361 research outputs found

    A Hybrid Classification Approach based on FCA and Emerging Patterns - An application for the classification of biological inhibitors

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    International audienceClassification is an important task in data analysis and learning. Classification can be performed using supervised or unsupervised methods. From the unsupervised point of view, Formal Concept Analysis (FCA) can be used for such a task in an efficient and well-founded way. From the supervised point of view, emerging patterns rely on pattern mining and can be used to characterize classes of objects w.r.t. a priori labels. In this paper, we present a hybrid classification method which is based both on supervised and unsupervised aspects. This method relies on FCA for building a concept lattice and then detects the concepts whose extents determines classes of objects sharing the same labels. These classes can then be used as reference classes for classifying unknown objects. This hybrid approach has been used in an experiment in chemistry for classifying inhibitors of the c-Met protein which plays an important role in protein interactions and in the development of cancer

    11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

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    Recent advances in computational epigenetics

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    31th International Conference on Information Modelling and Knowledge Bases

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    Information modelling is becoming more and more important topic for researchers, designers, and users of information systems.The amount and complexity of information itself, the number of abstractionlevels of information, and the size of databases and knowledge bases arecontinuously growing. Conceptual modelling is one of the sub-areas ofinformation modelling. The aim of this conference is to bring together experts from different areas of computer science and other disciplines, who have a common interest in understanding and solving problems on information modelling and knowledge bases, as well as applying the results of research to practice. We also aim to recognize and study new areas on modelling and knowledge bases to which more attention should be paid. Therefore philosophy and logic, cognitive science, knowledge management, linguistics and management science are relevant areas, too. In the conference, there will be three categories of presentations, i.e. full papers, short papers and position papers

    Population genetics and structure of the Sumatran tiger

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    The two key determinants of population persistence in fragmented landscapes are population size and connectivity. Populations with high levels of genetic variation and large population size are expected to have a lower risk of extinction. Similarly, populations with high rates of connectivity are expected to persist long-term. For many elusive landscape species it is difficult to obtain direct estimates of these parameters, but genetic sampling can offer powerful indirect assessments. Whilst these techniques have been applied to the study of many wide-ranging carnivores, this study represents the first example in the Sumatran tiger (Panthera tigris sumatrae). Extensive field surveys were conducted to collect faecal samples from several Tiger Conservation Landscapes and protected areas on Sumatra. Samples were then processed according to optimised protocols to obtain reliable results. In order to quantify extinction risk I first estimated genetic variation and effective population size using microsatellite loci. I also determined relative levels of connectivity using estimates of differentiation (FST), gene flow and genetic clustering. Results indicate that Sumatran tigers have high levels of genetic variation and that their effective population size is within the expected range. There is very little population structure and there is no obvious evidence for barriers to dispersal. The Batang Hari/Kerinci Seblat ecosystem emerged as a potential source population and in contrast there was some evidence of isolation affecting the population of Way Kambas NP in the extreme south of the island. Overall, despite high levels of human land cover conversion over the past 20-30 years, few genetic changes have been expressed in the Sumatran tiger. The immediate threat to tigers is not the loss of genetic diversity, but the rapidly declining area of suitable habitat in which they can survive

    Back to plants for drug discovery: from ethnomedicine to more conventional approaches

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    Over the last years, there is rekindling of interest in drug discovery from botanical resources. This thesis proposed two different approaches (from ethnomedicine to scholarly strategies) for drug discovery from medicinal plants, identifying the areas of knowledge involved and addressing the challenges encountered, with the aim of enhancing the chance of success of the overarching process. The first approach consists to review the literature to increase understanding of a plant of interest and generate strong hypotheses for future drug development research on this plant. Illustrating such an approach, we focused on Tithonia diversifolia (Hemsl.) A. Gray (TD). Knowledge about TD was collected from both online databases and non-electronic resources. Overall, a total of 1,804 reports have been collected. After subsequent duplicates removal and screening for relevant titles and abstracts, a total of 119 text articles were obtained and assessed for eligibility. Finally, 168 articles were selected, of which forty-nine were added after analyses of the reference lists of the included papers. We found that all parts of the plant are valued in several cultures for a wide scope of ailments ranging from topical issues \u2014wounds, skeleto-muscular disorders, abscesses, dermatological conditions, and stomach pains\u2014 to systemic disorders such as diabetes, malaria, fever, hepatitis and infectious diseases. Importantly, most of the ethnomedical claims of TD have been substantiated in several studies conducted in vitro and in vivo in animals. Sometimes, findings were conflicting and thanks to this review, we were able to assess the weight of evidence for each pharmacological effect of TD. The anti-inflammatory, antimalarial, antidiabetic, antioxidant and anticancer effects do stand out but there is also a stunning array of other relevant pharmacological effects. Chemically, a hundred of chemicals, mainly terpenoids and phenols, have been isolated from various TD extracts so far. Of these, some compounds including Tagitinin C have been linked to the pharmacology of TD. About the toxicological profile, we were able to conclude based on evidence that short-term oral administration of TD is relatively well-tolerated in animals when taken at doses less than 100 mg/kg. The second approach consists to screen the ethnomedical knowledge of indigenous people to select the best plant candidate to launch a drug discovery campaign. So, we carried out a 6-month cross-sectional questionnaire-based survey to explore the use of medicinal plants (MP) in People living with HIV (PLHIV) in the city of Dschang (West Region, Cameroon). Of the 247 HIV-infected respondents, 54.9% reported to use plants. MP users were then kindly invited to provide photographs and/or specimens of plants for botanical identification. A total of 70 MP, chiefly the herbs, were mentioned by informants (82.2% of total MP users, mean\ub1SEM: 2.2\ub10.2 MP/subject, min 1, max 11), of which forty-nine have been botanically identified. Commonly reported pathological conditions or symptoms treated with MP included malaria (n = 27, 18.4% of total citations), cough (n = 20, 13.6%) and abdominal pain (n = 16, 10.9%). The benefits of using MP reportedly ranged from moderate (n = 60, 57.7%) to complete (n = 35, 33.7%) relief, while only 8 subjects (7.7% of MP users) reported no change in their terms. Interestingly, 2 subjects (33.3 % of respondents) denounced fatigue and weight loss. We also observed that THPs were the main advisors of PLHIV on the use of MP. Thus, in the rest of our study, their knowledge and attitudes towards HIV/AIDS were surveyed aiming at understanding whether they may be an appropriate resource to assist in the scaling up of HIV prevention and treatment delivery services in Cameroon. 16 THPs were recruited by the chairperson of the Cooperative Society of Producers of Medicinal Plants of West Region based on their good reputation in traditional healing practice. Three of them acknowledged the use of MP to manage HIV diseases in their clients. All THPs who agreed to participate in the survey were also evaluated for their knowledge of HIV transmission, prevention and diagnosis. We found that their knowledge related to HIV was relatively low raising concern about their aptitude to effectively assist conventional health practitioners in fighting against HIV/AIDS. Resulting from literature mining and ethnomedical claims is the adoption of a relevant pharmacological testing system. In any case, the testing systems should represent the biological activities that best match the ethnomedical uses of the selected plant species. In addition, it is important to bear in mind that plant extracts are complex mixtures containing various components and, therefore, their overall activity results from interactions between their naturally occurring ingredients. It is with this background that we conducted a study of comparison of the effects of a whole extract of a particular strain of Cannabis sativa L. to that of cannabidiol (CBD). We knew cannabis is endowed with a potent anti-inflammatory effect attributable mainly to CBD, but also to its entourage. This mechanism by which other compounds occurring in cannabis may contribute to its clinical effects has been espoused as an \u201centourage effect\u201d. The concept of entourage effect was first introduced in 1998 by Ben-Shabat and Raphael Mechoulam but still, there was no hard evidence that the entourage effect is real. So, thanks to a collaboration with a pharmaceutical company, we grew a particular strain of cannabis deprived of THC and standardized in 5% CBD (CM5). Then, we tested the effects of an extract of CM5 in parallel to that of pure CBD at equimolar concentrations on neutrophil functions including oxidative metabolism, migration and production of proinflammatory cytokines. Results show that CM5 0.05-50 \u3bcg/mL and CBD 10-8-10-5 M inhibit the neutrophil functions including ROS production, cell migration, mRNA levels of proinflammatory cytokines (but at the protein level, only TNF-a was inhibited) to a comparable extent, indicating that CBD may be the main responsible of the anti-inflammatory effects of Cannabis. The effects of CBD and CM5 show however remarkable differences in terms of potency and efficacy, suggesting that beyond CBD, other components of cannabis may contribute to its biological effects. As a whole, such results support the use of cannabis and CBD to stem inflammation, however also warrant in-depth investigation of the underlying cellular and molecular mechanisms to better exploit their therapeutic potential

    Drinking water biofiltration: Removal of antibiotics and behaviour of antibiotic resistance genes

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    This research investigated the effectiveness of biofiltration systems for the attenuation of antibiotics and antibiotic resistance genes (ARGs) from drinking water. Five antibiotics, including amoxicillin, clarithromycin, oxytetracycline, sulfamethoxazole, and trimethoprim, and the relevant resistance genes (blaCTX-M, blaOXA-1, blaTEM, ermB, tetA, tetG, tetQ, tetW, tetX, sul 1, sul 2, dfrA1 and dfrA12) as well as integrase genes (intI 1 and intI 2) were targeted. In addition, the role the biofilm plays as a gene transfer site was also investigated. Both chemical (LC-MS/MS) and molecular biology (real-time qPCR, high-throughput qPCR and 16S rRNA amplicon sequencing) methodologies were used. A total of three biofiltration experiments using sand, granular activated carbon (GAC) and anthracite as filter media were set-up at bench-scale. Results showed that the target antibiotics were substantially removed (> 90%) by GAC-associated biofilters and partially removed (< 20%) by sand and anthracite-sand dual media biofilters. The position of GAC layer within the sand filter bed showed no effect on antibiotic removal. The absolute abundance of ARGs decreased (1.0-log reduction on average) after biofiltration, while ARGs’ normalised copy number remained unchanged or showed an increasing trend in the filtered water, especially when exposed to the target antibiotics, indicating that the biofilters did not contribute greatly to the elimination of ARG pollution from the feedwater despite the effective removal of antibiotics. Exposure to the target antibiotics affected the bacterial community in biofilm samples and the differences in bacterial community structure were correlated with the changes in the resistome. Plasmid conjugative transfer experiment based on biofiltration showed that the GAC media is more conducive to the horizontal transfer of ARGs in biofilms and the transfer occurred more frequently in biofilms than in the influents and effluents. Overall, the results of this study could enhance our understanding of the prevalence of ARGs during drinking water treatment
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