Miracle-dz/UniFAR-FTUs huggingface dataset:
Principles of diagnostic testing of animal populations

Along with almost everything else in the swine industry, the way veterinarians apply and interpret diagnostic tests has evolved as production systems have changed. Valid interpretation of diagnostic results requires integration of clinical, epidemiological and laboratory observations, and consideration of potential sources of error. Beyond their traditional application in outbreak investigation and disease diagnosis, diagnostic tests are increasingly used to quantify disease in defined populations in order to support decisions regarding population health management. The optimal strategy for population testing, including the tests selected and the numbers of animals sampled, is a function of the purpose of testing (Table 1). Fundamental objectives are to establish the disease status (positive or negative) of populations (groups, sites, studs, pods, companies, regions, countries), or to quantify disease trends in time or space. Demographic changes (particularly increased herd sizes) and persistent problems with PRRS have altered the needs for, and feasibility of, more intensive use of herd level diagnostics. Veterinarians must have a sound theoretical understanding of the relationships between diagnostic test performance, sampling theory, and disease prevalence that underpin population testing. This paper reviews some core principles that are essential for veterinarians to be able to meet these challenges. More detailed discussions of diagnostic testing of swine populations, and approaches to disease surveillance in swine are available elsewhere.
Presentation of secondary parasitic infection 37 years after primary infection

Abstract Echinococcus granulosus (EG) is a neglected pathology that causes cystic echinococcosis and primarily affects the liver and lung. EG infects ~6 million worldwide and mortality is quoted as 2–4% per 100 000 inhabitants. The increase in human traffic from endemic regions demands clinician’s awareness. Dogs are the most common definitive host for the EG tapeworm. Human infection requires ingestion of fecal parasitic eggs. Primary infection causes cysts to appear in affected organs, rupture of which leads to secondary infection. Ultrasound remains the mainstay of diagnosis. Treatment can be either; chemotherapeutic, radiological, surgical or a combination depending on the organ affected.
Natural Killer Cell Receptor Genes in the Family Equidae: Not only Ly49

Natural killer (NK) cells have important functions in immunity. NK recognition in mammals can be mediated through killer cell immunoglobulin-like receptors (KIR) and/or killer cell lectin-like Ly49 receptors. Genes encoding highly variable NK cell receptors (NKR) represent rapidly evolving genomic regions. No single conservative model of NKR genes was observed in mammals. Single-copy low polymorphic NKR genes present in one mammalian species may expand into highly polymorphic multigene families in other species. In contrast to other non-rodent mammals, multiple Ly49-like genes appear to exist in the horse, while no functional KIR genes were observed in this species. In this study, Ly49 and KIR were sought and their evolution was characterized in the entire family Equidae. Genomic sequences retrieved showed the presence of at least five highly conserved polymorphic Ly49 genes in horses, asses and zebras. These findings confirmed that the expansion of Ly49 occurred in the entire family. Several KIR-like sequences were also identified in the genome of Equids. Besides a previously identified non-functional KIR-Immunoglobulin-like transcript fusion gene (KIR-ILTA) and two putative pseudogenes, a KIR3DL-like sequence was analyzed. In contrast to previous observations made in the horse, the KIR3DL sequence, genomic organization and mRNA expression suggest that all Equids might produce a functional KIR receptor protein molecule with a single non-mutated immune tyrosine-based inhibition motif (ITIM) domain. No evidence for positive selection in the KIR3DL gene was found. Phylogenetic analysis including rhinoceros and tapir genomic DNA and deduced amino acid KIR-related sequences showed differences between families and even between species within the order Perissodactyla. The results suggest that the order Perissodactyla and its family Equidae with expanded Ly49 genes and with a potentially functional KIR gene may represent an interesting model for evolutionary biology of NKR genes.
Crowdsourced POI labelling: Location-aware result inference and Task Assignment

Identifying the labels of points of interest (POIs), aka POI labelling, provides significant benefits in location-based services. However, the quality of raw labels manually added by users or generated by artificial algorithms cannot be guaranteed. Such low-quality labels decrease the usability and result in bad user experiences. In this paper, by observing that crowdsourcing is a best-fit for computer-hard tasks, we leverage crowdsourcing to improve the quality of POI labelling. To our best knowledge, this is the first work on crowdsourced POI labelling tasks. In particular, there are two sub-problems: (1) how to infer the correct labels for each POI based on workers' answers, and (2) how to effectively assign proper tasks to workers in order to make more accurate inference for next available workers. To address these two problems, we propose a framework consisting of an inference model and an online task assigner. The inference model measures the quality of a worker on a POI by elaborately exploiting (i) worker's inherent quality, (ii) the spatial distance between the worker and the POI, and (iii) the POI influence, which can provide reliable inference results once a worker submits an answer. As workers are dynamically coming, the online task assigner judiciously assigns proper tasks to them so as to benefit the inference. The inference model and task assigner work alternately to continuously improve the overall quality. We conduct extensive experiments on a real crowdsourcing platform, and the results on two real datasets show that our method significantly outperforms state-of-the-art approaches.
Activation of Eosinophils Interacting with Dermal Fibroblasts by Pruritogenic Cytokine IL-31 and Alarmin IL-33: Implications in Atopic Dermatitis

Background IL-31 is a pruritogenic cytokine, and IL-33 is an alarmin for damaging inflammation. They together relate to the pathogenesis of atopic dermatitis (AD). Eosinophil infiltration into the inner dermal compartment is a predominant pathological feature of AD. We herein investigated the in vitro inflammatory effects of IL-31 and IL-33 on the activation of human eosinophils and dermal fibroblasts. Methodology/Principal Findings Receptors, adhesion molecules and signaling molecules were assessed by Western blot or flow cytometry. Chemokines and cytokine were quantitated by multiplex assay. Functional IL-31 receptor component IL-31RA, OSMR-β and IL-33 receptor component ST2 were constitutively expressed on the surface of eosinophils. Co-culture of eosinophils and fibroblasts significantly induced pro-inflammatory cytokine IL-6 and AD-related chemokines CXCL1, CXCL10, CCL2 and CCL5. Such inductions were further enhanced with IL-31 and IL-33 stimulation. IL-31 and IL-33 could significantly provoke the release of CXCL8 from eosinophils and fibroblasts, respectively, which was further enhanced upon co-culture. In co-culture, eosinophils and fibroblasts were the main source for the release of CCL5, and IL-6, CXCL1, CXCL8, CXCL10 and CCL2, respectively. Direct interaction between eosinophils and fibroblasts was required for CXCL1, CXCL10, CXCL8 and CCL5 release. Cell surface expression of intercellular adhesion molecule-1 on eosinophils and fibroblasts was up-regulated in co-culture upon IL-31 and IL-33 stimulation. The interaction between eosinophils and fibroblasts under IL-31 and IL-33 stimulation differentially activated extracellular signal-regulated kinase, c-Jun N-terminal kinase, p38 mitogen-activated protein kinase, nuclear factor-κB and phosphatidylinositol 3-kinase–Akt pathways. Using specific signaling molecule inhibitors, the differential induction of IL-31 and IL-33-mediated release of cytokines and chemokines such as IL-6 and CXCL8 from co-culture should be related to their distinct activation profile of intracellular signaling pathways. Conclusions/Significance The above findings suggest a crucial immunopathological role of IL-31 and IL-33 in AD through the activation of eosinophils-fibroblasts interaction via differential intracellular signaling mechanisms.
[Expression and role of nitric oxide synthase in the testis and epididymis of Macaca fascicularis].

OBJECTIVE To investigate the expression and the role of nitric oxide synthase (NOS) in the testis and epididymis of macaca fascicularis. METHODS The immunohistochemical ABC method was used to observe the localization of nitric oxide synthase in the testis and epididymis of the macaca fascicularis. RESULTS (1) nNOS immunoreactivity was found in the spermatogenic cells of seminiferous tubules, the epithelia of epididymal efferent ducts, sperm and the endothelia of blood vessels; (2) iNOS was expressed in the epididymal efferent duct, the sperm inside the duct, and the myoid cells and endothelia of blood vessels; (3) eNOS immunoreactivity was detected in the interstitial cells of the testis, the epididymal efferent duct, the sperm inside the duct, and the myoid cells and endothelia of blood vessels. CONCLUSION NOS is extensively expressed in the testis and epididymis of the macaca fascicularis and it may play an important role in such processes as spermatogenesis, sperm maturation and testosterone secretion.
Metabolic Myopathies: Update 2009

Metabolic myopathies are inborn errors of metabolism that result in impaired energy production due to defects in glycogen, lipid, mitochondrial, and possibly adenine nucleotide metabolism. Fatty acid oxidation defects (FAOD), glycogen storage disease, and mitochondrial myopathies represent the 3 main groups of disorders, and some consider myoadenylate deaminase (AMPD1 deficiency) to be a metabolic myopathy. Clinically, a variety of neuromuscular presentations are seen at different ages of life. Newborns and infants commonly present with hypotonia and multisystem involvement (liver and brain), whereas onset later in life usually presents with exercise intolerance with or without progressive muscle weakness and myoglobinuria. In general, the glycogen storage diseases result in high-intensity exercise intolerance, whereas the FAODs and the mitochondrial myopathies manifest predominately during endurance-type activity or under fasted or other metabolically stressful conditions. The clinical examination is often normal, and testing requires various combinations of exercise stress testing, serum creatine kinase activity and lactate concentration determination, urine organic acids, muscle biopsy, neuroimaging, and specific genetic testing for the diagnosis of a specific metabolic myopathy. Prenatal screening is available in many countries for several of the FAODs through liquid chromatography-tandem mass spectrometry. Early identification of these conditions with lifestyle measures, nutritional intervention, and cofactor treatment is important to prevent or delay the onset of muscle weakness and to avoid potential life-threatening complications such as rhabdomyolysis with resultant renal failure or hepatic failure. This article will review the key clinical features, diagnostic tests, and treatment recommendations for the more common metabolic myopathies, with an emphasis on mitochondrial myopathies.
A study on the spatial scaling properties of topographic index for China

Topographic Index (TI), ln(alpha/tanbeta) (alpha= upslope contributing area per unit contour; tanbeta= local slope angle), as an important parameter approximately characterizing the likely spatial distribution of soil water states within a watershed, has been widely applied in some topography-based land-surface schemes in recent decades. As TI concept and its computation was originally developed from hill slope hydrological process study and was most frequently utilized within small to middle sized watershed simulations, persistent disputation therefore has been concentrated on whether the TI computed from the coarse resolution DEM can be used to characterize the likely spatial distribution of moisture states in extensive areas effectively. The objective of this study was thus focused on investigating the statistical properties of TI computed from different resolution DEMs for clarifying the dynamic relations among them in whole territory of China. Statistical analyses were conducted to the TIs computed with an improved MFD algorithm from DEMs in different spatial resolution of 90 x 90 m, 1000 x 1000 m. Surprisingly, perfect linear relationships in almost the same form were found existed among the mean values of TI extensively sampled from these two different resolution DEMs under 0.1deg x 0.1deg, 0.5deg x 0.5deg and 1deg x 1deg block conditions respectively, which implies that accurate TI values can be obtained with coarse resolution DEMs usually employed in GCM or RCM simulations with an unique linear downscaling equation. Systematic analyses further point out that the algorithm for TI computation distinguishingly affects the form of this equation, while the size, location, and number of selected TI samples has minor affections.
Non-Destructive Quantification of Plastic Deformation in Steel: Employing X-Ray Diffraction Peak Broadening Analysis

Abstract : The X-ray diffraction (XRD) pattern of an alloy, such as steel, reveals, among other properties (ex., phase composition, crystal structure), information about the strain state, crystallite (domain) size and dislocation density. While well-established non-destructive methods are available to quantify elastic strain (and residual stress), dislocation density has proven to be a particularly elusive quantity to evaluate non-destructively. Dislocation density provides important information about the state of a material and the extent to which it was deformed. This has a strong influence on the mechanical behaviour of a material during and after deformation. The goal of this work is to examine the underpinning science behind XRD peak broadening analysis and develop a methodology for evaluating plastic deformation in ferromagnetic steel alloys. An overview of the principles of XRD, how the crystallographic structure of steel accommodates stress and how X-rays interact with steel structures are documented. A historical perspective on XRD peak broadening analysis is provided. Two approaches, the modified WilliamsonHall and WarrenAverbach, have been identified to enable quantification of dislocation density and crystallite size. Both approaches that account for strain anisotropy are believed to offer the best potential for success. A variety of potential defence applications have been identified and a possible way ahead for advancement of this technology has been mapped. It is thus recommended to modify the portable XRD hardware and software to enable calculation of the dislocation density and crystallite size using both these approaches. This, together with elastic strain / residual stress analysis, would enable better evaluation of the current state of health of steel structures and components as they near predetermined life limits and assess the risk in extending these limits.
Evidence for a Shared Etiological Mechanism of Psychotic Symptoms and Obsessive-Compulsive Symptoms in Patients with Psychotic Disorders and Their Siblings

The prevalence of obsessive-compulsive disorder in subjects with psychotic disorder is much higher than in the general population. The higher than chance co-occurrence has also been demonstrated at the level of subclinical expression of both phenotypes. Both extended phenotypes have been shown to cluster in families. However, little is known about the origins of their elevated co-occurrence. In the present study, evidence for a shared etiological mechanism was investigated in 3 samples with decreasing levels of familial psychosis liability: 987 patients, 973 of their unaffected siblings and 566 healthy controls. The association between the obsessive-compulsive phenotype and the psychosis phenotype c.q. psychosis liability was investigated. First, the association was assessed between (subclinical) obsessive-compulsive symptoms and psychosis liability. Second, in a cross-sib cross-trait analysis, it was examined whether (subclinical) obsessive-compulsive symptoms in the patient were associated with (subclinical) psychotic symptoms in the related unaffected sibling. Evidence was found for both associations, which is compatible with a partially shared etiological pathway underlying obsessive-compulsive and psychotic disorder. This is the first study that used a cross-sib cross-trait design in patients and unaffected siblings, thus circumventing confounding by disease-related factors present in clinical samples.
Loss of tumor suppressor Merlin results in aberrant activation of Wnt/β-catenin signaling in cancer

The expression of the tumor suppressor Merlin is compromised in nervous system malignancies due to genomic aberrations. We demonstrated for the first time, that in breast cancer, Merlin protein expression is lost due to proteasome-mediated elimination. Immunohistochemical analysis of tumor tissues from patients with metastatic breast cancer revealed characteristically reduced Merlin expression. Importantly, we identified a functional role for Merlin in impeding breast tumor xenograft growth and reducing invasive characteristics. We sought to determine a possible mechanism by which Merlin accomplishes this reduction in malignant activity. We observed that breast and pancreatic cancer cells with loss of Merlin show an aberrant increase in the activity of β-catenin concomitant with nuclear localization of β-catenin. We discovered that Merlin physically interacts with β-catenin, alters the sub-cellular localization of β-catenin, and significantly reduces the protein levels of β-catenin by targeting it for degradation through the upregulation of Axin1. Consequently, restoration of Merlin inhibited β-catenin-mediated transcriptional activity in breast and pancreatic cancer cells. We also present evidence that loss of Merlin sensitizes tumor cells to inhibition by compounds that target β-catenin-mediated activity. Thus, this study provides compelling evidence that Merlin reduces the malignant activity of pancreatic and breast cancer, in part by suppressing the Wnt/β-catenin pathway. Given the potent role of Wnt/β-catenin signaling in breast and pancreatic cancer and the flurry of activity to test β-catenin inhibitors in the clinic, our findings are opportune and provide evidence for Merlin in restraining aberrant activation of Wnt/β-catenin signaling.
Chemical Composition, Antioxidant, and Antimicrobial Activities of Lichen Umbilicaria cylindrica (L.) Delise (Umbilicariaceae)

The phytochemical analysis of methanol and chloroform extracts of Umbilicaria cylindrica was determined by HPLC-UV method. The predominant phenolic compound in both extracts was depsidone, salazinic acid (1). Besides salazinic acid, the tested extracts of U. cylindrica contain norstictic acid (2), methyl-β-orcinol carboxylate (3), ethyl haematommate (4), atranorin (5), and usnic acid (6), in different amounts and relations. The lichen extracts showed comparable and strong antioxidant activity, exhibited higher DPPH and hydroxyl radical scavengings, chelating activity, and inhibitory activity towards lipid peroxidation. The lichen extracts demonstrated important antimicrobial activity against eight strains with MIC values from 15.62 to 62.50 μg/mL. This is the first report of the detail chemical composition and antioxidant activity of the lichen Umbilicaria cylindrica, and the results suggest that this lichen can be used as a new source of the natural antioxidants and the substances with antimicrobial features.
Attachment and Proliferation of Cultured Human Periodontal Ligament Cells on 75:25 Poly (DL-Lactide-co-ε-Caprolactone) Electrospun Resorbable Membrane

75:25 poly (DL-lactide-co-ε-caprolactone) electrospun resorbable membranes were prepared by electrospinning and film casting techniques. Primary cultures of human periodontal ligament (HPDL) fibroblasts cells were seeded on the electrospun membranes, film-cast membranes, and control glass cover slips. The number of cell attached was determined at 1, 3, 24 and 72 h after cell seeding. Cell proliferation on the membranes was determined by MTT assay at 1.5 h and 1, 3, 5 and 7 days after cell seeding. The morphology of cells was also determined by SEM. The results indicated that the cell attached number and cell proliferation on the electrospun membranes were significantly higher than that of the film-cast membranes at every time point. From an SEM study, HPDL cells could healthy attach on both, the electrospun membranes and the film-cast membranes. HPDL cells were firmly attached to the membrane matrix in the electrospun membrane group. In the film-cast group, HPDL were loosely attached to the membrane surfaces. In conclusion, an electrospun membrane had better ability to promote HPDL cell attachment and proliferation than did film-cast membranes.
MicroRNA-383-5p acts as a prognostic marker and inhibitor of cell proliferation in lung adenocarcinoma by cancerous inhibitor of protein phosphatase 2A

Lung cancer is the leading cause of cancer-associated mortality worldwide. MicroRNAs (miRNAs/miRs) serve a role in the occurrence and development of lung cancer. The aim of the present study was to analyze the expression and function of the proliferation-associated miR-383-5p in lung adenocarcinoma (LAC). Samples of human LAC and matched adjacent normal lung tissues were surgically removed, and miR-383-5p expression and the pathological characteristics of lung adenocarcinoma were investigated. The present study revealed that miR-383-5p expression level was significantly decreased in LAC tissues and its expression levels were markedly associated with tumor size and differentiation. Overexpression of miR-383-5p in A549 and H1299 LAC cell lines inhibited cell proliferation by G1 cell cycle phase arrest and induction of apoptosis. Cancerous inhibitor of protein phosphatase 2A (CIP2A), a potential target gene of miR-383-5p, was inversely associated with miR-383-5p expression level in LAC tissues and cell lines. Furthermore, the results of the present study demonstrated that CIP2A was directly regulated by miR-383-5p and the restoration of CIP2A expression reversed the inhibitory effects of miR-383-5p on LAC cell proliferation. In conclusion, the results of the present study demonstrated that miR-383-5p was downregulated in LAC tissues. By targeting CIP2A, miR-383-5p exerts its anti-proliferative function in LAC, suggesting its use a potential novel potential prognostic biomarker and therapeutic target for LAC.
Algebraic theories, monads, and arities

Monads are of interest both in semantics and in higher dimensional algebra. It turns out that the idea behind usual notion finitary monads (whose values on all sets can be computed from their values on finite sets) extends to a more general class of monads called monads with arities, so that not only algebraic theories can be computed from a proper set of arities, but also more general structures like n-categories, the computing process being realized using Kan extensions. This Master thesis compiles the required material in order to understand this question of arities and reconstruction of monads, and tries to give some examples of relevant interest from both semantics and higher category theory. A discussion on the promising field of operads is then provided as appendix.