Web Query Reformulation via Joint Modeling of Latent Topic Dependency and Term Context

An important way to improve users’ satisfaction in Web search is to assist them by issuing more effective queries. One such approach is query reformulation, which generates new queries according to the current query issued by users. A common procedure for conducting reformulation is to generate some candidate queries first, then a scoring method is employed to assess these candidates. Currently, most of the existing methods are context based. They rely heavily on the context relation of terms in the history queries and cannot detect and maintain the semantic consistency of queries. In this article, we propose a graphical model to score queries. The proposed model exploits a latent topic space, which is automatically derived from the query log, to detect semantic dependency of terms in a query and dependency among topics. Meanwhile, the graphical model also captures the term context in the history query by skip-bigram and n-gram language models. In addition, our model can be easily extended to consider users’ history search interests when we conduct query reformulation for different users. In the task of candidate query generation, we investigate a social tagging data resource—Delicious bookmark—to generate addition and substitution patterns that are employed as supplements to the patterns generated from query log data

Effectiveness of Traditional Chinese Medicine in Primary Care

Includes bibliographical references

Local structural alignment of RNA with affine gap model

Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.The project is partially supported by the Seed Funding Programme for Basic Research (Project number: 200911159065) of the University of Hong Kong

Integrative analysis workflow for the structural and functional classification of C-type lectins

<p>Abstract</p> <p>Background</p> <p>It is important to understand the roles of C-type lectins in the immune system due to their ubiquity and diverse range of functions in animal cells. It has been observed that currently confirmed C-type lectins share a highly conserved domain known as the C-type carbohydrate recognition domain (CRD). Using the sequence profile of the CRD, an increasing number of putative C-type lectins have been identified. Hence, it is highly needed to develop a systematic framework that enables us to elucidate their carbohydrate (glycan) recognition function, and discover their physiological and pathological roles.</p> <p>Results</p> <p>Presented herein is an integrated workflow for characterizing the sequence and structural features of novel C-type lectins. Our workflow utilizes web-based queries and available software suites to annotate features that can be found on the C-type lectin, given its amino acid sequence. At the same time, it incorporates modeling and analysis of glycans - a major class of ligands that interact with C-type lectins. Thereafter, the results are analyzed together with context-specific knowledge to filter off unlikely predictions. This allows researchers to design their subsequent experiments to confirm the functions of the C-type lectins in a systematic manner.</p> <p>Conclusions</p> <p>The efficacy and usefulness of our proposed immunoinformatics workflow was demonstrated by applying our integrated workflow to a novel C-type lectin -CLEC17A - and we report some of its possible functions that warrants further validation through wet-lab experiments.</p

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE". Comments most welcom

Adiponectin Prevents Diabetic Premature Senescence of Endothelial Progenitor Cells and Promotes Endothelial Repair by Suppressing the p38 MAP Kinase/p16INK4A Signaling Pathway

OBJECTIVE - A reduced number of circulating endothelial progenitor cells (EPCs) are casually associated with the cardiovascular complication of diabetes. Adiponectin exerts multiple protective effects against cardiovascular disease, independent of its insulin-sensitizing activity. The objective of this study was to investigate whether adiponectin plays a role in modulating the bioavailability of circulating EPCs and endothelial repair. RESEARCH DESIGN AND METHODS - Adiponectin knockout mice were crossed with db+/- mice to produce db/db diabetic mice without adiponectin. Circulating number of EPCs were analyzed by flow cytometry. Reendothelialization was evaluated by staining with Evans blue after wire-induced carotid injury. RESULTS - In adiponectin knockout mice, the number of circulating EPCs decreased in an age-dependent manner compared with the wild-type controls, and this difference was reversed by the chronic infusion of recombinant adiponectin. In db/db diabetic mice, the lack of adiponectin aggravated the hyperglycemia-induced decrease in circulating EPCs and also diminished the stimulatory effects of the PPARγ agonist rosiglitazone on EPC production and reendothelialization. In EPCs isolated from both human peripheral blood and mouse bone marrow, treatment with adiponectin prevented high glucose-induced premature senescence. At the molecular level, adiponectin decreased high glucose-induced accumulation of intracellular reactive oxygen species and consequently suppressed activation of p38 MAP kinase (MAPK) and expression of the senescence marker p16INK4A. CONCLUSIONS - Adiponectin prevents EPC senescence by inhibiting the ROS/p38 MAPK/p16 INK4A signaling cascade. The protective effects of adiponectin against diabetes vascular complications are attributed in part to its ability to counteract hyperglycemia-mediated decrease in the number of circulating EPCs. © 2010 by the American Diabetes Association.published_or_final_versio

Tsuchime-like Aluminum Film to Enhance Absorption in Ultra-Thin Photovoltaic Cells

Ultra-thin solar cells enable materials to be saved, reduce deposition time, and promote carrier collection from materials with short diffusion lengths. However, light absorption efficiency in ultra-thin solar panels remains a limiting factor. Most methods to increase light absorption in ultra-thin solar cells are either technically challenging or costly, given the thinness of the functional layers involved. We propose a cost-efficient and lithography-free solution to enhance light absorption in ultra-thin solar cells—a Tsuchime-like self-forming nanocrater (T-NC) aluminum (Al) film. T-NC Al film can be produced by the electrochemical anodization of Al, followed by etching the nanoporous alumina. Theoretical studies show that T-NC film can increase the average absorbance by 80.3%, depending on the active layer’s thickness. The wavelength range of increased absorption varies with the active layer thickness, with the peak of absolute absorbance increase moving from 620 nm to 950 nm as the active layer thickness increases from 500 nm to 10 µm. We have also shown that the absorbance increase is retained regardless of the active layer material. Therefore, T-NC Al film significantly boosts absorbance in ultra-thin solar cells without requiring expensive lithography, and regardless of the active layer material

A Gramaticalização do Verbo Ir e a Variação de Formas para Expressar o Futuro do Presente: uma Fotografia Capixaba

Esta pesquisa verifica o estágio do processo de gramaticalização do verbo IR, que tem assumido a função de auxiliar em construções perifrásticas para expressar tempo. Para isso, investiga-se a variação entre as formas sintética e perifrástica com IR para expressão do futuro do presente. Temos por hipótese que a forma perifrástica já atinge todos os gêneros das duas modalidades da língua, uma vez que já se especializou para codificar tempo. São examinados dois gêneros, tomando-os como prototípicos do continuun oral/escrito: entrevistas com informantes universitários e editoriais de jornal. Partindo de uma orientação teórica Funcionalista, num quadro mais geral, concebe-se a língua como flexível ao uso, passível de influências cognitivas, sociais e também individuais, embora haja nela forças que atuam no sentido de regularizar a estrutura. Seguindo algumas pesquisas que têm se mostrado frutíferas, o modelo funcionalista estará em diálogo com outro modelo que procura dar conta da heterogeneidade estruturada da língua e de seus processos de mudança: a Teoria Variacionista. Num quadro mais específico, os fundamentos que orientam a pesquisa são os da Gramaticalização. Os dados extraídos dos gêneros selecionados serão submetidos ao programa computacional GOLDVARB 2001 e, em seguida, interpretados à luz das teorias lingüísticas que fundamentam esta pesquisa

Ad hoc influenza vaccination during years of significant antigenic drift in a tropical city with 2 seasonal peaks

We evaluated the acceptability of an additional ad hoc influenza vaccination among the health care professionals following seasons with significant antigenic drift. Self-administered, anonymous surveys were performed by hard copy questionnaires in public hospitals, and by an on-line platform available to all healthcare professionals, from April 1st to May 31st, 2015. A total of 1290 healthcare professionals completed the questionnaires, including doctors, nurses, and allied health professionals working in both the public and private systems. Only 31.8% of participating respondents expressed an intention to receive the additional vaccine, despite that the majority of them agreed or strongly agreed that it would bring benefit to the community (88.9%), save lives (86.7%), reduce medical expenses (76.3%), satisfy public expectation (82.8%), and increase awareness of vaccination (86.1%). However, a significant proportion expressed concern that the vaccine could disturb the normal immunization schedule (45.5%); felt uncertain what to do in the next vaccination round (66.0%); perceived that the summer peak might not occur (48.2%); and believed that the summer peak might not be of the same virus (83.5%). Furthermore, 27.8% of all respondents expected that the additional vaccination could weaken the efficacy of previous vaccinations; 51.3% was concerned about side effects; and 61.3% estimated that there would be a low uptake rate. If the supply of vaccine was limited, higher priority groups were considered to include the elderly aged ≥65 years with chronic medical conditions (89.2%), the elderly living in residential care homes (87.4%), and long-stay residents of institutions for the disabled (80.7%). The strongest factors associated with accepting the additional vaccine included immunization with influenza vaccines in the past 3 years, higher perceived risk of contracting influenza, and higher perceived severity of the disease impact. The acceptability to an additional ad hoc influenza vaccination was low among healthcare professionals. This could have a negative impact on such additional vaccination campaigns since healthcare professionals are a key driver for vaccine acceptance. The discordance in perceived risk and acceptance of vaccination regarding self versus public deserves further evaluation

Association of Genetic Variants Related to Combined Exposure to Higher Body Mass Index and Waist-to-Hip Ratio on Lifelong Cardiovascular Risk in UK Biobank

OBJECTIVE: This study examines the individual and combined association of body mass index (BMI) and 7 waist-to-hip ratio (WHR) with cardiovascular diseases (CVD) risk using genetic scores of the 8 obesity measurements as proxies. DESIGN: A 2×2 factorial analysis approach was applied, with participants divided into four groups of lifetime exposure to low BMI and WHR, high BMI, high WHR, and high BMI and WHR based on weighted genetic risk scores. The difference in CVD risk across groups was evaluated using multivariable logistic regression. SETTING: Cohort study. PARTICIPANTS: A total of 408,003 participants were included from the prospective observational UK Biobank study. RESULTS: A total of 58,429 of CVD events were recorded. Compared to the low BMI and WHR genetic scores group, higher BMI or higher WHR genetic scores were associated with an increase in CVD risk (high BMI: odds ratio (OR), 1.07; 95%CI, 1.04-1.10; high WHR: OR, 1.12; 95%CI, 1.09-1.16). A weak additive effect on CVD risk was found between BMI and WHR (high BMI and WHR: OR, 1.16; 95%CI, 1.12-1.19). Subgroup analysis showed similar patterns between different sex, age (<65, ≥65 years old), smoking status, Townsend deprivation index, fasting glucose level and medication uses, but lower systolic blood pressure was associated with higher CVD risk in obese participants. CONCLUSIONS: High BMI or WHR were associated with increased CVD risk, and their effects are weakly additive. Even though there were overlapping of effect, both BMI and WHR are important in assessing the CVD risk in the general population