Applying Biomedical Ontologies on Semantic Query Expansion

*1- Introduction*

The interpretation of a question (or information need) depends, among other things, of a series of lexicalsemantic relations that complement and help the cognitive process of answering that information need. Despite this fact, currently used information retrieval mechanisms take few advantages of the semantic interpretation of users’ information needs (usually specified through keywords). In most of the cases, those mechanisms are based on keyword matching, and thus are excessively dependant on the query and document terms.

There are several past results showing that, in general, information retrieval based on domain knowledge decreases the accuracy of keyword based search engines. We believe this approach deserves further discussion and experimentation, looking for more strong evidences that these negative results can really be generalized. Moreover, there are some questions left unanswered by previous work that our experiment is addressing:

(_i_) Using a scientific ontology, with formal construction and maintenance processes, such as the OBO ontologies, would produce better results? 

(_ii_) Are there more efficient query expansion techniques using available domain knowledge?

(_iii_) Is a scientific ontology complete enough to fulfill the information retrieval researchers’ needs, in general?

*2- Semantic Query Expansion*

To try to answer some of these questions, we run a query expansion experiment using the Gene Ontology (GO) as domain knowledge. As the document repository, we used an extraction of 10 years of PubMed publications (from 1994 to 2004), which contains approximately 4.6 Million documents. This dataset is a test collection used by the information retrieval community, called Genomic TREC.

*3- Results*
To evaluate our ontology-based semantic query expansion technique, we measured the effectiveness of the information retrieval mechanism with and without expansion. In a nutshell, the average result showed an increase of 28% on synonyms relations and a small decrease on other relations.

Our results show a lot of consistence with past related work. In fact, if the expansion strategy does not selectively choose when and how to expand, only synonym relations are worth to be used. However, looking further, it is possible to find several opportunities to try other expansion strategies. For example, the problem with query expansion using generalization/specialization relationships is that, if it is always applied, the bad results are more frequent than the good ones. But, if the strategy is to be selective on when to use these relations for expansion, the increasing on accuracy can be outstanding. As shown by our experiment, there was a query with 98% increment on effectiveness. 

*4- Conclusion*
We strongly believe that it is premature to assume that semantics-based query expansion is, in general, a recall-enhancing, precision-degrading technique. Our experiments suggest that by using scientific based ontologies (like OBO ontologies) with formal relations, it is possible to increase both recall and precision. Our group is currently revising this first experiment towards a better semantic query expansion strategy.

*5- Acknowledgements*
This work was partially funded by CAPES and CNPq research grants 311454/2006-2, 306889/2007-2 and 484713/2007-8.

*References*
_Fox E. Lexical relations enhancing effectiveness of information retrieval systems. SIGIR Forum, New York, v.15, n.3, p.5-3._

_Voorhees E. Query expansion using lexicalsemantic relations. In: ACM SIGIR conference on research and development in information retrieval, Proceedings, Dublin:17, p.61–69, 1994

Reduced dimension modeling of leading edge turbulent interaction noise

A computational aeroacoustics approach is used to model the effects of real airfoil geometry on leading edge turbulent interaction noise for symmetric airfoils at zero angle of attack. For the first time, one-component (transverse), two-component (transverse and streamwise), and three-component (transverse, streamwise, and spanwise) synthesized turbulent disturbances are modeled instead of single frequency transverse gusts, which previous computational studies of leading edge noise have been confined to. The effects of the inclusion of streamwise and spanwise disturbances on the noise are assessed, and it is shown that accurate noise predictions for symmetric airfoils can be made by modeling only the transverse disturbances, which reduces the computational expense of simulations. Additionally, the two-component turbulent synthesis method is used to model the effects of airfoil thickness on the noise for thicknesses ranging from 2% to 12%. By using sufficient airfoil thicknesses to show trends, it is found that airfoil thickness will reduce the noise at high frequency, and that the sound power P will reduce linearly with increasing airfoil thickness

The Cognitive Processes Underlying Affective Decision-Making Predicting Adolescent Smoking Behaviors in a Longitudinal Study

This study investigates the relationship between three different cognitive processes underlying the Iowa Gambling Task (IGT) and adolescent smoking behaviors in a longitudinal study. We conducted a longitudinal study of 181 Chinese adolescents in Chengdu City, China. The participants were followed from 10th to 11th grade. When they were in the 10th grade (Time 1), we tested these adolescents’ decision-making using the IGT and working memory capacity using the Self-ordered Pointing Test (SOPT). Self-report questionnaires were used to assess school academic performance and smoking behaviors. The same questionnaires were completed again at the 1-year follow-up (Time 2). The Expectancy-Valence (EV) Model was applied to distill the IGT performance into three different underlying psychological components: (i) a motivational component which indicates the subjective weight the adolescents assign to gains vs. losses; (ii) a learning-rate component which indicates the sensitivity to recent outcomes vs. past experiences; and (iii) a response component which indicates how consistent the adolescents are between learning and responding. The subjective weight to gains vs. losses at Time 1 significantly predicted current smokers and current smoking levels at Time 2, controlling for demographic variables and baseline smoking behaviors. Therefore, by decomposing the IGT into three different psychological components, we found that the motivational process of weight gain vs. losses may serve as a neuropsychological marker to predict adolescent smoking behaviors in a general youth population

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This study investigates the respiratory physiology of bioluminescent larvae of Pyrearinus termitilluminans in relation to their tolerance to hypoxia and hyperoxia and to the supply of oxygen for bioluminescence. The partial pressure of oxygen (P(O2)) was measured within the bioluminescent prothorax by in vivo electron paramagnetic resonance (EPR) oximetry following acclimation of larvae to hypoxic, normoxic and hyperoxic (normobaric) atmospheres and during periods of bioluminescence (during normoxia). The P(O2) in the prothorax during exposure to an external P(O2) of 15.2, 160 and 760 mmHg was 10.3+/-2.6, 134+/-0.9 and 725+/-73 mmHg respectively (mean +/- s.d., N=5; 1 mmHg=0.1333 kPa). Oxygen supply to the larvae via gas exchange through the spiracles, measured by determining the rate of water loss, was also studied in the above atmospheres and was found not to be dependent upon P(O2). The data indicated that there is little to no active control of extracellular tissue P(O2) within the prothorax of these larvae. The reduction in prothorax P(O2) observed during either attack-response-provoked bioluminescence or sustained feeding-related bioluminescence in a normoxic atmosphere was variable, but fell within the range 10-25 mmHg. The effect of hypoxic atmospheres on bioluminescence was measured to estimate the intracellular P(O2) within the photocytes of the prothorax. Above a threshold value of 50-80 mmHg, bioluminescence was unaffected by P(O2). Below this threshold, an approximately linear relationship between P(O2) and bioluminescence was observed. Taken together with the extracellular P(O2) measurements, this suggests that control of P(O2) within the photocyte may occur. This work establishes that EPR oximetry is a valuable technique for long-term measurement of tissue P(O2) in insects and can provide valuable insights into their respiratory physiology. It also raises questions regarding the hypothesis that bioluminescence can have a significant antioxidative effect by reduction of prothorax P(O2 )through oxygen consumption

The sensory acceptability of a tilapia (Oreochromis niloticus) mechanically separated meat-based spread.

A carne mecanicamente separada (CMS) é uma alternativa para a diversificação de novos produtos à base de pescado e também se mostra como um destino para os resíduos da indústria de filetagem. A carne mecanicamente separada de tilápia foi utilizada, neste estudo, na formulação de patê, com o objetivo de investigar a aceitabilidade desse produto pelos consumidores. Duas formulações de patê foram preparadas, com diferentes tipos de sais comerciais: sal temperado (A) e sal comum (B). Consumidores (112) avaliaram a aceitação em relação à impressão global, à espalhabilidade, à aparência e ao sabor em escala hedônica de nove pontos. A análise microbiológica da carne mecanicamente separada de tilápia e a composição química da formulação de patê de tilápia também foram determinadas. Quando a aceitação de todos os consumidores foi considerada, a impressão global, a aparência e o sabor foram significativamente (p < 0,05) inferiores para o patê de tilápia com sal comum (B). No entanto, três diferentes grupos de consumidores foram encontrados a partir da aceitabilidade da impressão global do patê de tilápia. O maior segmento também preferiu o patê de tilápia com sal temperado (A), mas ambos tiveram alta aceitabilidade. A CMS de tilápia apresentou qualidade como matéria-prima de acordo com regulamento técnico sobre padrões microbiológicos. O produto final apresentou a seguinte composição química: umidade - 62,17%; cinzas - 2,11%; proteína - 9,75%, e lipídios - 18,81%. Esses resultados podem ser de grande importância para a indústria no desenvolvimento e na comercialização de novos produtos obtidos a partir da carne mecanicamente separada de tilápia

Affective Decision-making Predictive of Chinese Adolescent Drinking Behaviors

The goal of the current investigation was to address whether affective decision making would serve as a unique neuropsychological marker to predict drinking behaviors among adolescents. We conducted a longitudinal study of 181 Chinese adolescents in Chengdu city, China. In their 10th grade (ages 15–16), these adolescents were tested for their affective decision-making ability using the Iowa Gambling Task (IGT) and working memory capacity using the Self-Ordered Pointing Test. Self-report questionnaires were used to assess academic performance and drinking behaviors. At 1-year follow-up, questionnaires were completed to assess drinking behaviors, and the UPPS Impulsive Behavior Scale was used to examine four dimensions of impulsivity: urgency, lack of premeditation, lack of perseverance, and sensation seeking. Results indicated that those adolescents who progressed to binge drinking or exhibited consistent binge drinking not only performed poorly on the IGT but also scored significantly higher in urgency compared to those who never or occasionally drank. Moreover, better IGT scores predicted fewer drinking problems and fewer drinks 1 year later after controlling for demographic variables, the previous drinking behaviors, working memory, and impulsivity. These findings suggest that deficits in affective decision making may be important independent determinants of compulsive drinking and potentially addictive behavior in adolescents. (JINS, 2009, 15, 547–557.

A pedagogic appraisal of the Priority Heuristic

We have explored how science and mathematics teachers made decisions when confronted with a dilemma in which a fictitious young woman, Deborah, may choose to have an operation that might address a painful spinal condition. We sought to explore the extent to which psychological heuristic models, in particular the Priority Heuristic, might successfully describe the decision-making process of these teachers and how an analysis of the role of personal and emotional factors in shaping the decision-making process might inform pedagogical design. A novel aspect of this study is that the setting in which the decision-making process is examined contrasts sharply with those used in psychological experiments. We found that to some extent, even in this contrasting setting, the Priority Heuristic could describe these teachers' decision-making. Further analysis of the transcripts yielded some insights into limitations on scope as well the richness and complexity in how personal factors were brought to bear. We see these limitations as design opportunities for educational intervention

Ferricytochrome c Directly Oxidizes Aminoacetone to Methylglyoxal, a Catabolite Accumulated in Carbonyl Stress

Age-related diseases are associated with increased production of reactive oxygen and carbonyl species such as methylglyoxal. Aminoacetone, a putative threonine catabolite, is reportedly known to undergo metal-catalyzed oxidation to methylglyoxal, NH4+ ion, and H2O2 coupled with (i) permeabilization of rat liver mitochondria, and (ii) apoptosis of insulin-producing cells. Oxidation of aminoacetone to methylglyoxal is now shown to be accelerated by ferricytochrome c, a reaction initiated by one-electron reduction of ferricytochrome c by aminoacetone without amino acid modifications. the participation of O-2(center dot-) and HO center dot radical intermediates is demonstrated by the inhibitory effect of added superoxide dismutase and Electron Paramagnetic Resonance spin-trapping experiments with 5,5'-dimethyl-1-pyrroline-N-oxide. We hypothesize that two consecutive one-electron transfers from aminoacetone (E-0 values = -0.51 and -1.0 V) to ferricytochrome c (E-0 = 0.26 V) may lead to aminoacetone enoyl radical and, subsequently, imine aminoacetone, whose hydrolysis yields methylglyoxal and NH4+ ion. in the presence of oxygen, aminoacetone enoyl and O-2(center dot-) radicals propagate aminoacetone oxidation to methylglyoxal and H2O2. These data endorse the hypothesis that aminoacetone, putatively accumulated in diabetes, may directly reduce ferricyt c yielding methylglyoxal and free radicals, thereby triggering redox imbalance and adverse mitochondrial responses.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)INCT Processos Redox em Biomedicina (Brazil)Univ São Paulo, Dept Bioquim, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Bioquim & Biol Mol, São Paulo, BrazilUniversidade Federal de São Paulo, Inst Ciencias Ambientais Quim & Farmaceut, São Paulo, BrazilUniv São Paulo, Dept Fis & Informat, São Paulo, BrazilUniv Fed ABC, Ctr Ciencias Nat & Humanas, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Bioquim & Biol Mol, São Paulo, BrazilUniversidade Federal de São Paulo, Inst Ciencias Ambientais Quim & Farmaceut, São Paulo, BrazilWeb of Scienc

Decision-making, cognitive distortions and alcohol use in adolescent problem and non-problem gamblers: an experimental study

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