Query routing in cooperative semi-structured peer-to-peer information retrieval networks

Conventional web search engines are centralised in that a single entity crawls and indexes the documents selected for future retrieval, and the relevance models used to determine which documents are relevant to a given user query. As a result, these search engines suffer from several technical drawbacks such as handling scale, timeliness and reliability, in addition to ethical concerns such as commercial manipulation and information censorship. Alleviating the need to rely entirely on a single entity, Peer-to-Peer (P2P) Information Retrieval (IR) has been proposed as a solution, as it distributes the functional components of a web search engine – from crawling and indexing documents, to query processing – across the network of users (or, peers) who use the search engine. This strategy for constructing an IR system poses several efficiency and effectiveness challenges which have been identified in past work. Accordingly, this thesis makes several contributions towards advancing the state of the art in P2P-IR effectiveness by improving the query processing and relevance scoring aspects of a P2P web search. Federated search systems are a form of distributed information retrieval model that route the user’s information need, formulated as a query, to distributed resources and merge the retrieved result lists into a final list. P2P-IR networks are one form of federated search in routing queries and merging result among participating peers. The query is propagated through disseminated nodes to hit the peers that are most likely to contain relevant documents, then the retrieved result lists are merged at different points along the path from the relevant peers to the query initializer (or namely, customer). However, query routing in P2P-IR networks is considered as one of the major challenges and critical part in P2P-IR networks; as the relevant peers might be lost in low-quality peer selection while executing the query routing, and inevitably lead to less effective retrieval results. This motivates this thesis to study and propose query routing techniques to improve retrieval quality in such networks. Cluster-based semi-structured P2P-IR networks exploit the cluster hypothesis to organise the peers into similar semantic clusters where each such semantic cluster is managed by super-peers. In this thesis, I construct three semi-structured P2P-IR models and examine their retrieval effectiveness. I also leverage the cluster centroids at the super-peer level as content representations gathered from cooperative peers to propose a query routing approach called Inverted PeerCluster Index (IPI) that simulates the conventional inverted index of the centralised corpus to organise the statistics of peers’ terms. The results show a competitive retrieval quality in comparison to baseline approaches. Furthermore, I study the applicability of using the conventional Information Retrieval models as peer selection approaches where each peer can be considered as a big document of documents. The experimental evaluation shows comparative and significant results and explains that document retrieval methods are very effective for peer selection that brings back the analogy between documents and peers. Additionally, Learning to Rank (LtR) algorithms are exploited to build a learned classifier for peer ranking at the super-peer level. The experiments show significant results with state-of-the-art resource selection methods and competitive results to corresponding classification-based approaches. Finally, I propose reputation-based query routing approaches that exploit the idea of providing feedback on a specific item in the social community networks and manage it for future decision-making. The system monitors users’ behaviours when they click or download documents from the final ranked list as implicit feedback and mines the given information to build a reputation-based data structure. The data structure is used to score peers and then rank them for query routing. I conduct a set of experiments to cover various scenarios including noisy feedback information (i.e, providing positive feedback on non-relevant documents) to examine the robustness of reputation-based approaches. The empirical evaluation shows significant results in almost all measurement metrics with approximate improvement more than 56% compared to baseline approaches. Thus, based on the results, if one were to choose one technique, reputation-based approaches are clearly the natural choices which also can be deployed on any P2P network.

Effects of modality, urgency and situation on responses to multimodal warnings for drivers

Signifying road-related events with warnings can be highly beneficial, especially when imminent attention is needed. This thesis describes how modality, urgency and situation can influence driver responses to multimodal displays used as warnings. These displays utilise all combinations of audio, visual and tactile modalities, reflecting different urgency levels. In this way, a new rich set of cues is designed, conveying information multimodally, to enhance reactions during driving, which is a highly visual task. The importance of the signified events to driving is reflected in the warnings, and safety-critical or non-critical situations are communicated through the cues. Novel warning designs are considered, using both abstract displays, with no semantic association to the signified event, and language-based ones, using speech. These two cue designs are compared, to discover their strengths and weaknesses as car alerts. The situations in which the new cues are delivered are varied, by simulating both critical and non-critical events and both manual and autonomous car scenarios. A novel set of guidelines for using multimodal driver displays is finally provided, considering the modalities utilised, the urgency signified, and the situation simulated.

Theoretical investigation of electronic excitation transfer between chlorophylls in light-harvesting antenna of photosystem ii using quantum computers

The excitation energy transfer between chlorophylls in major and minor antenna complexes of photosystem II (PSII) was investigated using quantum Fourier transforms. These transforms have an important role in the efficiency of quantum algorithms of quantum computers. The equation 2n=N was used to make the connection between excitation energy transfers using quantum Fourier transform, where n is the number of qubits required for simulation of transfers and N is the number of chlorophylls in the antenna complexes.

Oxidative Leaching of metals from electronic waste with solutions based on quaternary ammonium salts

The treatment of electric and electronic waste (WEEE) is a problem which receives ever more attention. An inadequate treatment results in harmful products ending up in the environment. This project intends to investigate the possibilities of an alternative route for recycling of metals from printed circuit boards (PCBs) obtained from rejected computers. The process is based on aqueous solutions composed of an etchant, either 0.2 M CuCl2.2H2O or 0.2 M FeCl3.6H2O, and a quaternary ammonium salt (quat) such as choline chloride or chlormequat. These solutions are reminiscent of deep eutectic solvents (DES) based on quats. DES are quite similar to ionic liquids (ILs) and are used as well as alternative solvents with a great diversity of physical properties, making them attractive for replacement of hazardous, volatile solvents (e.g. VOCs). A remarkable difference between genuine DES and ILs with the solutions used in this project is the addition of rather large quantities of water. It is shown the presence of water has a lot of advantages on the leaching of metals, while the properties typical for DES still remain. The oxidizing capacities of Cu(II) stem from the existence of a stable Cu(I) component in quat based DES and thus the leaching stems from the activity of the Cu(II)/Cu(I) redox couple. The advantage of Fe(III) in combination with DES is the fact that the Fe(III)/Fe(II) redox couple becomes reversible, which is not true in pure water. This opens perspectives for regeneration of the etching solution. In this project the leaching of copper was studied as a function of gradual increasing water content from 0 - 100w% with the same concentration of copper chloride or iron(III) chloride at room temperature and 80ºC. The solutions were also tested on real PCBs. At room temperature a maximum leaching effect for copper was obtained with 30w% choline chloride with 0.2 M CuCl2.2H2O. The leaching effect is still stronger at 80°C, b ut of course these solutions are more energy consuming. For aluminium, tin, zinc and lead, the leaching was faster at 80ºC. Iron and nickel dissolved easily at room temperature. The solutions were not able to dissolve gold, silver, rhodium and platinum.

Sorting out measures and definitions of screening participation to improve comparability: The example of colorectal cancer.

Participation is a key indicator of the potential effectiveness of any population-based intervention. Defining, measuring and reporting participation in cancer screening programmes has become more heterogeneous as the number and diversity of interventions have increased, and the purposes of this benchmarking parameter have broadened. This study, centred on colorectal cancer, addresses current issues that affect the increasingly complex task of comparing screening participation across settings. Reports from programmes with a defined target population and active invitation scheme, published between 2005 and 2012, were reviewed. Differences in defining and measuring participation were identified and quantified, and participation indicators were grouped by aims of measure and temporal dimensions. We found that consistent terminology, clear and complete reporting of participation definition and systematic documentation of coverage by invitation were lacking. Further, adherence to definitions proposed in the 2010 European Guidelines for Quality Assurance in Colorectal Cancer Screening was suboptimal. Ineligible individuals represented 1% to 15% of invitations, and variable criteria for ineligibility yielded differences in participation estimates that could obscure the interpretation of colorectal cancer screening participation internationally. Excluding ineligible individuals from the reference population enhances comparability of participation measures. Standardised measures of cumulative participation to compare screening protocols with different intervals and inclusion of time since invitation in definitions are urgently needed to improve international comparability of colorectal cancer screening participation. Recommendations to improve comparability of participation indicators in cancer screening interventions are made.

Sorting out measures and definitions of screening participation to improve comparability : the example of colorectal cancer.

Participation is a key indicator of the potential effectiveness of any population-based intervention. Defining, measuring and reporting participation in cancer screening programmes has become more heterogeneous as the number and diversity of interventions have increased, and the purposes of this benchmarking parameter have broadened. This study, centred on colorectal cancer, addresses current issues that affect the increasingly complex task of comparing screening participation across settings. Reports from programmes with a defined target population and active invitation scheme, published between 2005 and 2012, were reviewed. Differences in defining and measuring participation were identified and quantified, and participation indicators were grouped by aims of measure and temporal dimensions. We found that consistent terminology, clear and complete reporting of participation definition and systematic documentation of coverage by invitation were lacking. Further, adherence to definitions proposed in the 2010 European Guidelines for Quality Assurance in Colorectal Cancer Screening was suboptimal. Ineligible individuals represented 1% to 15% of invitations, and variable criteria for ineligibility yielded differences in participation estimates that could obscure the interpretation of colorectal cancer screening participation internationally. Excluding ineligible individuals from the reference population enhances comparability of participation measures. Standardised measures of cumulative participation to compare screening protocols with different intervals and inclusion of time since invitation in definitions are urgently needed to improve international comparability of colorectal cancer screening participation. Recommendations to improve comparability of participation indicators in cancer screening interventions are made.

The E3 ubiquitin ligase Itch regulates sorting nexin 9 through an unconventional substrate recognition domain.

The level of intracellular proteins is mainly regulated through modifications by ubiquitin ligases that target them for degradation. Members of the NEDD4 family of E3 ubiquitin ligases, such as Itch (atrophin-1 interacting protein 4), possess up to four WW domains for specific association with PY motif-containing substrates. We have identified sorting nexin 9 (SNX9), a protein involved in endocytic processes, as a new substrate of Itch. Itch ubiquitylates SNX9 and regulates intracellular SNX9 levels. Using truncated proteins, we found that the interaction with SNX9 is mediated by the proline-rich domain (PRD) of Itch, a domain distinct from the conventional WW recognition domain, and the SH3 domain of SNX9. Interaction with the PRD of Itch is essential for SNX9 ubiquitylation and degradation. Furthermore, this effect is specific for Itch, as NEDD4, a related PRD-containing E3 ligase, does not bind SNX9. SNX18, a second member of the SNX family containing an SH3 domain, was also found to bind to Itch. Our results indicate that the pool of substrates of NEDD4 family E3 ubiquitin ligases extends beyond proteins containing PY motifs.

Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green fluorescent protein-based flow cytometry and cell sorting.

Mutants were produced in the A-domain of HbpR, a protein belonging to the XylR family of σ(54)-dependent transcription activators, with the purpose of changing its effector recognition specificity from 2-hydroxybiphenyl (2-HBP, the cognate effector) to 2-chlorobiphenyl (2-CBP). Mutations were introduced in the hbpR gene part for the A-domain via error-prone polymerase chain reaction, and assembled on a gene circuitry plasmid in Escherichia coli, permitting HbpR-dependent induction of the enhanced green fluorescent protein (egfp). Cells with mutant HbpR proteins responsive to 2-CBP were enriched and separated in a flow cytometry-assisted cell-sorting procedure. Some 70 mutants were isolated and the A-domain mutations mapped. One of these had acquired true 2-CBP recognition but reacted hypersensitively to 2-HBP (20-fold more than the wild type), whereas others had reduced sensitivity to 2-HBP but a gain of 2-CBP recognition. Sequencing showed that most mutants carried double or triple mutations in the A-domain gene part, and were not located in previously recognized conserved residues within the XylR family members. Further selection from a new mutant pool prepared of the hypersensitive mutant did not result in increased 2-CBP or reduced 2-HBP recognition. Our data thus demonstrate that a one-step in vitro 'evolutionary' adaptation of the HbpR protein can result in both enhancement and reduction of the native effector recognition.

Reversible major histocompatibility complex I-peptide multimers containing Ni(2+)-nitrilotriacetic acid peptides and histidine tags improve analysis and sorting of CD8(+) T cells.

MHC-peptide multimers containing biotinylated MHC-peptide complexes bound to phycoerythrin (PE) streptavidin (SA) are widely used for analyzing and sorting antigen-specific T cells. Here we describe alternative T cell-staining reagents that are superior to conventional reagents. They are built on reversible chelate complexes of Ni(2+)-nitrilotriacetic acid (NTA) with oligohistidines. We synthesized biotinylated linear mono-, di-, and tetra-NTA compounds using conventional solid phase peptide chemistry and studied their interaction with HLA-A*0201-peptide complexes containing a His(6), His(12), or 2×His(6) tag by surface plasmon resonance on SA-coated sensor chips and equilibrium dialysis. The binding avidity increased in the order His(6) < His(12) < 2×His(6) and NTA(1) < NTA(2) < NTA(4), respectively, depending on the configuration of the NTA moieties and increased to picomolar K(D) for the combination of a 2×His(6) tag and a 2×Ni(2+)-NTA(2). We demonstrate that HLA-A2-2×His(6)-peptide multimers containing either Ni(2+)-NTA(4)-biotin and PE-SA- or PE-NTA(4)-stained influenza and Melan A-specific CD8+ T cells equal or better than conventional multimers. Although these complexes were highly stable, they very rapidly dissociated in the presence of imidazole, which allowed sorting of bona fide antigen-specific CD8+ T cells without inducing T cell death as well as assessment of HLA-A2-peptide monomer dissociation kinetics on CD8+ T cells.

Sorting live stem cells based on sox2 mRNA expression.

While cell sorting usually relies on cell-surface protein markers, molecular beacons (MBs) offer the potential to sort cells based on the presence of any expressed mRNA and in principle could be extremely useful to sort rare cell populations from primary isolates. We show here how stem cells can be purified from mixed cell populations by sorting based on MBs. Specifically, we designed molecular beacons targeting Sox2, a well-known stem cell marker for murine embryonic (mES) and neural stem cells (NSC). One of our designed molecular beacons displayed an increase in fluorescence compared to a nonspecific molecular beacon both in vitro and in vivo when tested in mES and NSCs. We sorted Sox2-MB(+)SSEA1(+) cells from a mixed population of 4-day retinoic acid-treated mES cells and effectively isolated live undifferentiated stem cells. Additionally, Sox2-MB(+) cells isolated from primary mouse brains were sorted and generated neurospheres with higher efficiency than Sox2-MB(-) cells. These results demonstrate the utility of MBs for stem cell sorting in an mRNA-specific manner.

Old world arenaviruses enter the host cell via the multivesicular body and depend on the endosomal sorting complex required for transport.

The highly pathogenic Old World arenavirus Lassa virus (LASV) and the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) use α-dystroglycan as a cellular receptor and enter the host cell by an unusual endocytotic pathway independent of clathrin, caveolin, dynamin, and actin. Upon internalization, the viruses are delivered to acidified endosomes in a Rab5-independent manner bypassing classical routes of incoming vesicular trafficking. Here we sought to identify cellular factors involved in the unusual and largely unknown entry pathway of LASV and LCMV. Cell entry of LASV and LCMV required microtubular transport to late endosomes, consistent with the low fusion pH of the viral envelope glycoproteins. Productive infection with recombinant LCMV expressing LASV envelope glycoprotein (rLCMV-LASVGP) and LCMV depended on phosphatidyl inositol 3-kinase (PI3K) as well as lysobisphosphatidic acid (LBPA), an unusual phospholipid that is involved in the formation of intraluminal vesicles (ILV) of the multivesicular body (MVB) of the late endosome. We provide evidence for a role of the endosomal sorting complex required for transport (ESCRT) in LASV and LCMV cell entry, in particular the ESCRT components Hrs, Tsg101, Vps22, and Vps24, as well as the ESCRT-associated ATPase Vps4 involved in fission of ILV. Productive infection with rLCMV-LASVGP and LCMV also critically depended on the ESCRT-associated protein Alix, which is implicated in membrane dynamics of the MVB/late endosomes. Our study identifies crucial cellular factors implicated in Old World arenavirus cell entry and indicates that LASV and LCMV invade the host cell passing via the MVB/late endosome. Our data further suggest that the virus-receptor complexes undergo sorting into ILV of the MVB mediated by the ESCRT, possibly using a pathway that may be linked to the cellular trafficking and degradation of the cellular receptor.

Electronic Bulletin Board System, HR-345, 1998

The primary objectives of the Electronic Bulletin Board System (BBS) project were to: (1) Provide an electronic communication tool which would link city and county engineering offices to each other and to other governmental agencies for messaging and data sharing; (2) Provide a dial-up site for reference information or files accessible on-demand; and (3) Provide a "stepping stone" to the world of electronic data transfer, recognizing that most local government employees face a huge complex of technology with limited knowledge of computers and communications tools. The system was designed to be as simple as possible, and to require minimal equipment and software cost to the users. The original system was an Apex 386/25 computer with MS-DOS 5.0 software and the final configuration was an HP Vectra XM Pentium 90 with MS-NT 3.51 and Mustang - Wildcat 5.0 software. The users of the BBS were county engineers and their staff, offices in the central office of the Iowa Department of Transportation (DOT) and Resident Construction Engineers at the Iowa DOT. Much of the activity was between the county engineers, and their staffs, and the Iowa DOT offices with which they have ongoing business activities. The BBS contained files for mapping, Internet e-mail service, Accident Location Analysis System (ALAS) data, Iowa DOT bid lettings, and Autocad and Intergraph maps and standards. The 800 line calls were recorded and gave the best indication of the usage and the trends that were being followed. The usage tended to be higher in the winter months when design activities are occurring and lower in the summer months when the construction is in progress. The project was judged a success. The BBS did provide a "stepping stone" to the world of electronic data transfer.

How to prescribe nutritional support using computers.

As other intensive care unit (ICU) therapies, nutritional support has become more complex requiring tight supervision and monitoring. It has repeatedly been shown that despite awareness of guidelines and prescription of the recommended amounts of energy (25 kcal/kg), underfeeding remains a prominent problem worldwide. In patients with prolonged stays, overfeeding has also become an issue. This lack of fit between prescription and delivery is largely caused by the lack of visibility of the nutritional results to nurses and clinicians. Computerized systems have brought major improvements, mainly through the customization of nutrition relevant variables in a single place, making them visible. Another important point is the possibility to change the ICU time constant to days and weeks which is the delay relevant for nutritional changes to appear, instead of minutes and hours which are more relevant for critical care.

Attitudes of second year diploma nurses in three community colleges toward the use of computers in the nursing role /

The effectiveness of various kinds of computer programs is of concern to nurse-educators. Using a 3x3 experimental design, ninety second year diploma student nurses were randomly selected from a total population at three community colleges in Ontario. Data were collected via a 20-item valid and reliable Likert-type questionnaire developed by the nursing profession to measure perceptions of nurses about computers in the nursing role. The groups were pretested and posttested at the beginning and end of one semester. Subjects attending College A group received a computer literacy course which comprised word processing with technology awareness. College B students were exposed to computer-aided instruction primarily in nursing simulations intermittently throughout the semester. College C subjects maintained their regular curriculum with no computer involvement. The student's t-test (two-tailed) was employed to assess the attitude scores data and a one-way analysis of variance was performed on the attitude scores. Posttest analysis revealed that there was a significant difference (p<.05) between attitude scores on the use of computers in the nursing role between College A and C. No significant differences (p>.05) were seen between College B and A in posttesting. Suggestions for continued computer education of diploma student nurses are provided.

Nurses' attitudes toward computers before and two months after training

This study examined nurses' attitudes toward computers before training and 2 months after training. A quantitative approach and a nonexperimental survey design were used in this study. Stronge and Brodt's (1985) instrument, Nurses' Attitudes Toward Computerization Questionnaire, was used to assess 27 nurses' attitudes prior to and 2 months after computer training. Demographic variables also were collected on the questionnaires. The results of this study showed that, overall, nurses had positive attitudes towards computers in both questionnaires. The results of the first questionnaire were consistent with other studies. There were no studies that involved a follow-up questionnaire using Stronge and Brodt's (1985) instrument. Attitude scores of Questionnaire 2 were higher than attitude scores of Questionnaire 1. More time for nursing tasks, less time for quality patient care, and threat to job security questions were found to be statistically significant. This study found no statistical significance between attitudes and demographic variables. Younger nurses a~d nurses with fewer years of computer experience were most likely to exhibit positive attitudes. Implications for practice and future research were discussed. Some limitations were identified and discussed.