Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic Ontology Extension : Resolving Inconsistencies – Extended

Ontologies are widely used in text technology and artificial intelligence. The need to develop large ontologies for real-life applications provokes researchers to automatize ontology extension procedures. Automatic updates without the control of a human expert can generate potential conflicts between original and new knowledge resulting in inconsistencies occurring in the ontology. We propose an algorithm that models the process of the adaptation of an ontology to new information. 1 Automatic Ontology Extension There is an increasing interest in applying ontological knowledge in text technologies and artificial intelligence. Since the manual development of large ontologies proved to be a time-consuming task many current investigations are devoted to automatic ontology learning methods (see [6] for an overview). Several formalisms have been proposed to represent ontological knowledge. Probably the most important one of the existing markup languages for ontology design is the Web Ontology Language (OWL) based on the logical formalism called Description Logics (DL) [1]. In particular, description logics were designed for the representation of terminological knowledge and reasoning processes. Although most of the tools extracting or extending ontologies automatically output knowledge in the OWL-format, they usually use only a small subset of DL. The core ontologies generated in practice usually contain the subsumption relation defined on concepts (taxonomy) and general relations (such as part-of and others). At present complex ontologies making use of the whole expressive power and advances of the various versions of DLs can be achieved only manually or semi-automatically. However, several approaches appeared recently tending not only to learn taxonomic and general relations but also state which concepts in the knowledge base are equivalent or disjoint [5]. In the present paper, we concentrate on these approaches. We will consider only terminological knowledge (called TBox in DL) leaving the information about assertions in the knowledge base (called ABox in DL) for further investigations. 3 See the documentation at http://www.w3. org/TR/owl-features/
Ovary and ovulation: Cell-specific localization of nitric oxide synthases (NOS) in the rat ovary during follicular development, ovulation and luteal formation

: Nitric oxide (NO) has emerged as one of several important intraovarian regulatory factors. In particular, NO has been implicated in the processes of ovulation and atresia-related apoptosis. The aim of the present study was to investigate the presence and distribution of the NO-generating nitric oxide synthase (NOS) enzymes in the ovary during follicular development, ovulation and luteal formation of the equine chorionic gonadotrophin (ECG)/human chorionic gonadotrophin (HCG)-primed rat. NADPH diaphorase activity was used as a histochemical marker for NOS within the ovary. Diaphorase reactivity was most abundant in the stroma (S) of the ovary and in the theca (T) layer of the follicle. In luteinized ovaries, weaker diaphorase reactivity was present within the corpora lutea (CL). Two different isoforms of NOS, the constitutively expressed endothelial NOS (eNOS) and the inducible isoform of NOS (iNOS), were immunolocalized in ovaries of immature rats and in ECG/HCG-primed rats during the periovulatory period from HCG injection until 2 days after ovulation. In addition, ovarian concentrations of eNOS and iNOS were quantified by immunoblotting. Immunoblotting with a monoclonal anti-eNOS antibody demonstrated the presence of eNOS mainly in the residual ovary (ROV) during the periovulatory period. In luteinized ovaries, higher concentrations of eNOS were seen in CL, while those in the ROV at this stage were lower than in the periovulatory ovary. Immature ovaries contained diminutive amounts of eNOS, detectable mostly in the ROV compartment. In contrast, iNOS was barely detectable during follicular development to the preovulatory stage. A slight elevation of iNOS was observed in the granulosa cells at 6 h after the HCG injection. The levels of iNOS during the luteal phase were also low. Immunohistochemical analysis using polyclonal eNOS and iNOS antibodies revealed the localization of these two isoforms primarily in the S and the T of the periovulatory ovary. In luteinized ovaries, positive immunoreactivity was also seen within the CL. With a monoclonal antibody against eNOS, intense immunoreactivity was observed in the S, T and within CL. There was a particularly strong staining in blood vessels. These data demonstrate the presence of an intraovarian NO-generating system. The localization of this system to the S, T and CL suggests a role for NO in the ovulatory process and in the regulation of CL function.
Role of urea in microbial metabolism in aquatic systems: a biochemical and molecular review

Urea synthesized commercially and formed naturally as a by-product of cellular metab- olism is an important source of nitrogen (N) for primary producers in aquatic ecosystems. Although urea is usually present at ambient concentrations below 1 µM-N, it can contribute 50% or more of the total N used by planktonic communities. Urea may be produced intracellularly via purine catabolism and/or the urea cycle. In many bacteria and eukaryotes, urea in the cell can be broken down by ure- ase into NH4 + and CO2. In addition, some bacteria and eukaryotes use urea amidolyase (UALase) to decompose urea. The regulation of urea uptake appears to differ from the regulation of urease activ- ity, and newly available genomic sequence data reveal that urea transporters in eukaryotic phyto- plankton are distinct from those present in Cyanobacteria and heterotrophic bacteria with different energy sources and possibly different enzyme kinetics. The diverse metabolic pathways of urea transport, production, and decomposition may contribute to differences in the role that urea plays in the physiology and ecology of different species, and in the role that each species plays in the biogeo- chemistry of urea. This review summarizes what is known about urea sources and availability, use of urea as an organic N growth source, rates of urea uptake, enzymes involved in urea metabolism (i.e. urea transporters, urease, UALase), and the biochemical and molecular regulation of urea transport and metabolic enzymes, with an emphasis on the potential for genomic sequence data to continue to provide important new insights.
Role of 5´-AMP-Activated Protein Kinase Activators in Regulating Nuclear Factor Kappa B Signaling

The role of nuclear factor kappa B (NF-κB) is well known in immunity, inflammation, and cancer. Because NF-κB is associated with various diseases, such as arthritis, atherosclerosis, asthma, diabetes, and inflammatory bowel disease, many studies have focused on the IκB kinase (IKK)/NF-κB pathway as a treatment target [1]. In the bladder urothelium, NF-κB is associated with interstitial cystitis (IC) and bladder cancer. IC occurs as a result of inflammation and disruption of urothelium integrity. In addition, bladder inflammation induced by lipopolysaccharide (LPS) is mediated by the IKK/NF-κB pathway, and studies have shown that down regulation of NF-κB, using anti-inflammatory drugs, can aid in treating such inflammation [2,3]. However, anti-inflammatory drug use aimed at reducing the symptoms of IC has yielded no significant results in true clinical practice.
Identification of disease activity and health status cut-off points for the symptom state acceptable to patients with rheumatoid arthritis

Background: Established thresholds for low levels of disease activity need to be examined from a patients’ perspective. Objective: To identify new cut-off points for patients’ perception of satisfactory condition (patient acceptable symptom state (PASS)) in composite indices and patient-reported outcomes, and to examine the agreement between the new PASS cut-off points for composite indices and existing thresholds for remission, low and moderate disease activity. Methods: Patients with rheumatoid arthritis from a treatment register (n = 1496, 72.1% women, mean (SD) age 53.9 (13.5) years, disease duration 7.6 (9.1) years, 28-joint Disease Activity Score (DAS28) 4.98 (1.36)) responded during follow-up (12, 24 and 52 weeks) to a global dichotomised question on satisfactory condition (PASS). New PASS cut-off points were identified with the 75th centile estimation and receiver operating characteristic analyses for a variety of outcome measures, and cut-off points for composite indices were examined for agreement with the low disease activity threshold (1.625) of the Patient Activity Scale (PAS) and thresholds for remission, low and moderate disease activity in DAS28, Simplified Disease Activity Index (SDAI) and Clinical Disease Activity Index (CDAI). Results: New PASS cut-off points for DAS28, SDAI and CDAI were in the moderate range of disease activity, and the cut-off point was 3.56 for PAS. Agreement between thresholds for disease activity levels and the PASS cut-off points was best for low disease activity (accuracy 64.5–74.6), and better for moderate disease activity (accuracy 61.3–67.2) than for remission (accuracy 30.7–45.8). Conclusion: The current PASS concept seems to be in the range of moderate disease activity.
Classification and Salt-tolerance of Actinomycetes in the Qinghai Lake Water and Lakeside Saline Soil

Mesophilic and cryogenic actinomycetes were isolated from water, quagmire soil , lakeside soil and saline wasteland soil in the Qinghai Lake by spreading samples on three kinds of agar media , in which content of NaCl was 70 g/ L. They were characterized according to routine methods, and detected their salt-tolerance. The results indicated that there were salt-tolerant, mesophilic and cryogenic actinomycetes in quagmire and lakeside soil of the Qinghai Lake and in saline wasteland soil nearby the Qinghai Lake. The amount in wasteland soil was the largest , followed by lakeside and swamp soil. All of the salt-tolerant actinomycetes identified were Streptomyces (92. 6 % of total) , and they were all albsporus. And 47.6 %, 19.0 %, and 33.3 % of the tested actinomycetes could tolerant NaCl concentration at 70 g/ L, 100 g/ L, and 150 g/ L respectively.
MRI-Based Topographic Parcellation of Human Cerebral White Matter and Nuclei II. Rationale and Applications with Systematics of Cerebral Connectivity

We describe a system for parcellation of the human cerebral white matter and nuclei, based upon magnetic resonance images. An algorithm for subdivision of the cerebral central white matter according to topographic criteria is developed in the companion manuscript. In the present paper we provide a rationale for this system of parcellation of the central white matter and we extend the system of cerebral parcellation to include principal subcortical gray structures such as the thalamus and the basal ganglia. The volumetric measures of the subcortical gray and white matter parcellation units in 20 young adult brains are computed and reported here as well. In addition, with the comprehensive system for cerebral gray and white matter structure parcellation as reference, we formulate a systematics of forebrain connectivity. The degree to which functionally specific brain areas correspond to topographically specific areas is an open empirical issue. The resolution of this issue requires the development of topographically specific anatomic analyses, such as presented in the current system, and the application of such systems to a comprehensive set of functional-anatomic correlation studies in order to establish the degree of structural-functional correspondence. This system is expected to be applied in both cognitive and clinical neuroscience as an MRI-based topographic systematics of human forebrain anatomy with normative volumetric reference and also as a system of reference for the anatomic organization of specific neural systems as disrupted by focal lesions in lesion-deficit correlations.
Clinical factors that impair health-related quality of life in ulcerative colitis patients vary with the disease duration

Background and aim The health-related quality of life (HRQOL) of patients with ulcerative colitis (UC) can be impaired because of the chronic symptoms. Although UC patients suffer from such symptoms over the long term, there have been few reports on the changes of HRQOL with disease duration. The aim of this study was to clarify these changes. Methods The HRQOL of 331 Japanese UC patients was examined using the validated Japanese version of the Inflammatory Bowel Disease Questionnaire (J-IBDQ). HRQOL and factors affecting HRQOL identified using multiple linear regression analysis were stratified by disease duration. Results Of the 15 clinical factors examined, the clinical activity index score was the strongest determinant (P<0.0001) of all the scores of IBDQ regardless of disease duration. HRQOL did not differ significantly among patients with different disease durations. The factors, however, that affected HRQOL varied according to disease duration. In patients with disease duration of less than 5 years, the clinical activity index score was the predominant factor affecting HRQOL. Being ‘on sick leave or hospitalized’ was a significant factor impairing HRQOL in patients with disease duration of 5–9 years. Moreover, complications due to corticosteroids significantly impaired all of the IBDQ scores in patients with disease duration of 10 years or more. Conclusion Factors that affected the HRQOL of UC patients varied according to the patients' disease duration. Our findings should assist in the development of a long-term strategy for the treatment of UC patients.
Inhaled Cissampelos sympodialis Down‐Regulates Airway Allergic Reaction by Reducing Lung CD3+T Cells

Cissampelos sympodialis Eichl. (Menispermaceae) root infusion is used in Northeast Brazil to treat allergic asthma. We have previously shown that oral use of the plant extract reduces eosinophil infiltration into the lung of ovalbumin (OVA)‐ sensitized mice. However, drugs taken by inhalation route to treat asthma achieve better outcomes. Thereby, in this study, we evaluated the inhaled C. sympodialis alcoholic extract as a therapeutic treatment in OVA‐sensitized BALB/c mice. The parameters which were analyzed consisted of leukocyte recruitment to the airway cavity, tissue remodeling and cell profile. The inhaled extract inhibited mainly eosinophil recruitment to the pleural cavity, bronchoalveolar lavage and peripheral blood. This treatment reduced the OVA‐specific IgE serum titer and leukocyte infiltration in the peribronchiolar and pulmonary perivascular areas as well as mucus production. In addition, we also tested isolated alkaloids from the plant extract. The flow cytometric analysis showed that methylwarifteine (MW) and, mainly, the inhaled extract reduced the number of CD3+T cells and eosinophil‐like cells. Therefore, inhaled C. sympodialis extract and MW lead to down‐regulation of inflammatory cell infiltration with remarkable decrease in the number of T cells in an experimental model of respiratory allergy, suggesting that the plant can be delivered via inhalation route to treat allergic asthma. Copyright © 2012 John Wiley & Sons, Ltd.
TGF- SIGNAL TRANSDUCTION

The transforming growth factor β (TGF-β) family of growth factors control the development and homeostasis of most tissues in metazoan organisms. Work over the past few years has led to the elucidation of a TGFβ signal transduction network. This network involves receptor serine/threonine kinases at the cell surface and their substrates, the SMAD proteins, which move into the nucleus, where they activate target gene transcription in association with DNA-binding partners. Distinct repertoires of receptors, SMAD proteins, and DNA-binding partners seemingly underlie, in a cell-specific manner, the multifunctional nature of TGFβ and related factors. Mutations in these pathways are the cause of various forms of human cancer and developmental disorders.
Reduced quadriceps strength relative to body weight: a risk factor for knee osteoarthritis in women?

OBJECTIVE To determine whether baseline lower extremity muscle weakness is a risk factor for incident radiographic osteoarthritis (OA) of the knee. METHODS This prospective study involved 342 elderly community-dwelling subjects (178 women, 164 men) from central Indiana, for whom baseline and followup (mean interval 31.3 months) knee radiographs were available. Lower extremity muscle strength was measured by isokinetic dynamometry and lean tissue (i.e., muscle) mass in the lower extremities by dual x-ray absorptiometry. RESULTS Knee OA was associated with an increase in body weight in women (P = 0.0014), but not in men. In both sexes, lower extremity muscle mass exhibited a strong positive correlation with body weight. In women, after adjustment for body weight, knee extensor strength was 18% lower at baseline among subjects who developed incident knee OA than among the controls (P = 0.053), whereas after adjustment for lower extremity muscle mass, knee extensor strength was 15% lower than in the controls (P not significant). In men, in contrast, adjusted knee extensor strength at baseline was comparable to that in the controls. Among the 13 women who developed incident OA, there was a strong, highly significant negative correlation between body weight and extensor strength (r = -0.740, P = 0.003), that is, the more obese the subject, the greater the reduction of quadriceps strength. In contrast, among the 14 men who developed incident OA, a modest positive correlation existed between weight and quadriceps strength (r = 0.455, P = 0.058). No correlation between knee flexor (hamstring) strength and knee OA was seen in either sex. CONCLUSION Reduced quadriceps strength relative to body weight may be a risk factor for knee OA in women.
Colour Correction for Assessing Plant Pathology using Low Quality Cameras

We describe a framework for standardising the colour of plant images taken using both mobile phones and compact cameras. This is with a view to maximising the accuracy of plant pathology diagnosis. Rather than attempt to characterise each camera, we place cheap and easily portable custom colour targets in the scene being captured. We propose a novel weighted least squares formulation for optimising the transformation function deduced for each image, where the relative contribution for each patch is proportional to the number of closely matching pixels in the image to be transformed. We also introduce our custom colour target which has been designed to preferentially map plant colours and facilitate simple automatic extraction from the image being processed. We provide subjective and objective results demonstrating the efficacy of our approach. It is anticipated that the methods described here could be applied to any application where perceptual consistency
Ciguatera food poisoning linked to the consumption of imported barracuda--Montreal, Quebec, 1998.

On 17 June 1998, several cases of ciguatera food poisoning were reported by a physician in a medical clinic to the infectious disease unit of the Direction de la santé publique de Montréal-Centre. On 26 June 1998, other cases believed to be part of the same event were reported by a physician working in a hospital. This report summarizes the investigation of this outbreak which occurred among members of Sri-Lankan families residing in Montreal.
A Concrete Categorical Model for the Lambek Syntactic Calculus

We present a categorical/denotational semantics for the Lambek Syntactic Calculus (LSC), indeed for a λlD‐typed version Curry‐Howard isomorphic to it. The main novelty of our approach is an abstract noncommutative construction with right and left adjoints, called sequential product. It is defined through a hierarchical structure of categories reflecting the implicit permission to sequence expressions and the inductive construction of compound expressions. We claim that Lambek's noncommutative product corresponds to a noncommutative bi‐endofunctor into a category, which encloses all categories of such hierarchical structure. A soundness theorem for LSC is shown with respect to this semantical framework.
Degree‐based statistic and center persistency for brain connectivity analysis

Brain connectivity analyses have been widely performed to investigate the organization and functioning of the brain, or to observe changes in neurological or psychiatric conditions. However, connectivity analysis inevitably introduces the problem of mass‐univariate hypothesis testing. Although, several cluster‐wise correction methods have been suggested to address this problem and shown to provide high sensitivity, these approaches fundamentally have two drawbacks: the lack of spatial specificity (localization power) and the arbitrariness of an initial cluster‐forming threshold. In this study, we propose a novel method, degree‐based statistic (DBS), performing cluster‐wise inference. DBS is designed to overcome the above‐mentioned two shortcomings. From a network perspective, a few brain regions are of critical importance and considered to play pivotal roles in network integration. Regarding this notion, DBS defines a cluster as a set of edges of which one ending node is shared. This definition enables the efficient detection of clusters and their center nodes. Furthermore, a new measure of a cluster, center persistency (CP) was introduced. The efficiency of DBS with a known “ground truth” simulation was demonstrated. Then they applied DBS to two experimental datasets and showed that DBS successfully detects the persistent clusters. In conclusion, by adopting a graph theoretical concept of degrees and borrowing the concept of persistence from algebraic topology, DBS could sensitively identify clusters with centric nodes that would play pivotal roles in an effect of interest. DBS is potentially widely applicable to variable cognitive or clinical situations and allows us to obtain statistically reliable and easily interpretable results. Hum Brain Mapp 38:165–181, 2017. © 2016 Wiley Periodicals, Inc.
Audit Risk Assessment Based on Case-Based Reasoning Model in an Extended Environment

The complexity of contemporary business organiza-tions has caused the audit profession to radically alter their audit process over the past decade. Because of the impact of e-business partnerships, outsourcing and co-sourcing relationships, and co-dependence with business partners on the extending of the business risk faced by a client, auditors have to alter their procedures in accordance with this vision, and adopt some new methods to assess audit risks. This study presents a case-based reasoning approach to support auditors to assess audit risks in an extended environment. Case-based reasoning performs similarity-based matching to find the most similar case in case base to the new problem. The method presented is applied to data of audit cases of an accounting firm.
Retroviruses and microtubule‐associated motor proteins

Retroviruses are obligate intracellular parasites of eukaryotic cells. After reverse transcription, the viral DNA contained in the preintegration complex is delivered to the nucleus of the host cell, where it integrates. Before reaching the nucleus, the incoming particle and the preintegration complex must travel throughout the cytoplasm. Likewise, the newly synthesized viral proteins and viral particles must transit the cytoplasm during exit. The cytoplasm is a crowded environment, and simple diffusion is difficult. Therefore, viruses have evolved to utilize the cellular mechanisms of movement through the cytoplasm, where microtubules are the roads, and the ATP‐dependent motors dynein and kinesin are the vehicles for retrograde and anterograde trafficking.