Problem Solving Evolutionary Method for Ontology Knowledge Representation with Protégé-2000

This paper studies the knowledge representation with ontology method in the Protégé 2000 system. We first analyzed the various ontological methods for knowledge representation. Then we described the OWL method used in Protégé 2000 for knowledge representation. We proposed the new method named problem-solving evolutionary method (PSEM) for knowledge representation in which it is based the OWL of Protégé 2000. Then we design the interface between the Racer inference engine and the Protégé 2000. Based on the interface built, we can use the Racer inferring engine to reasoning the knowledge. We use the PSEM to experiment the professional domain knowledge of MIS in which it is based undergraduate level. Experiments have shown that PSEM based on the Protégé 2000 is able to represent some domain knowledge well and built knowledge with OWL can be inferred by the Racer

Ambient CFCs and HCFC-22 observed concurrently at 84 sites in the Pearl River Delta region during the 2008–2009 grid studies

Air samples were collected concurrently at 05:00 A.M. and 10:00 A.M. local Beijing time (geomagnetic time + 8) at 84 sites during two grid-study campaigns on 29 September 2008 and 1 March 2009 in the Pearl River Delta region, in order to offer snapshots of ambient CFCs and hydrochlorofluorocarbons (HCFCs) in different seasons and to indicate the presence of local emission sources. Compared to the subtropical northern hemisphere background levels, mean mixing ratios of CFC-11, CFC-12, CFC-113, CFC-114, and HCFC-22 were enhanced by 7%–11%, 8%–11%, 5%–6%, 8%–9%, and 71%–135%, respectively. When data from this tudy were pooled together with previous observations in the region, ambient CFC-11, CFC-12, and CFC-113 unambiguously showed declines in mixing ratios, while HCFC-22 showed an increase. Spatial variations revealed potential emission hot spots in the region, and levels of CFCs and HCFC-22 were higher in September than in March due to many more refrigeration and air-conditioning activities during summer. Source apportioning by positive matrix factorization revealed that new input of CFCs and HCFC-22 into the ambient air was largely attributed to emission from air-conditioning and refrigerating activities instead of industry activities. Average emissions in the region estimated by the CO-tracer method were 0.8 ± 0.2, 1.4 ± 0.6, 0.2 ± 0.1, 0.1 ± 0.02, and 4.4 ± 1.0 Gg/yr for CFC-11, CFC-12, CFC-113, CFC-114, and HCFC-22, respectively, and they accounted for 5.5%–25.5% of the total estimated CFC and HCFC-22 emissions in China

2DPSK Signal Detection Based on Cascaded Stochastic Resonance

In the case of poor channel environment, the detection and reception of digital signal often appear errors. In view of this situation, by reducing the error rate of coherent reception of 2D PSK signals, we propose a new method based on the detection efficiency and improved cascaded stochastic resonance theory.A cascaded bistable stochastic resonance model was established by using stochastic resonance theory. The nonlinear receiver was used to receive 2DPSK signal under small signal-to-noise ratio (SNR). The experimental results show that the spectrum peak of the output signal of cascade stochastic resonance system is 5.70 times that of the traditional model. The output error rate of cascaded nonlinear system model can be reduced by 92.31% compared to the traditional model when the input signal to noise ratio is -7dB. Consequently, the output signal of the system is more likely to be detected and the accuracy can be greatly improved

Scientific Publications on Primary Biliary Cirrhosis from 2000 through 2010: An 11-Year Survey of the Literature

BACKGROUND: Primary biliary cirrhosis (PBC) is a chronic liver disease characterized by intrahepatic bile-duct destruction, cholestasis, and fibrosis. It can lead to cirrhosis and eventually liver failure. PBC also shows some regional differences with respect to incidence and prevalence that are becoming more pronounced each year. Recently, researchers have paid more attention to PBC. To evaluate the development of PBC research during the past 11 years, we determined the quantity and quality of articles on this subject. We also compared the contributions of scientists from the US, UK, Japan, Italy, Germany, and China. METHODS: The English-language papers covering PBC published in journals from 2000 through 2010 were retrieved from the PubMed database. We recorded the number of papers published each year, analyzed the publication type, and calculated the accumulated, average impact factors (IFs) and citations from every country. The quantity and quality of articles on PBC were compared by country. We also contrasted the level of PBC research in China and other countries. RESULTS: The total number of articles did not significantly increase during the past 11 years. The number of articles from the US exceeded those from any other country; the publications from the US also had the highest IFs and the most citations. Four other countries showed complex trends with respect to the quantity and quality of articles about PBC. CONCLUSION: The researchers from the US have contributed the most to the development of PBC research. They currently represent the highest level of research. Some high-level studies, such as RCTs, meta-analyses, and in-depth basic studies should be launched. The gap between China and the advanced level is still enormous. Chinese investigators still have a long way to go

Common polymorphisms of the hOGG1, APE1 and XRCC1 genes correlate with the susceptibility and clinicopathological features of primary angle-closure glaucoma Running title: hOGG1, APE1 and XRCC1 genes in PACG patients

Synopsis This case study aims to elucidate the correlation between the hOGG1, APE1 and XRCC1 gene polymorphisms to the susceptibility and clinicopathological features of primary angle-closure glaucoma (PACG) in a Chinese Han population. Blood samples were obtained from 258 PACG patients (case group) and 272 healthy volunteers (control group). Polymerase chain reaction with sequence specific primer (PCR-SSP) was used to determine the allele frequencies and genotype distributions of the hOGG1, APE1 and XRCC1 genes. The risk factors of PACG were determined using logistic regression analysis. The results indicated that hOGG1 Ser326Cys, APE1 Asp148Glu and XRCC1 Arg399Gln polymorphisms are correlated with the risk of PACG. Furthermore, there were thicker corneas, higher intraocular pressure (IOP) and a shorter axial length in patients carrying the mutant genotypes of hOGG1 Ser326Cys (Ser/Cys + Cys/Cys), APE1 Asp148Glu (Asp/Glu + Glu/Glu) and XRCC1 Arg399Gln (Arg/Gln + Glu/Glu) than those carrying the corresponding wild-type genotypes. According to the logistic regression analysis, Asp148Glu and Arg399Gln polymorphisms, a short axial length and high IOP are major risk factors of PACG. These findings reveal that hOGG1 Ser326Cys, APE1 Asp148Glu and XRCC1 Arg399Gln polymorphisms are correlated with the risk and clinicopathological features of PACG in a Chinese Han population

Monotonicity of Fitness Landscapes and Mutation Rate Control

A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the performance of evolutionary algorithms. Much biological theory in this area is based on Ronald Fisher's work, who used Euclidean geometry to study the relation between mutation size and expected fitness of the offspring in infinite phenotypic spaces. Here we reconsider this theory based on the alternative geometry of discrete and finite spaces of DNA sequences. First, we consider the geometric case of fitness being isomorphic to distance from an optimum, and show how problems of optimal mutation rate control can be solved exactly or approximately depending on additional constraints of the problem. Then we consider the general case of fitness communicating only partial information about the distance. We define weak monotonicity of fitness landscapes and prove that this property holds in all landscapes that are continuous and open at the optimum. This theoretical result motivates our hypothesis that optimal mutation rate functions in such landscapes will increase when fitness decreases in some neighbourhood of an optimum, resembling the control functions derived in the geometric case. We test this hypothesis experimentally by analysing approximately optimal mutation rate control functions in 115 complete landscapes of binding scores between DNA sequences and transcription factors. Our findings support the hypothesis and find that the increase of mutation rate is more rapid in landscapes that are less monotonic (more rugged). We discuss the relevance of these findings to living organisms

Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum

Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3) of A. suum was constructed by suppressive-subtractive hybridization (SSH), and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498) shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer). Using gene ontology (GO), 235 of these molecules were assigned to ‘biological process’ (n = 68), ‘cellular component’ (n = 50), or ‘molecular function’ (n = 117). Of the 91 clusters assembled, 56 molecules (61.5%) had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5%) had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors), and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein–protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50) to be involved in apoptosis and insulin signaling (2%), ATP synthesis (2%), carbon metabolism (6%), fatty acid biosynthesis (2%), gap junction (2%), glucose metabolism (6%), or porphyrin metabolism (2%), although 34 (68%) of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%), anchored (2%), and/or transmembrane (12%) proteins. Functionally, 17 (34%) of them were predicted to be associated with (non-wild-type) RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb) (13 types; 58.8%), larval arrest (Lva) (23.5%) and larval lethality (Lvl) (47%). A genetic interaction network was predicted for these 17 C. elegans orthologues, revealing highly significant interactions for nine molecules associated with embryonic and larval development (66.9%), information storage and processing (5.1%), cellular processing and signaling (15.2%), metabolism (6.1%), and unknown function (6.7%). The potential roles of these molecules in development are discussed in relation to the known roles of their homologues/orthologues in C. elegans and some other nematodes. The results of the present study provide a basis for future functional genomic studies to elucidate molecular aspects governing larval developmental processes in A. suum and/or the transition to parasitism

Higher Height, Higher Ability: Judgment Confidence as a Function of Spatial Height Perception

Based on grounded cognition theories, the current study showed that judgments about ability were regulated by the subjects' perceptions of their spatial height. In Experiment 1, we found that after seeing the ground from a higher rather than lower floor, people had higher expectations about their performance on a knowledge test and assigned themselves higher rank positions in a peer comparison evaluation. In Experiment 2, we examined the boundary conditions of the spatial height effects and showed that it could still occur even if we employed photos rather than actual building floors to manipulate the perceptions of spatial heights. In addition, Experiment 2 excluded processing style as an explanation for these observations. In Experiment 3, we investigated a potential mechanism for the spatial height effect by manipulating the scale direction in the questionnaire. Consequently, consistent with our representational dependence account, the effect of spatial heights on ability judgments was eliminated when the mental representation of ability was disturbed by a reverse physical representation. These results suggest that people's judgments about their ability are correlated with their spatial perception

The effect of word sense disambiguation accuracy on literature based discovery

Background The volume of research published in the biomedical domain has increasingly lead to researchers focussing on specific areas of interest and connections between findings being missed. Literature based discovery (LBD) attempts to address this problem by searching for previously unnoticed connections between published information (also known as “hidden knowledge”). A common approach is to identify hidden knowledge via shared linking terms. However, biomedical documents are highly ambiguous which can lead LBD systems to over generate hidden knowledge by hypothesising connections through different meanings of linking terms. Word Sense Disambiguation (WSD) aims to resolve ambiguities in text by identifying the meaning of ambiguous terms. This study explores the effect of WSD accuracy on LBD performance. Methods An existing LBD system is employed and four approaches to WSD of biomedical documents integrated with it. The accuracy of each WSD approach is determined by comparing its output against a standard benchmark. Evaluation of the LBD output is carried out using timeslicing approach, where hidden knowledge is generated from articles published prior to a certain cutoff date and a gold standard extracted from publications after the cutoff date. Results WSD accuracy varies depending on the approach used. The connection between the performance of the LBD and WSD systems are analysed to reveal a correlation between WSD accuracy and LBD performance. Conclusion This study reveals that LBD performance is sensitive to WSD accuracy. It is therefore concluded that WSD has the potential to improve the output of LBD systems by reducing the amount of spurious hidden knowledge that is generated. It is also suggested that further improvements in WSD accuracy have the potential to improve LBD accuracy

Proteomic Analysis of Rat Hypothalamus Revealed the Role of Ubiquitin–Proteasome System in the Genesis of DR or DIO

Obesity has become a global epidemic, contributing to the increasing burdens of cardiovascular disease and type 2 diabetes. However, the precise molecular mechanisms of obesity remain poorly elucidated. The hypothalamus plays a major part in regulating energy homeostasis by integrating all kinds of nutritional signals. This study investigated the hypothalamus protein profile in diet-induced obese (DIO) and diet-resistant (DR) rats using two dimensional gel electrophoresis (2-DE) combined with MALDI-TOF/TOF–MS analysis. Twenty-two proteins were identified in the hypothalamus of DIO or DR rats. These include metabolic enzymes, antioxidant proteins, proteasome related proteins, and signaling proteins, some of which are related to AMP-activated protein kinase (AMPK) signaling or mitochondrial respiration. Among these proteins, in comparison with the normal-diet group, Ubiquitin was significantly decreased in DR rats but not changed in DIO rats, while Ubiquitin carboxyl-terminal esterase L1 (UCHL-1) was decreased in DIO rats but not changed in DR rats. The expression level of Ubiquitin and UCHL-1 were further validated using Western blot analysis. Our study reveals that Ubiquitin and UCHL-1 are obesity-related factors in the hypothalamus that may play an important role in the genesis of DR or DIO by interfering with the integrated signaling network that control energy balance and feeding