Biochemical network matching and composition

This paper looks at biochemical network matching and compositio

Composition of Biochemical Networks using Domain Knowledge

Graph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge known networks and examine topological variants arising from such composition. Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can help with network design and optimisation. The problem of network composition has not received much attention in algorithm and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work and the possible solutions to the graph merge problem. We show that our XML graph merge solution performs well in practice and improves on the existing toolsets. This leads us into future work directions and the plan of research which will aim to implement graph merging primitives using domain knowledge to perform composition and decomposition on specific graphs in the biological domain

reSearch : enhancing information retrieval with images

Combining image and text search is an open research question. The main issues are what technologies to base this solution on, and what measures of relevance to employ. Our reSearch prototype mashes up papers indexed using information retrieval techniques (Terrier) with Google image search for faces and Google book search. The user can interactively employ query expansion with additional terms suggested by Terrier, and use those terms to expand both the text and image search. We test this solution with a selection of recent publications and queries concerning people engaged in research. We report on the effectiveness of this solution. It seems that the combination works to a large extent, as testified by our observations

Karren of the Kamenjak Hum (Dalmatian Karst, Croatia); from the initial dissection of flat surfaces by rain to rocky points

Rock relief is an important trace of the formation and development of karst phenomena on various carbonate rock. The existing current state is usually in a rich and diverse stage of homogeneous or heterogeneous development. The various forms of rock relief represent different ways and conditions a karst phenomenon formed and the developmental levels under the same conditions and with the same factors. Research into the connections between different developmental models is therefore necessary. Over time, not only rock relief but also rock forms begin to merge with one another. We are looking at the initial period of the development of a thick rock strata due to rain. On gently sloping rock strata, which tend to disintegrate at the edges, especially when they are inclined downwards, characteristic rock relief forms on the flat surfaces of larger planes, initially due to rainwater and sheets of creeping water and later through three-dimensional dissection and primarily the direct action of rainwater.Škraplje huma Kamenjak (Dalmatinski kras, Hrvaška); od začetnega obdobja členjenja ravnih površin z dežjem do skalnih konicSkalni relief je pomembna sled načina oblikovanja in razvoja kraških pojavov na različnih karbonatnih kamninah. Je pa zatečeno, trenutno stanje v največkrat bogatem in pestrem oblikovnem enovrstnem ali večvrstnem razvoju. Različna oblika skalnega reliefa torej predstavlja različne načine in razmere oblikovanja kraškega pojava in razvojne stopnje znotraj istih razmer in z istimi dejavniki. Zatorej je neobhodno proučevanje znotraj povezav v različne razvojne modele. Ne samo skalni relief, temveč tudi skalne oblike same se skozi čas prelivajo ena v drugo. Pred nami je začetno obdobje razvoja debelih skladov kamnine z dežjem. Na položnih skladih kamnine, ki na robovih, zlasti nagnjenih navzdol razpadajo, na njihovih ravnih površinah večjih ploskev pa se sprva z deževnico in s ploskovno polzečo vodo in nato s trirazsežnim razčlenjevanjem in predvsem neposrednim delovanjem deževnice oblikuje značilen skalni relief. Iz skalnih oblik, ki ga tvorijo, je moč natančno razbrati najbolj značilna obdobja razvoja škrapelj z odločilnimi dejavniki njihovega oblikovanja.

Morphometric analysis of dolines — the problem of delineation and calculation of basic parameters

So far reported unstable correlations between environmental settings and doline geometry require a revision of doline delineating methods and morphometric analyses that follows from such input data. We examine the reliability of the most accessible data sources for doline delineation, namely basic topographic maps at a scale of 1:5,000 and ortho-rectified aerial photographs (digital orthophotos) of 0.5 m resolution. Their reliability has been quantified in the Dinaric karst (Krk Island, NE Adriatic Sea). The adequacy of most commonly used morphometric parameters (viz. elongation and circularity) and their variations applied in previous studies are mathematically verified and practically tested. The simulation of an individual method behaviour performed on polygons with increasing circularity and elongation demonstrated their ranges of validity. The efficiency of a particular method was verified by the application to the real dataset of dolines. The optimal variation of an individual parameter (circularity = Pcc/Pd; elongation = ε of the best fitting ellipse) is identified and suggested for use in order to provide uniform results and increase the comparability of future morphometric analyses. Asymmetry (the distance between the centroid of doline ground plan and the centroid of the largest inscribed circle) as an additional parameter for describing doline ground plans has been developed and is proposed for further use.Key words: karst, doline delineating, morphometric analyses, measurement errors, Krk Island.Morfometrične analize vrtač – problem določanja oboda in računanja osnovnih parametrovNezanesljivost korelacij med okoljskimi dejavniki in geometrijo vrtač je spodbudila pregled do sedaj uporabljenih metod določanja oboda vrtač in primernosti morfometričnih analiz, ki sledijo iz teh podatkov. V prispevku preverjamo zanesljivost najširše dostopnih podatkovnih virov za določanje oboda vrtač, in sicer topografskih kart v merilu 1 : 5000 in ortofotov z ločljivostjo 0,5 m. Zanesljivost smo določali na primeru Dinarskega krasa (otok Krk, SV Jadransko morje). Primernost do sedaj najpogosteje uporabljenih parametrov (tj. sploščenost in krožnost) in njunih različic, ki se pojavljajo v literaturi, smo matematično preverili in preizkusili pri realnem naboru vrtač. Simulacija delovanja posamezne metode na poligonih z naraščajočo krožnostjo in sploščenostjo je pokazala njihova območja veljavnosti. Učinkovitost metod smo nato preverili še pri realnem vzorcu vrtač, pri katerem smo ugotovili, katera je najprimernejša različica posameznega parametra (krožnost = Pcc/Pd; sploščenost = ε prilegajoče elipse), in jo, da bi zagotovili večjo usklajenost in primerljivost rezultatov, predlagali za nadaljnjo rabo v prihodnjih morfometričnih analizah vrtač. Kot dodaten parameter za analizo tlorisa vrtač smo razvili in preizkusili indeks asimetrije oboda vrtač, tj.razdaljo med težiščem tlorisa vrtače in težiščem največjega včrtanega kroga.Ključne besede: kras, določanje oboda vrtač, morfometrične analize, merske napake, otok Krk.Unstable correlations between environmental settings and doline geometry have inspired a revision of previously applied doline delineating methods, and the adequacy of morphometric analysis that follows from such input data. We examine reliability of the most accessible data sources for remote doline delineation, namely basic topographic maps at scale of 1:5,000 and ortho-rectified aerial photographs (digital orthophotos) of 0.5 m resolution. Their reliability has been quantified in the Dinaric karst (Krk Island, NE Adriatic Sea). The adequacy of most commonly used morphometric parameters (viz. elongation and circularity) and their variations applied in previous studies are mathematically verified and practically tested. The optimal variation of an individual parameter (circularity = Pcc/Pd ; elongation = ε of the best fitting ellipse) is identified and suggested for use in order to provide uniform results and increase the comparability of future morphometric analyses. Asymmetry as an additional parameter for describing doline ground plans has been developed and is proposed for use in further research

VisGenome: visualization of single and comparative genome representations

Summary: VisGenome visualizes single and comparative representations for the rat, the mouse and the human chromosomes at different levels of detail. The tool offers smooth zooming and panning which is more flexible than seen in other browsers. It presents information available in Ensembl for single chromosomes, as well as homologies (orthologue predictions including ortholog one2one, apparent ortholog one2one, ortholog many2many) for any two chromosomes from different species. The application can query supporting data from Ensembl by invoking a link in a browser. Availability: http://www.dcs.gla.ac.uk/~asia/VisGenome Contact: [email protected]

Measuring Student Attitudes and Performance in order to Improve Future Performance and Enrolments in Senior Science Subjects.

With increased demands for scientific literacy with the impending changes to external assessment in Queensland, whereby 50% of a student’s results in senior science and mathematics will be based on external assessment, it is important to incorporate more standardised assessment into a middle school’s program so that students have the requisite literacy skills and self-efficacy to be successful throughout the process. This project aimed to examine whether external examinations such as the International Competitions and Assessments for Schools (ICAS) Science test, could correlate with internal assessment outcomes, and whether the increased use of scientific literacy through these leads to greater confidence when selecting senior science subjects. Two cohorts of students (Year 9 and Year 10) were included in the research and student learning outcomes post intervention were analysed to determine correlations between the ICAS science results and internal school-based assessment. The results suggest that targeted intervention does improve student self-efficacy and furthermore showed a positive correlation between the external ICAS science test and internal assessment

Strong Post-Compromise Secure Proxy Re-Encryption

Proxy Re-Encryption (PRE), introduced by Bellare et. al, allows a ciphertext encrypted using a key pki to be re-encrypted by a third party so that it is an encryption of the same message under a new key pkj , without revealing the message. Post-Compromise Security (PCS) was first introduced for messaging protocols, and ensures that a ciphertext remains confidential even when past keys have been corrupted. We define PCS in the context of PRE, which ensures that an adversary cannot distinguish which ciphertext a re-encryption was created from even given the old secret key, potential old ciphertexts and update token used to perform the re-encryption. We argue that this formal notion accurately captures the most intuitive form of PCS. We give separating examples demonstrating how our definition is stronger than existing ones, before showing that PCS can be met using a combination of existing security definitions from the literature. In doing so, we show that there are existing PRE schemes that satisfy PCS. We also show that natural modifications of more practical PRE schemes can be shown to be PCS without relying on this combination of existing security definitions. Finally, we discuss the relationship between PCS with selective versus adaptive key corruptions, giving a theorem that shows how adaptive security can be met for certain re-encryption graphs

Identification of hepatitis a virus mimotopes by phage display, antigenicity and immunogenicity

A phage-displayed peptide approach was used to identify ligands mimicking antigenic determinants of hepatitis A virus (HAV) for the first time. Bacteriophages displaying HAV mimotopes were isolated from a phage-display peptide library by affinity selection on serum antibodies from hepatitis A patients. Selected phage-peptides were screened for reactivity with sera from HAV infected patients and healthy controls. Four cloned peptides with different sequences were identified as mimotopes of HAV; three of them showed similarity in their amino acid sequences with at least one of the VP3 and VP1 antigenic proteins of HAV. One clone was recognised by 92% of the positive sera. The phagotopes competed effectively with HAV for absorption of anti-HAV-specific antibodies in human sera, as determined by ELISA. The four phage clones induced neutralising anti-HAV antibodies in immunised mice. These results demonstrate the potential of this method to elucidate the disease related epitopes of HAV and to use these mimotopes in diagnostic applications or in the development of a mimotope-based hepatitis A vaccine without the necessity of manipulation of the virus