Identifying collaborations among researchers: a pattern-based approach

In recent years a huge amount of publications and scientific reports has become available through digital libraries and online databases. Digital libraries commonly provide advanced search interfaces, through which researchers can find and explore the most related scientific studies. Even though the publications of a single author can be easily retrieved and explored, understanding how authors have collaborated with each other on specific research topics and to what extent their collaboration have been fruitful is, in general, a challenging task. This paper proposes a new pattern-based approach to analyzing the correlations among the authors of most influential research studies. To this purpose, it analyzes publication data retrieved from digital libraries and online databases by means of an itemset-based data mining algorithm. It automatically extracts patterns representing the most relevant collaborations among authors on specific research topics. Patterns are evaluated and ranked according to the number of citations received by the corresponding publications. The proposed approach was validated in a real case study, i.e., the analysis of scientific literature on genomics. Specifically, we first analyzed scientific studies on genomics acquired from the OMIM database to discover correlations between authors and genes or genetic disorders. Then, the reliability of the discovered patterns was assessed using the PubMed search engine. The results show that, for the majority of the mined patterns, the most influential (top ranked) studies retrieved by performing author-driven PubMed queries range over the same gene/genetic disorder indicated by the top ranked pattern

SIIMCO: A forensic investigation tool for identifying the influential members of a criminal organization

Members of a criminal organization, who hold central positions in the organization, are usually targeted by criminal investigators for removal or surveillance. This is because they play key and influential roles by acting as commanders, who issue instructions or serve as gatekeepers. Removing these central members (i.e., influential members) is most likely to disrupt the organization and put it out of business. Most often, criminal investigators are even more interested in knowing the portion of these influential members, who are the immediate leaders of lower level criminals. These lower level criminals are the ones who usually carry out the criminal works; therefore, they are easier to identify. The ultimate goal of investigators is to identify the immediate leaders of these lower level criminals in order to disrupt future crimes. We propose, in this paper, a forensic analysis system called SIIMCO that can identify the influential members of a criminal organization. Given a list of lower level criminals in a criminal organization, SIIMCO can also identify the immediate leaders of these criminals. SIIMCO first constructs a network representing a criminal organization from either mobile communication data that belongs to the organization or crime incident reports. It adopts the concept space approach to automatically construct a network from crime incident reports. In such a network, a vertex represents an individual criminal, and a link represents the relationship between two criminals. SIIMCO employs formulas that quantify the degree of influence/importance of each vertex in the network relative to all other vertices. We present these formulas through a series of refinements. All the formulas incorporate novelweighting schemes for the edges of networks. We evaluated the quality of SIIMCO by comparing it experimentally with two other systems. Results showed marked improvement

Trusting (and Verifying) Online Intermediaries\u27 Policing

All is not well in the land of online self-regulation. However competently internet intermediaries police their sites, nagging questions will remain about their fairness and objectivity in doing so. Is Comcast blocking BitTorrent to stop infringement, to manage traffic, or to decrease access to content that competes with its own for viewers? How much digital due process does Google need to give a site it accuses of harboring malware? If Facebook censors a video of war carnage, is that a token of respect for the wounded or one more reflexive effort of a major company to ingratiate itself with the Washington establishment? Questions like these will persist, and erode the legitimacy of intermediary self-policing, as long as key operations of leading companies are shrouded in secrecy. Administrators must develop an institutional competence for continually monitoring rapidly-changing business practices. A trusted advisory council charged with assisting the Federal Trade Commission (FTC) and Federal Communications Commission (FCC) could help courts and agencies adjudicate controversies concerning intermediary practices. An Internet Intermediary Regulatory Council (IIRC) would spur the development of expertise necessary to understand whether companies’ controversial decisions are socially responsible or purely self-interested. Monitoring is a prerequisite for assuring a level playing field online

Structure based drug design for the discovery of promising inhibitors of human Bcl-2 and Streptococcus dysgalactiae LytR proteins

Drug research has evolved significantly in the last decades toward the concept of the rational design of drugs. The capability to study molecular interactions at the atomic level and to rationalize this knowledge to construct and improve drug candidates provided the premises of structure-based drug design (SBDD). This approach allied to the computational methods available nowadays yields the opportunity to expedite the intricate process of drug discovery. In the present thesis, the SBDD approach was implemented to study promising candidate inhibitors of the human Bcl-2 and the Streptococcus dysgalactiae LytR proteins. Half of the cancers in humans are estimated to be related with overexpression of Bcl-2 protein. This macromolecule is responsible for the inhibition of the apoptotic process, which is pivotal for the elimination of abnormal cells. When Bcl-2 is overexpressed, these abnormal cells don’t respond to death stimuli, either endogenous or exogenous, such as chemotherapeutic, and become immortal. Promising 4H-chromene and indole derivatives were studied regarding their potential to inhibit Bcl-2. Molecular docking studies revealed sub-micromolar binding of the 4Hchromene activemethine and the indole derivatives in the binding groove essential for Bcl-2 biological function. Biophysical characterization did not demonstrate significant evidence of binding between Bcl-2 and the compounds under study, probably due to their small network of interactions with the binding pocket residues. The structure determination process of the proteinligand complexes achieved preliminary co-crystallization conditions that require further optimization. Numerous infectious diseases are associated to the bacterial biofilm phenotype, which consists of agglomerates of cells enclosed in a self-produced matrix. Biofilms confer bacteria improved resistance to the host’s innate immune system and to conventional antibiotics. LytR belongs to the LCP family of proteins, which are thought to be responsible for the attachment of anionic polymers to the peptidoglycan, protecting the Gram-positive bacteria from phagocytosis and lysis. Previous virtual screening studies yielded ellagic acid and fisetin has promising inhibitors of LytR, displaying anti-biofilm activity. Molecular docking revealed binding of these compounds in the hypothetical active site of LytR, with micromolar affinities, and specific interactions with crucial protein residues for catalysis. Biophysical techniques failed to provide evidence of protein-ligand interactions, although this may be related to the possible co-purification with a lipidic substrate, which has been reported before. Mass spectrometry or structural determination, through X-ray crystallography or NMR, should be pivotal to establish evidence of this molecule’s accommodation in the binding pocket

Molecular modeling study of the testosterone metabolizing enzyme UDP-glucuronosyltransferase 2B17

The dominant sex hormone testosterone is mainly metabolized by liver enzymes belonging to the uridine-diphospho (UDP) glucuronosyltransferase (UGT) family. These enzymes are the main phase II enzymes, and they have an important role in the detoxification of endogenous and exogenous compounds in humans. The aim of the present study was to improve the understanding of the binding properties of UGT2B17. A homology modelling procedure was used to generate models of the UGT2B17 enzyme based on templates with known crystal structures. Molecular docking of inhibitors was performed to gain further insights in the interactions between ligand and binding site, and to determine which of the models had the best accuracy. ROC curves were made to evaluate the ability of the models to differentiate between binders (inhibitors) and non-binders (decoys). When comparing the four models, which were based on four different crystal structures, the model based on the 4AMG crystal structure was the most accurate in distinguishing between true binders and non-binders. Investigating pharmacological UGT2B17 inhibition may provide novel treatment for patients with low testosterone levels. Such treatment may elevate endogenous testosterone levels and provide a more predictable increase in serum concentrations rather than un-physiological elevation of serum levels through direct treatment with testosterone, and this could be favorable both for giving a predictable treatment regime with reduced chances of serious adverse effects. The present study may serve as a tool in the search for novel drugs aiming for increasing testosterone levels

10381 Summary and Abstracts Collection -- Robust Query Processing

Dagstuhl seminar 10381 on robust query processing (held 19.09.10 - 24.09.10) brought together a diverse set of researchers and practitioners with a broad range of expertise for the purpose of fostering discussion and collaboration regarding causes, opportunities, and solutions for achieving robust query processing. The seminar strove to build a unified view across the loosely-coupled system components responsible for the various stages of database query processing. Participants were chosen for their experience with database query processing and, where possible, their prior work in academic research or in product development towards robustness in database query processing. In order to pave the way to motivate, measure, and protect future advances in robust query processing, seminar 10381 focused on developing tests for measuring the robustness of query processing. In these proceedings, we first review the seminar topics, goals, and results, then present abstracts or notes of some of the seminar break-out sessions. We also include, as an appendix, the robust query processing reading list that was collected and distributed to participants before the seminar began, as well as summaries of a few of those papers that were contributed by some participants

Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens

<p>Abstract</p> <p>Background</p> <p>Duplication, followed by fixation or random loss of novel genes, contributes to genome evolution. Particular outcomes of duplication events are possibly associated with pathogenic life histories in fungi. To date, differential gene gain and loss have not been studied at genomic scales in fungal pathogens, despite this phenomenon's known importance in virulence in bacteria and viruses.</p> <p>Results</p> <p>To determine if patterns of gene duplication differed between pathogens and non-pathogens, we identified gene families across nine euascomycete and two basidiomycete species. Gene family size distributions were fit to power laws to compare gene duplication trends in pathogens <it>versus </it>non-pathogens. Fungal phytopathogens showed globally altered patterns of gene duplication, as indicated by differences in gene family size distribution. We also identified sixteen examples of gene family expansion and five instances of gene family contraction in pathogenic lineages. Expanded gene families included those predicted to be important in melanin biosynthesis, host cell wall degradation and transport functions. Contracted families included those encoding genes involved in toxin production, genes with oxidoreductase activity, as well as subunits of the vacuolar ATPase complex. Surveys of the functional distribution of gene duplicates indicated that pathogens show enrichment for gene duplicates associated with receptor and hydrolase activities, while euascomycete pathogens appeared to have not only these differences, but also significantly more duplicates associated with regulatory and carbohydrate binding functions.</p> <p>Conclusion</p> <p>Differences in the overall levels of gene duplication in phytopathogenic species <it>versus </it>non-pathogenic relatives implicate gene inventory flux as an important virulence-associated process in fungi. We hypothesize that the observed patterns of gene duplicate enrichment, gene family expansion and contraction reflect adaptation within pathogenic life histories. These adaptations were likely shaped by ancient, as well as contemporary, intimate associations with monocot hosts.</p