Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models

Background: Biological entities such as genes, promoters, mRNA, metabolites or proteins do not act alone, but in concert in their network context. Modules, i.e., groups of nodes with similar topological properties in these networks characterize important biological functions of the underlying biomolecular system. Edges in such molecular networks represent regulatory and physical interactions, and comparing them between conditions provides valuable information on differential molecular mechanisms. However, biological data is inherently noisy and network reduction techniques can propagate errors particularly to the level of edges. We aim to improve the analysis of networks of biological molecules by deriving modules together with edge relevance estimations that are based on global network characteristics. Methods: The key challenge we address here is investigating the capability of stochastic block models (SBMs) for representing and analyzing different types of biomolecular networks. Fitting them to SBMs both delivers modules of the networks and enables the derivation of edge confidence scores, and it has not yet been investigated for analyzing biomolecular networks. We apply SBM-based analysis independently to three correlation-based networks of breast cancer data originating from high-throughput measurements of different molecular layers: either transcriptomics, proteomics, or metabolomics. The networks were reduced by thresholding for correlation significance or by requirements on scale-freeness. Results and discussion: We find that the networks are best represented by the hierarchical version of the SBM, and many of the predicted blocks have a biologically and phenotypically relevant functional annotation. The edge confidence scores are overall in concordance with the biological evidence given by the measurements. We conclude that biomolecular networks can be appropriately represented and analyzed by fitting SBMs. As the SBM-derived edge confidence scores are based on global network connectivity characteristics and potential hierarchies within the biomolecular networks are considered, they could be used as additional, integrated features in network-based data comparisons

Ontological Clarity, Cognitive Engagement, and Conceptual Model Quality Evaluation: An Experimental Investigation

When analysts build information systems, they document their understanding of users’ work domains via conceptual models. Once a model has been developed, analysts should then check it has no defects. The literature provides little guidance about approaches to improve the effectiveness of conceptual model quality evaluation work. In this light, we propose a theory in which two factors have a material impact on the effectiveness of conceptual model quality evaluation work: (a) the ontological clarity of the conceptual models prepared, and (b) the extent to which analysts use a quality evaluation method designed to cognitively engage stakeholders with the semantics of the domain represented by a conceptual model. We tested our theory using an experiment involving forty-eight expert data modeling practitioners. Their task was to find as many defects as possible in a conceptual model. Our results showed that participants who received the conceptual model with greater ontological clarity on average detected more defects. However, participants who were given a quality evaluation method designed to cognitively engage them more with the semantics of the domain did not detect more defects. Nonetheless, during our analysis of participants’ protocols, we found that those who manifested higher levels of cognitive engagement with the model detected more defects. Thus, we believe that our treatment for the level of cognitive engagement evoked by the quality evaluation method did not take effect. Based on our protocol analyses, we argue that cognitive engagement appears to be an important factor that affects the quality of conceptual model evaluation work

FOOD HABITS OF ASIAN ELEPHANT (Elephas maximus maximus) IN HANDAPANAGALA , SOUTH EAST SRI LANKA

Handapanagala tank area is home for the largest Elephant aggregation(Elephas maxim us maxim us) in Wellawaya area during the dry season. Mostof these Elephants come from different areas mainly from adjacent protectedareas such as Yala, Udawalawe and Lunugamwehera National parks. Themain traditional migratory route lies across the study area connecting Yala -through Demodara. The local migration is mainly due to lack of food andwater within the protected areas.The study attempted to find the food habits of elephants in Handapanagalaarea during dry season. This study was carried out for six months. The mainobjectives were to determine both food availability and feeding habits inrelation to the habitats. Food availability and their Relative ImportanceValues (RIV) were estimated using line transect and direct observationmethod within study area. Relative importance values were comparativelyhigh in species like Bauhinia racemosa (12.39 %), Fleuggea leucocarpa(17.32 %), Securinrega leucopyrus (14.3 %). Relative frequency valueindicated that most common species distributed in the study area wereBauhinia racemosa, Dichrostachys cinera, Phyllanthus sp., Premna sp. Themicro histological analysis was done to determine food habits of elephants.The major food plant parts in dung samples were analyzed to identify thecategories of plants consumed by elephants. This study revealed that themajor food items consumed by elephant during dry season were themonocotyledon leaves (65 %), Culm (12 %), Sheath (6 %) and DicotylidensBark (7 %) and, Woody fiber (2%). The predominant grasses identified indung samples were Imperata cylindrica (Gini grass) and Panicum maximum(Illuk). The field observations revealed that the elephants were mainlyconsuming plants in families such as Leguminosae, Graminae,Euphorbiaceae and Verbenaceae. Majority of bark damages were seen inplants such as Bauhinia racemosa (RIV - 12.39), Treminalia arjuna(Kumbuk) and Phyllanthus spp. A total of 112 plant species were identifiedand 35 species (31% of the available plants) were consumed by elephants.The results indicate that the Elephants in the Handapanagala are grazers andmainly feed on tall grasses during the dry season. Results also indicated that there is an impact on forest tree species like Bauhinia racemosa, Fleuggealeucocarpa and Securinrega leucopyrus, which have high RIV. Since thepresent study was carried out during dry season, this should be continuedduring wet season to get a hroad idea about the seasonal changes in foodhabits of Elephants.

EFFECT OF GLUTEN ADDITION TO RICE FLOUR IN DEVELOPING A NEW RICE FLOUR :BREAD

It was observed that the minimum quantity of vital wheat gluten requiredto mix with rice flour in bread making to be 20 %. Studies on the chemicalcomposition of this bread showed higher moisture and protein levels than wheatbread. Farinograph absorption curves of wheat gluten/rice flour mixesshowed that stable doughs could be made with mixes having 20 % and 25 %wfw Gluten. It was observed that such doughs needed 70% water. Amylographviscosity data showed the above mixture to behave like rice flour onheating, but on cooling it did not show a sharp increase in viscosity like riceflour. The extensibility of the above dough was lower and the resistence washigher than in a wheat flour dough. Gluten/rice flour dough tended to collapseand became porous after two hours. This dough gave a good loaf whendeveloped by a combination of chemical and activated dough developmentmethods. Lecithin when used at 0.5 % (w/w) concentration in the form of aliquid crystaline lipid phase was found to improve the loaf volume further

IMPACT OF SAMBAR DEER(Cervus unicoior unicoior) ON THE VEGETATION AT THE HORTON PLAINS NATIONAL PARK

A survey was carried out at the Horton Plains National Park to investigate the influenceof sambar deer on grassland and fares' vegetation. The method adopted was, comparisonof the dominant grassland communities and seedlings in the forested areas with andwithout the effect of deer. Three enclosures (20 m x 5 m) were erected in the grasslandand four enclosures (20 In x 15 m) were erected in the forest to serve as controls (nograzing). Similar areas adjoining the plots were marked with pegs as test areas (withgrazing). Field surveys were carried ou. during the years 1997 and 1998. Incidence andextent of bark damage by sambar deer \Y<JS also examined using a scoring method on sixtransects each measuring 250 lJ1. GSN (Grazing Susceptibility Number) was used as anindicator of the the phytosociological behaviour of sambar in the grassland SummedDominance Ratio (SDR)) was used to calculate the GSN. During the months of January,March. July and October 1997, GSN values for dominant species in the grassland vizPennicetum and Chrysopogon were 184,20,23.75, -3.06 and 18.6,8.1, 17.23, 19.0respectively. The minus GSN value of ).06 indicates that during October Pcnnicctumgrass was not damaged by deer which coincided with the flowering period of thatspecies. Grazing presusure values obtained during the periods July-Sep 97, Sep-Nov 97 .Nov-Jan 98, Jan-Mar 98 for Pennicetum and Chrysopogon were 17, 5.6, -17.6, 5.8 andI, I I, -0.5, 0.9 respectively. Here the minus values indicates heavy grazing. During theperiods of less rain and also during peak lactation periods of sambar, the grazingpressure is high (July-September and November-January) compared to positive values ofgrazing pressure which coincides well with the comparatively high rainfall periods Studiesof the forest vegetation revealed that after a period of two years (1997-1999) 88'% ofseedlings survived (N=1499) in the enclosure but only 73% of the seedlings survived(N= 1488) in the open area. Bark damage is distinct on plants like Cinnamomumovalifolium, Neolitsea fucata, Calopiiyllum walkeri, Eurya japonica, Eleocarpussubvillosus, Syzigium revolutum and rJedyotis lawsoniae all of which have high IV)(Importance Value Indices). Trees with average gbh 28 cm and average height 7 m weremore prone to damage by deer. Only S% of a total of 921 trees were dead due to barkdamage

Synthesis of New 4-Aminoquinolines and Evaluation of Their In Vitro Activity against Chloroquine-Sensitive and Chloroquine-Resistant Plasmodium falciparum

International audienceThe efficacy of chloroquine, once the drug of choice in the fight against Plasmodium falcipa-rum, is now severely limited due to widespread resistance. Amodiaquine is one of the most potent antimalarial 4-aminoquinolines known and remains effective against chloroquine-resistant parasites, but toxicity issues linked to a quinone-imine metabolite limit its clinical use. In search of new compounds able to retain the antimalarial activity of amodiaquine while circumventing quinone-imine metabolite toxicity, we have synthesized five 4-amino-quinolines that feature rings lacking hydroxyl groups in the side chain of the molecules and are thus incapable of generating toxic quinone-imines. The new compounds displayed high in vitro potency (low nanomolar IC 50), markedly superior to chloroquine and comparable to amodiaquine, against chloroquine-sensitive and chloroquine-resistant strains of P. falcipa-rum, accompanied by low toxicity to L6 rat fibroblasts and MRC5 human lung cells, and metabolic stability comparable or higher than that of amodiaquine. Computational studies indicate a unique mode of binding of compound 4 to heme through the HOMO located on a biphenyl moeity, which may partly explain the high antiplasmodial activity observed for this compound

Porphyromonas gingivalis and Treponema denticola Mixed Microbial Infection in a Rat Model of Periodontal Disease

Porphyromonas gingivalis and Treponema denticola are periodontal pathogens that express virulence factors associated with the pathogenesis of periodontitis. In this paper we tested the hypothesis that P. gingivalis and T. denticola are synergistic in terms of virulence; using a model of mixed microbial infection in rats. Groups of rats were orally infected with either P. gingivalis or T. denticola or mixed microbial infections for 7 and 12 weeks. P. gingivalis genomic DNA was detected more frequently by PCR than T. denticola. Both bacteria induced significantly high IgG, IgG2b, IgG1, IgG2a antibody levels indicating a stimulation of Th1 and Th2 immune response. Radiographic and morphometric measurements demonstrated that rats infected with the mixed infection exhibited significantly more alveolar bone loss than shaminfected control rats. Histology revealed apical migration of junctional epithelium, rete ridge elongation, and crestal alveolar bone resorption; resembling periodontal disease lesion. These results showed that P. gingivalis and T. denticola exhibit no synergistic virulence in a rat model of periodontal disease

High Efficient Dye-Sensitized Solar Cells Based on Synthesized SnO 2

In this study, SnO2 semiconductor nanoparticles were synthesized for DSC applications via acid route using tin(ii) chloride as a starting material and hydrothermal method through the use of tin(iv) chloride. Powder X-ray diffraction studies confirmed the formation of the rutile phase of SnO2 with nanoranged particle sizes. A quasi-solid-state electrolyte was employed instead of a conventional liquid electrolyte in order to overcome the practical limitations such as electrolyte leakage, solvent evaporation, and sealing imperfections associated with liquid electrolytes. The gel electrolytes were prepared incorporating lithium iodide (LiI) and tetrapropylammonium iodide (Pr4N+I−) salts, separately, into the mixture which contains polyacrylonitrile as a polymer, propylene carbonate and ethylene carbonate as plasticizers, iodide/triiodide as the redox couple, acetonitrile as the solvent, and 4-tertiary butylpyridine as an electrolyte additive. In order to overcome the recombination problem associated with the SnO2 due to its higher electron mobility, ultrathin layer of CaCO3 coating was used to cover the surface recombination sites of SnO2 nanoparticles. Maximum energy conversion efficiency of 5.04% is obtained for the device containing gel electrolyte incorporating LiI as the salt. For the same gel electrolyte, the ionic conductivity and the diffusion coefficient of the triiodide ions are 4.70 × 10−3 S cm−1 and 4.31 × 10−7 cm2 s−1, respectively