Miracle-dz/UniFAR-FTUs huggingface dataset:
Tabulator Redux: writing Into the Semantic Web

A first category of Semantic Web browsers were designed to present a given dataset (an RDF graph) for perusal, in various forms. These include mSpace, Exhibit, and to a certain extent Haystack. A second category tackled mechanisms and display issues around linked data gathered on the fly. These include Tabulator, Oink, Disco, Open Link Software's Data Browser, and Object Browser. The challenge of once that data is gathered, how might it be edited, extended and annotated has so far been left largely unaddressed. This is not surprising: there are a number of steep challenges for determining how to support editing information in the open web of linked data. These include the representation of both the web of documents and the web of things, and the relationships between them; ensuring the user is aware of and has control over the social context such as licensing and privacy of data being entered, and, on a web in which anyone can say anything about anything, helping the user intuitively select the things which they actually wish to see in a given situation. There is also the view update problem: the difficulty of reflecting user edits back through functions used to map web data to a screen presentation. In the latest version of the Tabulator project, described in this paper we have focused on providing the write side of the readable/writable web. Our approach has been to allow modification and addition of information naturally within the browsing interface, and to relay changes to the server triple by triple for least possible brittleness (there is no explicit 'save' operation). Challenges which remain include the propagation of changes by collaborators back to the interface to create a shared editing system. To support writing across (semantic) Web resources, our work has contributed several technologies, including a HTTP/SPARQL/Update-based protocol between an editor (or other system) and incrementally editable resources stored in an open source, world-writable 'data wiki'. This begins enabling the writable Semantic Web.
An industrial information integration approach to in-orbit spacecraft

ABSTRACT To operate an in-orbit spacecraft, the spacecraft status has to be monitored autonomously by collecting and analysing real-time data, and then detecting abnormities and malfunctions of system components. To develop an information system for spacecraft state detection, we investigate the feasibility of using ontology-based artificial intelligence in the system development. We propose a new modelling technique based on the semantic web, agent, scenarios and ontologies model. In modelling, the subjects of astronautics fields are classified, corresponding agents and scenarios are defined, and they are connected by the semantic web to analyse data and detect failures. We introduce the modelling methodologies and the resulted framework of the status detection information system in this paper. We discuss system components as well as their interactions in details. The system has been prototyped and tested to illustrate its feasibility and effectiveness. The proposed modelling technique is generic which can be extended and applied to the system development of other large-scale and complex information systems.
NEW POSSIBILITIES IN THE PHARMACOLOGICAL TREATMENT OF ABNORMAL CONVULSIVE ACTIVITY IN ACUTE ORGANOPHOSPHATE NERVE AGENTS INTOXICATION

Organophosphates, used as chemical warfare nerve agents and pesticides are the most toxic chemicals known to date. Despite the number of studies done on the subject matter, intoxication caused by such agents is among the most complicated problems in medicine because of the induced increase in abnormal electrical activity in the brain and the subsequent brain damage. The anticonvulsant and neuro-protective effects of conventional benzodiazepines are limited by their side effects, including sedation, amnesia, withdrawal, and anticonvulsant tolerance. Imidazenil is a proposed drug in the treatment of convulsions in acute cases of poisoning with organophosphate nerve agents and an alternative to the currently used benzodiazepines with an improved safety profile.
Selection of the Regularization Parameter in Graphical Models Using Network Characteristics

ABSTRACT Gaussian graphical models represent the underlying graph structure of conditional dependence between random variables, which can be determined using their partial correlation or precision matrix. In a high-dimensional setting, the precision matrix is estimated using penalized likelihood by adding a penalization term, which controls the amount of sparsity in the precision matrix and totally characterizes the complexity and structure of the graph. The most commonly used penalization term is the L1 norm of the precision matrix scaled by the regularization parameter, which determines the trade-off between sparsity of the graph and fit to the data. In this article, we propose several procedures to select the regularization parameter in the estimation of graphical models that focus on recovering reliably the appropriate network structure of the graph. We conduct an extensive simulation study to show that the proposed methods produce useful results for different network topologies. The approaches are also applied in a high-dimensional case study of gene expression data with the aim to discover the genes relevant to colon cancer. Using these data, we find graph structures, which are verified to display significant biological gene associations. Supplementary material is available online.
Antimicrobial resistance to disinfectants in biofilms

Microorganisms have a natural capacity to attach to surfaces, to multiply and to embed themselves in a slimy matrix, forming biofilms. These allow complex interactions among different species and surfaces. There is significant evidence that bacterial growth in attached communities constituted the first form of life on the planet, and it is estimated that the majority of microbial activity on earth is resultant from biofilms, rather than microbes growing isolated in the form of planktonic cells. Industrial units, particularly food processing plants, provide good environmental conditions for biofilm proliferation, such as an abundant source of nutrients, which can create a significant problem mainly because most of these microorganisms can be pathogens. Therefore, cleaning and disinfection in food processing plants are important issues that deserve full consideration. However, the phenotype of biofilms provides intrinsic resistance to cleaning and disinfection. Nowadays, there are no biofilm control strategies that inactivate, remove or prevent their regrowth after antimicrobial treatment.This study provides information on the problems of biofilm formation and on the main strategies used for their control. Information on the antimicrobial mode of action of biocides and biofilm resistance mechanisms is also provided.
The relationship between atherosclerosis and pulmonary emphysema.

INTRODUCTION The etiopathogenesis of atherosclerosis and subsequent pulmonary emphysema has not been fully elucidated. EXPERIMENTAL STUDIES Foam cells are of great importance in the development of these diseases. It is known that local cytokine secretion and modification of native lipoprotein particles, which are internalized by the vascular and alveolar macrophages via the scavenger receptors on the surfaces of these cells, lead to the formation of foam cells. Thus, the exacerbation of local inflammatory process in the vascular and lung tissue ensues due to a generation of reactive oxygen species, resulting in further lipoprotein modification and cytokine production. Accumulating evidence suggests that oxidants may facilitate the inflammatory response by impairing antiprotease function, directly attacking vascular and lung matrix proteins and by inactivating enzymes involved in elastin synthesis and vascular and lung repair. CLINICAL STUDIES Cigarette smoke is recognized as a rich source of oxidants. Nearly 90% of all patients with chronic obstructive pulmonary disease are smokers. The process of atherogenesis is also influenced by tobacco smoke. CONCLUSION The role of vascular and alveolar macrophages has become increasingly important in understanding the development of atherosclerosis and resulting pulmonary emphysema.
High Frequency of Genetic Recombination Is a Common Feature of Primate Lentivirus Replication

ABSTRACT Recent studies indicate that human immunodeficiency virus type 1 (HIV-1) recombines at exceedingly high rates, approximately 1 order of magnitude more frequently than simple gammaretroviruses such as murine leukemia virus and spleen necrosis virus. We hypothesize that this high frequency of genetic recombination is a common feature of primate lentiviruses. Alternatively, it is possible that HIV-1 is unique among primate lentiviruses in possessing high recombination rates. Among other primate lentiviruses, only the molecular mechanisms of HIV-2 replication have been extensively studied. There are reported differences between the replication mechanisms of HIV-1 and those of HIV-2, such as preferences for RNA packaging in cis and properties of reverse transcriptase and RNase H activities. These biological disparities could lead to differences in recombination rates between the two viruses. Currently, HIV-1 is the only primate lentivirus in which recombination rates have been measured. To test our hypothesis, we established recombination systems to measure the recombination rates of two other primate lentiviruses, HIV-2 and simian immunodeficiency virus from African green monkeys (SIVagm), in one round of viral replication. We determined that, for markers separated by 588, 288, and 90 bp, HIV-2 recombined at rates of 7.4%, 5.5%, and 2.4%, respectively, whereas SIVagm recombined at rates of 7.8%, 5.6%, and 2.7%, respectively. These high recombination rates are within the same range as the previously measured HIV-1 recombination rates. Taken together, our results indicate that HIV-1, HIV-2, and SIVagm all possess high recombination frequencies; hence, the high recombination potential is most likely a common feature of primate lentivirus replication.
Chloromethane-Induced Genes Define a Third C1 Utilization Pathway in Methylobacterium chloromethanicum CM4

ABSTRACT Methylobacterium chloromethanicum CM4 is an aerobic α-proteobacterium capable of growth with chloromethane as the sole carbon and energy source. Two proteins, CmuA and CmuB, were previously purified and shown to catalyze the dehalogenation of chloromethane and the vitamin B12-mediated transfer of the methyl group of chloromethane to tetrahydrofolate. Three genes located near cmuA and cmuB, designated metF, folD and purU and encoding homologs of methylene tetrahydrofolate (methylene-H4folate) reductase, methylene-H4folate dehydrogenase-methenyl-H4folate cyclohydrolase and formyl-H4folate hydrolase, respectively, suggested the existence of a chloromethane-specific oxidation pathway from methyl-tetrahydrofolate to formate in strain CM4. Hybridization and PCR analysis indicated that these genes were absent in Methylobacterium extorquens AM1, which is unable to grow with chloromethane. Studies with transcriptional xylE fusions demonstrated the chloromethane-dependent expression of these genes. Transcriptional start sites were mapped by primer extension and allowed to define three transcriptional units, each likely comprising several genes, that were specifically expressed during growth of strain CM4 with chloromethane. The DNA sequences of the deduced promoters display a high degree of sequence conservation but differ from the Methylobacterium promoters described thus far. As shown previously for purU, inactivation of the metF gene resulted in a CM4 mutant unable to grow with chloromethane. Methylene-H4folate reductase activity was detected in a cell extract of strain CM4 only in the presence of chloromethane but not in the metF mutant. Taken together, these data provide evidence that M. chloromethanicum CM4 requires a specific set of tetrahydrofolate-dependent enzymes for growth with chloromethane.
Characterization of the lacticin 481 operon: the Lactococcus lactis genes lctF, lctE, and lctG encode a putative ABC transporter involved in bacteriocin immunity

The lantibiotic lacticin 481 is a bacteriocin produced by Lactococcus lactis strains. The genetic determinants of lacticin 481 production are organized as an operon encoded by a 70-kb plasmid. We previously reported the first three genes of this operon, lctA, lctM, and lctT, which are involved in the bacteriocin biosynthesis and export (A. Rincé, A. Dufour, S. Le Pogam, D. Thuault, C. M. Bourgeois, and J.-P. Le Pennec, Appl. Environ. Microbiol. 60:1652-1657, 1994). The operon contains three additional open reading frames: lctF, lctE, and lctG. The hydrophobicity profiles and sequence similarities strongly suggest that the three gene products associate to form an ABC transporter. When the three genes were coexpressed into a lacticin 481-sensitive L. lactis strain, the strain became resistant to the bacteriocin. This protection could not be obtained when any of the three genes was deleted, confirming that lctF, lctE, and lctG are all necessary to provide immunity to lacticin 481. The quantification of the levels of immunity showed that lctF, lctE, and lctG could account for at least 6% and up to 100% of the immunity of the wild-type lacticin 481 producer strain, depending on the gene expression regulation. The lacticin 481 biosynthesis and immunity systems are discussed and compared to other lantibiotic systems.
Implications of Macroalgal Isolation by Distance for Networks of Marine Protected Areas

The global extent of macroalgal forests is declining, greatly affecting marine biodiversity at broad scales through the effects macroalgae have on ecosystem processes, habitat provision, and food web support. Networks of marine protected areas comprise one potential tool that may safeguard gene flow among macroalgal populations in the face of increasing population fragmentation caused by pollution, habitat modification, climate change, algal harvesting, trophic cascades, and other anthropogenic stressors. Optimal design of protected area networks requires knowledge of effective dispersal distances for a range of macroalgae. We conducted a global meta‐analysis based on data in the published literature to determine the generality of relation between genetic differentiation and geographic distance among macroalgal populations. We also examined whether spatial genetic variation differed significantly with respect to higher taxon, life history, and habitat characteristics. We found clear evidence of population isolation by distance across a multitude of macroalgal species. Genetic and geographic distance were positively correlated across 49 studies; a modal distance of 50–100 km maintained FST < 0.2. This relation was consistent for all algal divisions, life cycles, habitats, and molecular marker classes investigated. Incorporating knowledge of the spatial scales of gene flow into the design of marine protected area networks will help moderate anthropogenic increases in population isolation and inbreeding and contribute to the resilience of macroalgal forests.
New algorithm for colour image segmentation using hybrid k-means clustering

The traditional k–means algorithm is a classical clustering method which is widely used in variant application such as image processing, computer vision, pattern recognition and machine learning. However, the k–means method converges to one of many local minima. It is known that, the final result depends on the initial starting points (means). Generally initial cluster centres are selected randomly, so the algorithm could not lead to the unique result. In this paper, we present a new algorithm which includes three methods to compute initial centres for k–means clustering. First one is called geometric method which depends on equal areas of distribution. The second is called block method which segments the image into uniform areas. The last method is called hybrid and it is a combination between first and second methods. The experimental results appeared quite satisfactory.
CPR / MIS 2016 : G : Investigating the Role of Top Management Support between Institutional Pressures and Cloud Implementation Success

While cloud computing adoption is on the rise, barriers continue to play a critical role in delaying the progress of some cloud computing adoption efforts. In 2010 the United States federal government launched the ‘Cloud First’ policy which requires government agencies to consider the adoption of cloud computing when the solution is secure, reliable and cost effective (Kundra, 2010). Unfortunately, cloud computing adoption among federal agencies has been sluggish. This study investigates pressures asserted to facilitate cloud computing adoption. Although a vast amount of literature exists, very few studies empirically investigate cloud computing adoption from an institutional perspective in concert with top management support. This study aims to fill the gap where the literature is lacking concerning the adoption of cloud computing by federal agencies.
Reticulate Speciation and Barriers to Introgression in the Anopheles gambiae Species Complex

Abstract Speciation as a process remains a central focus of evolutionary biology, but our understanding of the genomic architecture and prevalence of speciation in the face of gene flow remains incomplete. The Anopheles gambiae species complex of malaria mosquitoes is a radiation of ecologically diverse taxa. This complex is well-suited for testing for evidence of a speciation continuum and genomic barriers to introgression because its members exhibit partially overlapping geographic distributions as well as varying levels of divergence and reproductive isolation. We sequenced 20 genomes from wild A. gambiae s.s. , Anopheles coluzzii, Anopheles arabiensis, and compared these with 12 genomes from the “GOUNDRY” subgroup of A. gambiae s.l. Amidst a backdrop of strong reproductive isolation, we find strong evidence for a speciation continuum with introgression of autosomal chromosomal regions among species and subgroups. The X chromosome, however, is strongly differentiated among all taxa, pointing to a disproportionately large effect of X chromosome genes in driving speciation among anophelines. Strikingly, we find that autosomal introgression has occurred from contemporary hybridization between A. gambiae and A. arabiensis despite strong divergence (∼5× higher than autosomal divergence) and isolation on the X chromosome. In addition to the X, we find strong evidence that lowly recombining autosomal regions, especially pericentromeric regions, serve as barriers to introgression secondarily to the X. We show that speciation with gene flow results in genomic mosaicism of divergence and introgression. Such a reticulate gene pool connecting vector taxa across the speciation continuum has important implications for malaria control efforts.
Venezuelan Equine Encephalitis Virus Capsid Protein Inhibits Nuclear Import in Mammalian but Not in Mosquito Cells

ABSTRACT Venezuelan equine encephalitis virus (VEEV) represents a continuous public health threat in the United States. It has the ability to cause fatal disease in humans and in horses and other domestic animals. We recently demonstrated that replicating VEEV interferes with cellular transcription and uses this phenomenon as a means of downregulating a cellular antiviral response. VEEV capsid protein was found to play a critical role in this process, and its ∼35-amino-acid-long peptide, fused with green fluorescent protein, functioned as efficiently as did the entire capsid. We detected a significant fraction of VEEV capsid associated with nuclear envelope, which suggested that this protein might regulate nucleocytoplasmic trafficking. In this study, we demonstrate that VEEV capsid and its N-terminal sequence efficiently inhibit multiple receptor-mediated nuclear import pathways but have no effect on the passive diffusion of small proteins. The capsid protein of the Old World alphavirus Sindbis virus and the VEEV capsid, with a previously defined frameshift mutation, were found to have no detectable effect on nuclear import. Importantly, the VEEV capsid did not noticeably interfere with nuclear import in mosquito cells, and this might play a critical role in the ability of the virus to develop a persistent, life-long infection in mosquito vectors. These findings demonstrate a new aspect of VEEV-host cell interactions, and the results of this study are likely applicable to other New World alphaviruses, such as eastern and western equine encephalitis viruses.
Tissue-nonspecific Alkaline Phosphatase Is Required for the Calcification of Collagen in Serum

Previous studies have shown that the type I collagen of tendon and demineralized bone both calcify rapidly in serum. The speed, collagen matrix-type specificity, and extent of the re-calcification of demineralized bone in serum suggest that the serum calcification activity identified in these studies may participate in normal biomineralization. Because of its presence in serum and its long history of association with the normal mineralization of the collagen matrix of bone, tissue-nonspecific alkaline phosphatase (TNAP) is an obvious candidate for a protein that could be a component of serum calcification activity, and experiments were therefore carried out to test this possibility. These experiments show that the inactivation of TNAP in serum prevents collagen calcification, and that the addition of physiological levels of purified TNAP restores the ability of TNAP-deficient serum to calcify collagen. Additional experiments show that the role of TNAP in collagen calcification is to activate a serum nucleator of apatite crystal formation. Based on these and earlier studies, the mechanism of collagen calcification in serum requires at least four elements as follows. 1) A matrix (collagen fibrils) that is accessible to small apatite crystals but not large molecules ( Toroian, D., Lim, J. E., and Price, P. A. (2007) J. Biol. Chem. 282, 22437-22447 ). 2) A large serum nucleator that generates small crystals, some of which diffuse into the fibrils. 3) A source of TNAP to activate the serum nucleator. 4) A large protein (fetuin) that selectively inhibits growth of crystals remaining in solution, thereby ensuring that only crystals within fibrils grow ( Toroian, D. T., and Price, P. A. (2008) Calcif. Tissue Int. 82, 116-126 ).
Insights into theory of mind from deafness and autism.

This paper summarizes the results of 11 separate studies of deaf children's performance on standard tests of false belief understanding, the results of which combine to show that deaf children from hearing families are likely to be delayed in acquiring a theory of mind. indeed, these children generally perform no better than autistic individuals of similar mental age. Conversational and neurological explanations for deficits in mental state understanding are considered in relation to recent evidence from studies of deaf, autistic, and normally developing children with varied levels of access to talk about mental states at home with family members during the preschool years.
Monte Carlo simulation of ion implantation damage process in silicon

In this paper is reported for the first time a rigorous physically based ion implantation damage model which successfully predicts both the as-implanted impurity profiles (SIMS) and the damage profiles (RBS) for a wide range of implant conditions for arsenic, boron and BF/sub 2/ implants. In addition, the amorphous layer thicknesses predicted by this new damage model for high dose implants are also in excellent agreement with experimental measurements. This new damage model explicitly simulates the defect production and its subsequent evolution into the experimentally observable profiles. The detailed nature of the new damage model has provided much insight into the fundamental physical processes involved in implantation damage, and could also serve as a basis for further applications such as defect engineering.