior aspects of cerebellum, and posterior temporal regions (e.g., fusiform gyrus, inferior and superior temporal gyri). In sum, we found prominent differences in the development of striatal connectivity in ASD, most notably, atypical development of connectivity in striatal networks that may underlie cognitive and social reward processing. Our findings highlight the need to identify the biological mechanisms of perturbations in brain reorganization over development, which may also help clarify discrepant findings in the literature.
A stochastic approach to diffusion model with asymmetric influence

A diffusion model with innovators and imitators is formulated by the use of the generalised birth process with immigration. In our formulation, the immigration rate and the birth rate have time dependence. The immigration process corresponds to the behaviour of innovators and the birth process to that of imitators. The Bass model is derived under the assumption that the ratio of the immigration rate to the birth rate is constant. An extension of the Bass model based on the stochastic process is proposed, by which data with broad peak or bimodal shape can be analysed. Data on the sales of new products and on hit phenomena are analysed by the diffusion model.
Improving software practice through education: Challenges and future trends

We argue that the software engineering (SE) community could have a significant impact on the future of the discipline by focusing its efforts on improving the education of software engineers. There are some bright spots such as the various projects to codify knowledge, and the development of undergraduate SE programs. However, there remain several key challenges, each of which is addressed in this paper: The challenges are 1) making programs attractive to students, 2) focusing education appropriately, 3) communicating industrial reality more effectively, 4) defining curricula that are forward-looking, 5) providing education for existing practitioners, 6) making SE education more evidence- based, 7) ensuring that SE educators have the necessary background, and 8) raising the prestige and quality of SE educational research. For each challenge, we provide action items and open research questions.
Municipal Wastewater Effluents as a Source of Listerial Pathogens in the Aquatic Milieu of the Eastern Cape Province of South Africa: A Concern of Public Health Importance

We evaluated the effluent quality of an urban wastewater treatment facility in South Africa and its impact on the receiving watershed for a period of 12 months. The prevalence and antimicrobial susceptibility of potential Listeria pathogens (L. ivanovii and L. innocua) and the physicochemical quality of the treated wastewater effluent was assessed, with a view to ascertain the potential health and environmental hazards of the discharged effluent. Total listerial density varied between 2.9 × 100 and 1.2 × 105 cfu/mL; free living Listeria species were more prevalent (84%), compared to Listeria species attached to planktons (59–75%). The treated effluent quality fell short of recommended standards for turbidity, dissolved oxygen, chemical oxygen demand, nitrite, phosphate and Listeria density; while pH, temperature, total dissolved solids and nitrate contents were compliant with target quality limits after treatment. The Listeria isolates (23) were sensitive to three (15%) of the 20 test antibiotics, and showed varying (4.5–91%) levels of resistance to 17 antibiotics. Of seven resistance gene markers assayed, only sulII genes were detected in five (22%) Listeria strains. The study demonstrates a potential negative impact of the wastewater effluent on the receiving environment and suggests a serious public health implication for those who depend on the receiving watershed for drinking and other purposes.
Development of Spirulina Based “Biscuits”: A Potential Method of Value Addition

Abstract The present study was undertaken to assess the nutritional composition of Spirulina powder, development of Spirulina based value added products and their nutritional composition and shelf life. Value added biscuitswere prepared by using refined wheat flour, sugar powder, ghee, milk, ammonia, baking powder, custard powder, milk powder, vanilla and pineapple essence and 10 per cent level of Spirulina powder. Mean score for overall acceptability of value added biscuitwas 7.5 against the control sample, 7.9 on nine point hedonic ranking scale. The developed value added biscuitcontained 2.95 per cent moisture, 19.6g protein, 26.71g fat, 2.08g crude fiber, 1.83g ash, 46.83 g carbohydrate and 506.11 kcal energy per 100g on dry weight basis. Spirulina supplemented biscuits had β-carotene, vitamin C, iron and potassium contents in the range of 349.75 μg/100g, 2.75 mg/100g, 17.62 mg/100g and 292 mg/100g, respectively. Fat acidity revealed satisfactory quality of the value added biscuitat the end of three months of storage period. Thus, Spirulina based value added products may be beneficial for vulnerable population due its high nutritive value. These would also be advantageous for those who are suffering from degenerative diseases because of its therapeutic properties.
Cyclooxygenase-2 Expression in Human Gliomas : Prognostic Significance and Molecular Correlations 1

Cyclooxygenase (COX)-2, the inducible isoform of prostaglandin H synthase, has been implicated in the growth and progression of a variety of human cancers. Although COX-2 overexpression has been observed in human gliomas, the prognostic or clinical relevance of this overexpression has not been investigated to date. In addition, no study has analyzed the relationship between COX-2 expression and other molecular alterations in gliomas. Consequently, we examined COX-2 expression by immunohistochemistry in tumor specimens from 66 patients with lowand high-grade astrocytomas and correlated the percentage of COX-2 expression with patient survival. We also analyzed the relative importance of COX-2 expression in comparison with other clinicopathological features (age and tumor grade) and other molecular alterations commonly found in gliomas (high MIB-1 level, p53 alteration, loss of retinoblastoma (Rb) protein or p16, and high bcl-2 level). Kaplan-Meier analyses demonstrated that high COX-2 expression ( >50% of cells stained positive) correlated with poor survival for the study group as a whole (P < 0.0001) and for those with glioblastoma multiforme in particular ( P < 0.03). Cox regression analyses demonstrated that COX-2 expression was the strongest predictor of outcome, independent of all other variables. In addition, high COX-2 expression correlated with increasing histological grade but did not correlate with positive p53 immunostaining, bcl-2 expression, loss of p16 or retinoblastoma protein expression, or high MIB-1 expression. These findings indicate that high COX-2 expression in tumor cells is associated with clinically more aggressive gliomas and is a strong predictor of poor survival.
Virgo High-Resolution CO Survey: V. Circumnuclear Elliptical Ring in NGC 4569

We present high-resolution (1. �� 8–4. 5) CO data of the Virgo spiral galaxy NGC 4569, obtained using the Nobeyama Millimeter Array. We found that the molecular gas is highly concentrated in the circumnuclear region with two off-center peaks. A CO image with the highest angular resolution of 2. �� 0 ×1. �� 8 shows that six blobs likely form a circumnuclear elliptical ring (CER) with a semimajor axis of 720pc. The CER shows a strongly twisted velocity field, and the position–velocity diagram shows significant forbidden velocity components. These kinetic features are understood as being non-circular motion due to a bar-potential. We found that the CER coincides with the Hα bright central core and that the mass ratio of the molecular gas to the dynamical mass is about 18%. These results support a gaseous inflow scenario induced by a weak bar potential and self-gravity of the gas.