Miracle-dz/UniFAR-FTUs huggingface dataset:
A Probabilistic-Logical Framework for Ontology Matching

Ontology matching is the problem of determining correspondences between concepts, properties, and individuals of different heterogeneous ontologies. With this paper we present a novel probabilistic-logical framework for ontology matching based on Markov logic. We define the syntax and semantics and provide a formalization of the ontology matching problem within the framework. The approach has several advantages over existing methods such as ease of experimentation, incoherence mitigation during the alignment process, and the incorporation of a-priori confidence values. We show empirically that the approach is efficient and more accurate than existing matchers on an established ontology alignment benchmark dataset.
Ultramorphological characteristics of immature stages of Chrysomya albiceps (Wiedemann 1819) (Diptera: Calliphoridae), a fly specie of forensic importance

Forensic entomology is an area of science that serves as a tool in crime scene investigations. Usually, flies are the first insects to reach a dead body and can oviposit just a few hours after arrival. Therefore the knowledge of immature stages is essential for correct identification of the species found on corpses. Scanning electron microscopy gives detailed information about morphological characters helping to identify the immature forms and consequently serves as a tool in crime scene investigations. C. albiceps is a very important fly for forensic entomologists because its larvae are almost always present on a dead body and it is facultative predators and therefore can alter the composition of species present at the carcass. The aim of this study is to identify eggs, larvae, and puparia of C. albiceps using SEM. Eggs were elongated with the anterior region ending in a “Y” shape and the posterior end was tapered. The micropyle was a well‐adorned orifice with some projections around it. The first instar larva was composed of 12 segments separated by spines. Only one spiracular opening could be seen at the posterior spiracle. Body tegument was smooth and tubercles were not seen. Antennae and maxillary palps were visible. Second and third larval instars were very similar to first instar, except for the presence of anterior spiracle. However, body tegument was composed of net‐like patches and tubercles were visible. Tubercles present at the third instar larvae were robust and erect. Puparia showed a retracted cephalic region and curved tubercles. Microsc. Res. Tech. 73:779–784, 2010. © 2010 Wiley‐Liss, Inc.
An Overview of the Analysis of DNA Methylation in Mammalian Genomes

Abstract DNA methylation at position C5 of the pyrimidine ring of cytosine in mammalian genomes has received a great deal of research interest due to its importance in many biological phenomena. It is associated with events such as epigenetic gene silencing and the maintenance of genome integrity. Aberrant DNA methylation, particularly that of chromosomal regions called CpG islands, is an important step in carcinogenesis. In order to elucidate methylation profiling of complex genomes, various methods have been developed. Many of these methods are based on the differential reactivity of cytosine and 5-methylcytosine to various chemicals. The combined use of these chemical reactions and other preexisting methods has enabled the discrimination of cytosine and 5- methylcytosine in complex genomes. The use of proteins that preferentially bind to methylated DNA has also successfully been used to discriminate between methylated and unmethylated sites. The chemical and structural dissection of the in vivo processes of enzymatic methylation and the binding of methyl CpG binding proteins provides evidence for the complex mechanisms that nature has acquired. In this review we summarize the methods available for the discrimination between cytosine and 5-methylcytosine in complex genomes.
AVSS2011 demo session: GPU enabled Smart Video Node

Summary form only given. This poster presents the educational Hard Choices board game that simulates design decision process to communicate the concepts of design strategies in the face of uncertainty. At the end of the game, players experience the implications of investing effort to gain an advantage or paying a price to take shortcuts during software development in the race to become market leader. The game has been played in academic and industrial contexts, in several countries around the world, and is available to the community under a creative commons license.
Whole-Brain Perfusion Measurement Using 320-Detector Row Computed Tomography in Patients With Cerebrovascular Steno-Occlusive Disease: Comparison With 15O-Positron Emission Tomography

Objective: The 320-detector row computed tomography (CT) can provide whole-brain CT perfusion (CTP) maps with continuous angiographic images by performing a single dynamic scan. We investigated the reliability of CTP cerebral blood flow (CTP-CBF) with 320-detector row CT by comparing findings with 15O-positron emission tomography (PET-CBF). Methods: Whole-brain CTP and PET were performed in 10 patients with chronic unilateral steno-occlusive disease. We compared absolute and relative CBF values of bilateral middle cerebral artery territories between CTP and PET. Results: Although mean CTP-CBF values were approximately 30% lower than mean PET-CBF values, the mean ischemic-to-nonischemic CBF ratios of CTP and PET were almost identical (P = 0.804). Regression analysis showed a significant correlation between CTP-CBF and PET-CBF values for each patient (r = 0.52-0.85, P < 0.001). Conclusions: Whole-brain CTP using 320-detector row CT is useful for evaluating the degree of ischemia for the entire brain with chronic cerebrovascular disease.
Verb Classification using Distributional Similarity in Syntactic and Semantic Structures

In this paper, we propose innovative representations for automatic classification of verbs according to mainstream linguistic theories, namely VerbNet and FrameNet. First, syntactic and semantic structures capturing essential lexical and syntactic properties of verbs are defined. Then, we design advanced similarity functions between such structures, i.e., semantic tree kernel functions, for exploiting distributional and grammatical information in Support Vector Machines. The extensive empirical analysis on VerbNet class and frame detection shows that our models capture meaningful syntactic/semantic structures, which allows for improving the state-of-the-art.
Comparison of the language networks from literature and blogs

In this paper we present the comparison of the linguistic networks from literature and blog texts. The linguistic networks are constructed from texts as directed and weighted co-occurrence networks of words. Words are nodes and links are established between two nodes if they are directly co-occurring within the sentence. The comparison of the networks structure is performed at global level (network) in terms of: average node degree, average shortest path length, diameter, clustering coefficient, density and number of components. Furthermore, we perform analysis on the local level (node) by comparing the rank plots of in and out degree, strength and selectivity. The selectivity-based results point out that there are differences between the structure of the networks constructed from literature and blogs.
Group sequential, sample size re‐estimation and two‐stage adaptive designs in clinical trials: a comparison

Recently there have been quite a few enthusiastic discussions on the topic about adaptive designs for clinical trials [1, 2]. Controversies have been generated among authors who favour versus those who do not quite favour adaptive designs (AD). Some of the controversies have involved group sequential (GS) designs, sample size re-estimation (SSR) procedures, and their variants and mixtures. In this commentary I would like to o er some comparisons with respect to the distinct purposes and key operating aspects of these types of designs. Perhaps a good starting point is their commonality: these designs or procedures all involve interim analysis. Interestingly, this is also where they begin to di er. First, it is important to recognize that the interim analyses they involve serve distinct purposes, hence have di erent operating characteristics. The familiar GS designs have been developed for guiding early stop to reject or accept the null hypothesis, primarily for ethical or economic reasons, that is, for saving lives or saving resources, respectively. Multiple interim analyses (more than two) are usually performed in this situation, typically starting at an early time during the trial, as practiced by an Independent Data Monitoring Committee (IDMC); see for example, Fleming and DeMets [3]. There is also another common reason to analyse the interim data, which is more for the science itself. Due to incomplete knowledge regarding the disease and treatment under study and the very nature of an investigative research, we often encounter uncertainty in the design of a clinical trial when planning the protocol. Therefore, an interim analysis is performed for checking the design assumptions and re-estimation of the sample size so as to reinforce the study power. Put it another way, the purpose of this type of interim analyses is to
Phytotoxicity Evaluation of Type B Trichothecenes Using a Chlamydomonas reinhardtii Model System

Type B trichothecenes, which consist of deoxynivalenol (DON) and nivalenol (NIV) as the major end products, are produced by phytotoxic fungi, such as the Fusarium species, and pollute arable fields across the world. The DON toxicity has been investigated using various types of cell systems or animal bioassays. The evaluation of NIV toxicity, however, has been relatively restricted because of its lower level compared with DON. In this study, the Chlamydomonas reinhardtii testing system, which has been reported to have adequate NIV sensitivity, was reinvestigated under different mycotoxin concentrations and light conditions. The best concentration of DON and NIV, and their derivatives, for test conditions was found to be 25 ppm (2.5 × 10−2 mg/mL). In all light test conditions, DON, NIV, and fusarenon-X (FusX) indicated significant growth inhibition regardless of whether a light source existed, or under differential wavelength conditions. FusX growth was also influenced by changes in photon flux density. These results suggest that C. reinhardtii is an appropriate evaluation system for type B trichothecenes.
In Silico Analysis for Transcription Factors With Zn(II)2C6 Binuclear Cluster DNA-Binding Domains in Candida albicans

A total of 6047 open reading frames in the Candida albicans genome were screened for Zn(II)2C6-type zinc cluster proteins (or binuclear cluster proteins) involved in DNA recognition. These fungal proteins are transcription regulators of genes involved in a wide range of cellular processes, including metabolism of different compounds such as sugars or amino acids, as well as multi-drug resistance, control of meiosis, cell wall architecture, etc. The selection criteria used in the sequence analysis were the presence of the CysX2CysX6CysX5-16CysX2CysX6-8Cys motif and a putative nuclear localization signal. Using this approach, 70 putative Zn(II)2C6 transcription factors have been found in the genome of C. albicans.
Differential methylation of the c‐H‐ras gene in normal mouse cells and during skin tumour progression.

We have previously shown that the mouse c‐H‐ras gene acquires transforming activity in chemically induced skin tumours. We have now investigated the pattern of DNA methylation at HpaII and XhoI sites around the c‐H‐ras locus in various tissues and stages of epidermal tumour progression. The results of this study suggest a correlation between the methylation state of the c‐H‐ras gene and its susceptibility to oncogenic conversion by a point‐mutation. The locus is substantially undermethylated in normal epidermis in comparison with NIH/3T3 fibroblasts. Intermediate levels of methylation were observed in the other tissues investigated. The undermethylation at HpaII sites in epidermal DNA persists through the morphologically distinct phases of hyperplasia, benign papilloma and malignant carcinoma. Methylation at a specific XhoI site close to the c‐H‐ras gene is significantly reduced with respect to normal epidermis in some, but not all epidermal tumours. The methylation state of the c‐H‐ras locus in specific tumours is stably maintained following transfection of these DNAs into NIH/3T3 cells and selection of transformed foci. Demethylation of the locus is not essential in vitro for the transforming activity of DNA from epidermal tumours. The significance of changes in the methylation pattern of the c‐H‐ras gene in different tissues and during tumour progression is discussed.
Do all children need intervention after exposure to tsunami?

Children are uniquely vulnerable in the context of a major natural disaster like tsunami. Post disaster intervention studies in children are few, especially from developing countries like India. An intervention programme for children was developed and conducted at Srinivasapuram, a coastal hamlet in Chennai, a year after tsunami. Sixty- five children who participated in all the six intervention modules were compared to 70 children who did not participate in the intervention. All the children were assessed before and after intervention using the Youth Self Report (YSR) form of Child Behaviour Check List (CBCL) in addition to PTSD symptoms. Children in the two groups were comparable in socio-demographic factors and exposure to tsunami. Prevalence of family psychopathology was more in the intervention group. Only hyperactivity problems were significantly reduced after intervention (z = 2.41 p = 0.016). Children in the intervention group appreciated expression of positive emotions (F = 8.044 p = 0.005) and were also more likely to desist from smoking (F = 6.102 p = 0.003) compared to the control group. The majority of the children are likely to be resilient and only children with pre-existing vulnerability require specific and specialized interventions.
“Leaving it to chance”—Passive risk taking in everyday life

While risk research focuses on actions that put people at risk, this paper introduces the concept of “passive risk”—risk brought on or magnified by inaction. We developed a scale measuring personal tendency for passive risk taking (PRT), validated it using a 150 undergraduate student sample, and obtained three factors indicating separate domains of passive risk taking: risk involving resources, medical risks and ethical risks. The scale has criterion validity, as it is correlated with reported passive risk taking in everyday life, and also has high test-retest reliability. While correlated with the DOSPERT scale, the PRT shows divergent validity from classic risk taking constructs like sensation seeking, and convergent validity with tendencies previously not linked to risk taking, such as procrastination and avoidance. The results indicate that passive risk is a separate and unique domain of risk taking, which merits further research to understand the cognitive and motivational mechanism perpetuating it.
Homology Modeling and Domain Analysis Studies on (CHRNA5) Lung Cancer Protein using Bioinformatics Methods

Globally, lung cancer is the most common cancer among men in terms of both incidence and mortality and among women has the third highest incidence, and is second after breast cancer in mortality. The aim of the research work is to find out the potential mutation gene involved in human lung cancer. Based on literature studies, we identified the potential gene candidate for drug docking studies. Our protein modeling results show the molecular structural regions present in CHRNA5 protein. We also identified the potential domain regions of the protein sequences of the CHRNA5 protein. The results clearly elucidate that the modeled protein candidate acts as a very good candidate for introducing the various novel chemical molecules
A modified version of a Fos-associated cluster in HBZ affects Jun transcriptional potency

Like c-Fos, HBZ (HTLV-I bZIP factor) is able to interact with c-Jun but differs considerably from c-Fos in its ability to activate AP-1-responsive genes since HBZ rather inhibits transcriptional activity of c-Jun. To better understand the molecular mechanisms involved in this down-regulation of c-Jun activity, a large number of HBZ/c-Fos chimeras was constructed and analyzed for their ability to interact with c-Jun, to bind to the AP-1 motif and to stimulate expression of a reporter gene containing the collagenase promoter. By this approach, we demonstrate that the DNA-binding domain of HBZ is responsible for its inhibitory effect on the trans-activation potential of c-Jun. However, unexpectedly, we found that exchange of a cluster of six charged amino acids immediately adjacent to the DNA contact region altered significantly transcriptional activity of chimeras. This particular subdomain could be involved in efficient presentation of the AP-1 complex to the transcriptional machinery. To confirm this role, specific residues present in the cluster of HBZ were substituted for corresponding amino acids in c-Fos. Unlike the JunD-activating potential of wild-type HBZ, this mutant was no longer able to stimulate JunD activity, confirming the key role of this particular cluster in regulation of Jun transcriptional potency.
A methodology for developing local smart diagnostic models using expert knowledge

This paper describes an innovative modular component-based modelling approach for diagnostics and condition-monitoring of manufacturing equipment. The approach is based on the use of object-oriented Bayesian networks, which supports a natural decomposition of a large and complex system into a set of less complex components. The methodology consists of six steps supporting the development process: Begin, Design, Implement, Test, Analyse, and Deploy. The process is iterative and the steps should be repeated until a satisfactory model has been achieved. The paper describes the details of the methodology as well as illustrates the use of the component-based modelling approach on a linear axis used in manufacturing. This application demonstrates the power and flexibility of the approach for diagnostics and condition-monitoring and shows a significant potential of the approach for modular component-based modelling in manufacturing and other domains.
Capsazepine concentration dependently inhibits currents in HEK 293 cells mediated by human hyperpolarization-activated cyclic nucleotide-gated 2 and 4 channels

Recent studies indicate that blockade of currents (Ih) mediated by hyperpolarization-activated cyclic nucleotide-gated (HCN) channels (particularly HCN1) may partly account for the antinociceptive effects of capsazepine (CPZ). Unfortunately, determining whether capsazepine is a selective HCN channel blocker and determining its adverse effects when it is used for the treatment of neuropathic pain, have been thus far understudied. In this study, we aimed to elucidate the effects of capsazepine on human HCN2 (hHCN2) and HCN4 (hHCN4) channels in HEK293 cells. The vectors that expressed hHCN2 and hHCN4 cDNA were constructed and transfected into HEK293 cells. Enhanced green fluorescent protein (EGFP) fluorescence and the reverse transcription polymerase chain reaction (RT-PCR) were used to confirm the successful transfection of the vectors. After G418 (neomycin) screening, cell lines that expressed hHCN2 and hHCN4 were obtained. The whole-cell voltage-clamp technique was used to determine the currents from hHCN2 and hHCN4 channels, which were perfused with five concentrations (0.1 µM, 1 µM, 5 µM, 10 µM and 50 µM) of capsazepine. The results showed that capsazepine at the range from 0.1 to 50 µM markedly inhibited hHCN2 and hHCN4 currents in a concentration-dependent manner, with most inhibition achieved at a concentration of 10 µM of capsazepine. When compared with the control group, a V0.5 for the hHCN2 and hHCN4 channel showed that 10 µM capsazepine significantly shifted the membrane potential towards hyperpolarization. The present results indicate that capsazepine is not a selective HCN1 channel blocker and that it may have adverse effects when used to treat neuropathic pain.
Image processing of particle detection for asbestos qualitative analysis support method -Particle counting system based on classification of background area-

In this paper, we propose the technique classifying background area automatically by calculating the color variance in the RGB space of the picture. By this technique, the background classification robust to change of the background brightness and the background color was enabled. Moreover, we show the effectiveness of this technique by performing particle detection and verifying the result of counting. We aim at development of the particle detector which performs particle counting automatically about the ldquodispersion staining methodrdquo which is one of the processes of asbestos analysis. We used the pictures taken by phase contrast microscopy used for a "dispersion staining method".
Skin Findings of Staphylococcus aureus Toxin-mediated Infection in Relation to Toxin Encoding Genes

Background: Staphylococcal scalded skin syndrome and toxic shock syndrome are associated with exfoliatins and superantigens, respectively; and are easy to distinguish in their usual presentation. However, there is confusion about the mild forms of these 2 staphylococcal diseases. These mild forms are both designated as “staphylococcal scarlet fever” despite differences in their pathophysiology and clinical presentation. Our study aimed to distinguish between the clinical characteristics of the rash associated with exfoliatins and the rash associated with superantigens. Methods: Patients were selected from the French National Reference Center for Staphylococci. We retrospectively compared the clinical characteristics of patients with a generalized rash during Staphylococcus aureus infection. Patients who met the criteria of staphylococcal scalded skin syndrome or toxic shock syndrome were excluded. The patients were classified into 2 groups depending on the presence of a gene coding for exfoliatin or for superantigenic toxin. Results: We included 13 cases with exfoliatin and 9 with superantigens. The patients of the exfoliatin group were more likely to have facial involvement, fold involvement and a superficial focus of infection. In the second group, S. aureus was isolated from a deeper focus in 8 of 9 patients. Conclusion: Mild forms of S. aureus toxin-mediated infection affect the pediatric population. Examination made it possible to distinguish an exanthema associated with an exfoliatin from one associated with a superantigen. This early clinical distinction results in differences in management.