-
[show abstract]
[hide abstract]
ABSTRACT: BACKGROUND: The Food- Frequency Questionnaire (FFQ) is a dietary assessment tool frequently used in large-scale nutritional epidemiology studies. The goal of the present study is to validate a self-administered version of the Hawaii FFQ modified for use in the general adult population of Newfoundland and Labrador (NL). METHODS: Over a one year period, 195 randomly selected adults completed four 24-hour dietary recalls (24-HDRs) by telephone and one subsequent self-administered FFQ. Estimates of energy and nutrients derived from the 24-HDRs and FFQs were compared (protein, carbohydrate, fibre, fat, vitamin A, carotene, vitamin D, and calcium). Data were analyzed using the Pearson's correlation coefficients, cross-classification method, and Bland--Altman plots. RESULTS: The mean nutrient intake values of the 24-HDRs were lower than those of the FFQs, except for protein in men. Sex and energy-adjusted de-attenuated Pearson correlation coefficients for each nutrient varied from 0.13 to 0.61. Except for protein in men, all correlations were statistically significant with p < 0.05. Cross-classification analysis revealed that on average, 74% women and 78% men were classified in the same or adjacent quartile of nutrient intake when comparing data from the FFQ and 24-HDRs. Bland--Altman plots showed no serious systematic bias between the administration of the two instruments over the range of mean intakes. CONCLUSION: This 169-item FFQ developed specifically for the adult NL population had moderate relative validity and therefore can be used in studies to assess food consumption in the general adult population of NL. This tool can be used to classify individual energy and nutrient intakes into quartiles, which is useful in examining relationships between diet and chronic disease.
Nutrition Journal 04/2013; 12(1):49. · 2.48 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: BACKGROUND: Transcription factors (TFs) and microRNAs (miRNAs) are primary metazoan gene regulators. Regulatory mechanisms of the two main regulators are of great interest to biologists and may provide insights into the causes of diseases. However, the interplay between miRNAs and TFs in a regulatory network still remains unearthed. Currently, it is very difficult to study the regulatory mechanisms that involve both miRNAs and TFs in a biological lab. Even at data level, a network involving miRNAs, TFs and genes will be too complicated to achieve. Previous research has been mostly directed at inferring either miRNA or TF regulatory networks from data. However, networks involving a single type of regulator may not fully reveal the complex gene regulatory mechanisms, for instance, the way in which a TF indirectly regulates a gene via a miRNA. RESULTS: We propose a framework to learn from heterogeneous data the three-component regulatory networks, with the presence of miRNAs, TFs, and mRNAs. This method firstly utilises Bayesian network structure learning to construct a regulatory network from multiple sources of data: gene expression profiles of miRNAs, TFs and mRNAs, target information based on sequence data, and sample categories. Then, in order to produce more meaningful results for further biological experimentation and research, the method searches the learnt network to identify the interplay between miRNAs and TFs and applies a network motif finding algorithm to further infer the network.We apply the proposed framework to the data sets of epithelial-to-mesenchymal transition (EMT). The results elucidate the complex gene regulatory mechanism for EMT which involves both TFs and miRNAs. Several discovered interactions and molecular functions have been confirmed by literature. In addition, many other discovered interactions and bio-markers are of high statistical significance and thus can be good candidates for validation by experiments. Moreover, the results generated by our method are compact, involving a small number of interactions which have been proved highly relevant to EMT. CONCLUSIONS: We have designed a framework to infer gene regulatory networks involving both TFs and miRNAs from multiple sources of data, including gene expression data, target information, and sample categories. Results on the EMT data sets have shown that the proposed approach is able to produce compact and meaningful gene regulatory networks that are highly relevant to the biological conditions of the data sets. This framework has the potential for application to other heterogeneous datasets to reveal the complex gene regulatory relationships.
BMC Bioinformatics 03/2013; 14(1):92. · 2.75 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: MOTIVATION: microRNAs (miRNAs) are known to play an essential role in the post-transcriptional gene regulation in plants and animals. Currently, several computational approaches have been developed with a shared aim to elucidate miRNA-mRNA regulatory relationships. While these existing computational methods discover the statistical relationships such as correlations and associations between miRNAs and mRNAs at data level, such statistical relationships are not necessarily the real causal regulatory relationships that would ultimately provide useful insights into the causes of gene regulations. The standard method for determining causal relationships is randomised controlled perturbation experiments. In practice, however, such experiments are expensive and time consuming. Our motivation for this study is to discover the miRNA-mRNA causal regulatory relationships from observational data. RESULTS: We present a causality discovery based method to uncover the causal regulatory relationship between miRNAs and mRNAs using expression profiles of miRNAs and mRNAs without taking into consideration the prior target information. We apply this method to the Epithelial to Mesenchymal Transition (EMT) datasets and validate the computational discoveries by a controlled biological experiment for the miR-200 family. A significant portion of the regulatory relationships discovered in data is consistent with those identified by experiments. In addition, the top genes that are causally regulated by miRNAs are highly relevant to the biological conditions of the datasets. The results indicate that the causal discovery method effectively discovers miRNA regulatory relationships in data. Although computational predictions may not completely replace intervention experiments, the accurate and reliable discoveries in data are cost effective for the design of miRNA experiments and the understanding of miRNA-mRNA regulatory relationships. AVAILABILITY: The R scripts are in the Supplementary material. CONTACT: thuc duy.le@mymail.unisa.edu.au; jiuyong.li@unisa.edu.au.
Bioinformatics 01/2013; · 5.47 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In this study, we evaluate the effect of HO-1 upregulation on blood pressure and cardiac function in the new model of infarct spontaneous hypertensive rats (ISHR). Male spontaneous hypertensive rats (SHR) at 13 weeks (n = 40) and age-matched male Wistar (WT) rats (n = 20) were divided into six groups: WT (sham + normal saline (NS)), WT (sham + Co(III) Protoporphyrin IX Chloride (CoPP)), SHR (myocardial infarction (MI) + NS), SHR (MI + CoPP), SHR (MI + CoPP + Tin Mesoporphyrin IX Dichloride (SnMP)), SHR (sham + NS); CoPP 4.5 mg/kg, SnMP 15 mg/kg, for six weeks, one/week, i.p., n = 10/group. At the sixth week, echocardiography (UCG) and hemodynamics were performed. Then, blood samples and heart tissue were collected. Copp treatment in the SHR (MI + CoPP) group lowered blood pressure, decreased infarcted area, restored cardiac function (left ventricular ejection fraction (LVEF), left ventricular fraction shortening (LVFS), +dp/dt(max), (-dp/dt(max))/left ventricular systolic pressure (LVSP)), inhibited cardiac hypertrophy and ventricular enlargement (downregulating left ventricular end-systolic diameter (LVEDD), left ventricular end-systolic diameter (LVESD) and heart weight/body weight (HW/BW)), lowered serum CRP, IL-6 and Glu levels and increased serum TB, NO and PGI2 levels. Western blot and immunohistochemistry showed that HO-1 expression was elevated in the SHR (MI + CoPP) group, while co-administration with SnMP suppressed the benefit functions mentioned above. In conclusion, HO-1 upregulation can lower blood pressure and improve post-infarct cardiac function in the ISHR model. These functions may be involved in the inhibition of inflammation and the ventricular remodeling process and in the amelioration of glucose metabolism and endothelial dysfunction.
International Journal of Molecular Sciences 01/2013; 14(2):2684-706. · 2.60 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: microRNAs (miRNAs) are small non-coding RNAs that cause mRNA degradation and translation inhibition. They are pivotal regulators of development and cellular homeostasis through their control of diverse processes. Recently, great efforts have been made to elucidate many targets that are affected by miRNAs, but the functions of most miRNAs and their precise regulatory mechanisms remain elusive. With more and more matched expression profiles of miRNAs and mRNAs having been made available, it is of great interest to utilize both expression profiles and sequence information to discover the functional regulatory networks of miRNAs and their target mRNAs for potential biological processes that they may participate in. In this chapter, we first briefly review the computational methods for discovering miRNA targets and miRNA-mRNA regulatory modules, and then focus on a method of identifying functional miRNA-mRNA regulatory modules by integrating multiple data sets from different sources.
Advances in experimental medicine and biology 01/2013; 774:267-90. · 1.09 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Discovering causal relationships in large databases of observational data is challenging. The pioneering work in this area was rooted in the theory of Bayesian network (BN) learning, which however, is a NP-complete problem. Hence several constraint-based algorithms have been developed to efficiently discover causations in large databases. These methods usually use the idea of BN learning, directly or indirectly, and are focused on causal relationships with single cause variables. In this paper, we propose an approach to mine causal rules in large databases of binary variables. Our method expands the scope of causality discovery to causal relationships with multiple cause variables, and we utilise partial association tests to exclude noncausal associations, to ensure the high reliability of discovered causal rules. Furthermore an efficient algorithm is designed for the tests in large databases. We assess the method with a set of real-world diagnostic data. The results show that our method can effectively discover interesting causal rules in large databases.
Data Mining (ICDM), 2012 IEEE 12th International Conference, Brussel, Belgium; 12/2012
-
[show abstract]
[hide abstract]
ABSTRACT: microRNAs (miRNAs) are small non-coding RNAs that cause mRNA degradation and translation inhibition. They are pivotal regulators of development and cellular homeostasis through their control of diverse processes. Recently, great efforts have been made to elucidate many targets that are affected by miRNAs, but the functions of most miRNAs and their precise regulatory mechanisms remain elusive. With more and more matched expression profiles of miRNAs and mRNAs having been made available, it is of great interest to utilize both expression profiles and sequence information to discover the functional regulatory networks of miRNAs and their target mRNAs for potential biological processes that they may participate in. In this chapter, we first briefly review the computational methods for discovering miRNA targets and miRNA-mRNA regulatory modules, and then focus on a method of identifying functional miRNA-mRNA regulatory modules by integrating multiple data sets from different sources.
12/2012; , ISBN: 978-9400755895
-
[show abstract]
[hide abstract]
ABSTRACT: Background: Cardiovascular disease (CVD) is an important cause of mortality in elderly patients worldwide. Aspirin resistance has been well reported in CVD. Objective: The frequency, risk factors, prognosis, and genetic polymorphism of the cyclooxygenase-1 (COX-1) gene for aspirin resistance have not been reported in elderly patients with CVD. We therefore undertook this study to evaluate these associations among elderly Chinese patients with CVD. Methods: Four hundred thirty-one elderly Chinese patients with CVD receiving daily aspirin therapy (≥75 mg) over 1 month were enrolled. Platelet aggregation was measured by light transmission aggregometry (LTA) and thromboelastography platelet mapping assay (TEG) using arachidonic acid (AA) as a stimulus. The median follow-up was 1.8 years. Results: After the median follow-up, aspirin-resistant patients were at an increased risk of the composite endpoint compared to nonresistant patients by LTA(AA) + TEG(AA) (23.7 vs. 9.2%, p = 0.025). Additionally, Cox proportional hazards regression modeling demonstrated that aspirin resistance and cerebrovascular disease were associated with major adverse long-term outcomes (HR for aspirin resistance = 2.31, 95% CI 1.11-4.81, p = 0.026). The variant G-allele of COX-1 rs1330344 (-1676 A/G) significantly increased the risk of aspirin resistance defined by LTA(AA) + TEG(AA) (OR = 1.82, 95% CI 1.13- 2.92, p = 0.01). Conclusions: Aspirin resistance, evaluated by LTA(AA) + TEG(AA), is associated with an increased risk of adverse clinical events in elderly Chinese patients with CVD. The variant G-allele of COX-1 rs1330344 is significantly associated with aspirin resistance defined by LTA(AA) + TEG(AA).
Gerontology 09/2012; · 2.78 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: By comparisons of interface growth temperatures of different phases in eutectic systems, competitive growth between the primary
phase, halo structure and coupled eutectic has been discussed. The compositions for the formation of coupled eutectic have
been discussed at the coexisting with the primary phase in eutectic under directional solidification. Solidification conditions,
such as growth rate and composition required for the formation of the primary phase, halo structure and coupled eutectic have
been proposed. Numerical calculation results show that no halo structure formed in directionally solidified Sn−Pb eutectic,
but in Al−Si eutectic, competitive growth structures of the primary β-Si phase, α-Al halo structure and coupled eutectic (α+β)
may exist at the hypereutectic composition between 12.6% and 25% Si. The calculated results of Al−Si eutectic fit in with
the reported experiment results.
Science in China Series E Technological Sciences 05/2012; 48(3):270-281. · 1.02 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: To evaluate correlation between and agreement in light transmittance aggregation (LTA) and thromboelastography (TEG) in laboratory diagnosing aspirin resistance (AR), and to determine the prevalence of AR in old patients.
Patients in the Wanshoulu District of Beijing with ischemic atherothrombotic diseases were recruited. Inclusion criteria were age ≥ 65 years, and having received regular aspirin therapy (75-100 mg daily) for at least 4 weeks. On the basis of LTA assay, the definition of AR was taken as aggregation of ≥ 20% with AA (arachidonic acid), and of ≥ 70% with ADP (adenosine diphosphate). Aspirin-sensitivity was indicated by the absence of either of these criteria; aspirinsensitivity was indicated as both criteria being met. The definition of AR by TEG is ≥ 50% via AA-induced whole blood aggregation.
There were 13.69% prevalence of aspirin resistance for LTA using AA as the agonist, 30.16% prevalence of aspirin resistance for LTA using ADP as the agonist, and 23.67% prevalence of aspirin resistance for TEG using AA as the agonist. Results from these tests showed poor agreement (Kappa<0.4). However, by the method of LTA using AA and ADP as the agonists, prevalence of AR was 8.35%. By methods of AA-induced LTA and AA-induced TEG, prevalence of AR was 8.82%. Results from these two latter methods showed good agreement (Kappa = 0.793).
Combined methods, as described here, have good correlation and agreement in the assays of AR, and the results with them represent a realistic measure of the prevalence of AR. Prevalence of AR of elderly patients from Wanshoulu district of Beijing is about 9%.
Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences 04/2012; 37(4):338-42.
-
[show abstract]
[hide abstract]
ABSTRACT: To investigate the levels of sex hormones and androgen receptor (AR) in elderly male patients and to explore a possible correlation with obesity.
The cross-sectional study included 314 Elderly males (age ≥ 65 year). Of these subjects, 104 were healthy (age range 65-92 year; mean 71.38 ± 5.154 year), 74 were obese (65-87 year; 71.32 ± 4.74 year), and 111 were overweight (65-85 year; 71.43 ± 5.03 year). The following parameters were measured: total testosterone (TT), free testosterone, dehydroepiandrosterone sulfate, sex hormone-binding globulin (SHBG), estradiol (E2), luteinizing hormone, follicle-stimulating hormone and AR.
(i) The levels of TT and SHBG in the obesity group were significantly lower than those in non-obese subjects. (ii) Body mass index (BMI) negatively correlated with TT and SHBG. (iii) Multiple regression analysis revealed that TT (β: -0.230; p = 0.045) and SHBG (β: -0.163; p = 0.02) were statistically correlated with BMI.
Testosterone levels in the obese population were significantly lower than in the non-obese population and there is a significant association between testosterone levels and the extent of obesity.
The Aging Male 03/2012; 15(2):85-9. · 1.52 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Aspirin resistance is recognized in different population. However, the prevalence and clinical events of aspirin resistance in elderly male patients with cardiovascular disease (CVD) have not been reported.
We enrolled 304 elderly male patients with CVD receiving daily aspirin therapy (≥ 75 mg) more than 1 month. Platelet aggregation was measured by light transmission aggregometry (LTA) and thrombelastography platelet mapping assay (TEG). The median follow-up time was 1.8 years. The primary outcome was the composite of death, myocardial infarction, unstable angina, stroke and transient ischemic attack.
By LTA, 25 (8.2%) of elderly patients were aspirin resistant and 106 (34.9%) patients were semiresponders. According to TEG, 62 patients (20.4%) were found to be resistant to aspirin therapy. Of the 62 patients with aspirin resistance by TEG, 21 patients were aspirin resistant by LTA. Twenty-two of the 106 semiresponders by LTA were aspirin resistant by TEG. Patients with aspirin resistance or aspirin semiresponders were at increased risk of the composite outcome compared with aspirin-sensitive patients by LTA (18.3% vs 9.8%, Hazard ratio (HR) = 1.864, 95% confidence interval (CI): 1.046-3.324 p = 0.039). However, aspirin resistance was not associated with an increased risk of clinical vascular events compared to aspirin-sensitive patients by TEG (17.7% vs 10.9%, p = 0.452). In addition, Cox proportional hazard regression modeling demonstrated that aspirin resistance or semiresponders (HR = 3.050, 95% CI: 1.464-6.354, p = 0.003) and diabetes (HR = 2.055, 95% CI: 1.060-3.981, p = 0.033) were associated with major adverse long-term outcomes.
Aspirin resistance or semiresponders, defined by LTA, are associated with an increased risk of adverse clinical events in elderly male patients with CVD.
The Aging Male 03/2012; 15(3):140-7. · 1.52 Impact Factor
-
Zhuoyu Sun, Lin Liu,
Peizhong Peter Wang,
Barbara Roebothan,
Jin Zhao,
Elizabeth Dicks,
Michelle Cotterchio,
Sharon Buehler,
Peter T Campbell,
John R McLaughlin,
Patrick S Parfrey
[show abstract]
[hide abstract]
ABSTRACT: Diet is regarded as one of the most important environmental factors associated with colorectal cancer (CRC) risk. A recent report comprehensively concluded that total energy intake does not have a simple relationship with CRC risk, and that the data were inconsistent for carbohydrate, cholesterol and protein. The objective of this study was to identify the associations of CRC risk with dietary intakes of total energy, protein, fat, carbohydrate, fiber, and alcohol using data from a large case-control study conducted in Newfoundland and Labrador (NL) and Ontario (ON), Canada.
Incident colorectal cancer cases (n = 1760) were identified from population-based cancer registries in the provinces of ON (1997-2000) and NL (1999-2003). Controls (n = 2481) were a random sample of residents in each province, aged 20-74 years. Family history questionnaire (FHQ), personal history questionnaire (PHQ), and food frequency questionnaire (FFQ) were used to collect study data. Logistic regression was used to evaluate the association of intakes of total energy, macronutrients and alcohol with CRC risk.
Total energy intake was associated with higher risk of CRC (OR: 1.56; 95% CI: 1.21-2.01, p-trend = 0.02, 5th versus 1st quintile), whereas inverse associations emerged for intakes of protein (OR: 0.85, 95%CI: 0.69-1.00, p-trend = 0.06, 5th versus 1st quintile), carbohydrate (OR: 0.81, 95%CI: 0.63-1.00, p-trend = 0.05, 5th versus 1st quintile) and total dietary fiber (OR: 0.84, 95% CI:0.67-0.99, p-trend = 0.04, 5th versus 1st quintile). Total fat, alcohol, saturated fatty acids, monounsaturated fatty acids, polyunsaturated fatty acids, and cholesterol were not associated with CRC risk.
This study provides further evidence that high energy intake may increase risk of incident CRC, whereas diets high in protein, fiber, and carbohydrate may reduce the risk of the disease.
Nutrition Journal 03/2012; 11:18. · 2.48 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Hepatitis C virus (HCV) research is hampered by the use of arbitrary representative isolates in cell culture and immunology. The most replicative isolate in vitro is a subtype 2a virus (JFH-1); however, genotype 1 is more prevalent worldwide and represents about 70% of infections in the United States, and genotypes differ from one another by 31% to 33% at the nucleotide level. For phylogenetic and immunologic analyses, viruses H77 and HCV-1 (both subtype 1a) are commonly used based on their historic importance. In an effort to rationally design a representative subtype 1a virus (Bole1a), we used Bayesian phylogenetics, ancestral sequence reconstruction, and covariance analysis on a curated set of 390 full-length human HCV 1a sequences from GenBank. By design, Bole1a contains variations present in widely circulating strains and matches more epitope-sized peptides in a full-genome comparison to subtype 1a isolates than any other sequence studied. Parallel analyses confirm that selected epitopes from the Bole1a genome were able to elicit a robust T cell response. In a proof of concept for infectivity, the envelope genes (E1 and E2) of Bole1a were expressed in an HIV pseudoparticle system containing HCV envelope genes and HIV nonenvelope genes with luciferase expression. The resulting Bole1a pseudoparticle robustly infected Hep3B cells. In this study, we demonstrate that a rationally designed, fully synthetic HCV genome contains representative epitopes and envelope genes that assemble properly and mediate entry into target cells.
Journal of Virology 03/2012; 86(10):5915-21. · 5.40 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Diabetic retinopathy is a leading cause of reduced visual acuity and acquired blindness. Diabetes is known to alter the amount of retinal expression of the water-selective channels aquaporin 4 (AQP4). However, the function and impact of AQP4 in diabetic retinopathy is not well understood. In the present work, diabetes was induced by intraperitoneal injection of streptozotocin in Sprague-Dawley rats. Two weeks later, AQP4 shRNA (r) lentiviral particles or negative lentiviral particles were delivered by intravitreal injection to the eyes. Gene delivery was confirmed by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) and Western blotting analysis. Eight weeks later, BRB breakdown was measured using Evans blue dye. Images of retinal sections were obtained and the thicknesses of the retinas were determined. Retinal leukostasis measurement was performed using acridine orange leukocyte fluorography. The mRNA levels of IL-1β, IL-6, intercellular adhesion molecule 1 (ICAM-1), glial fibrillary acidic protein (GFAP) and vascular endothelial growth factor (VEGF) were determined using qRT-PCR method. AQP4 shRNA (r) lentiviral particles or negative lentiviral particles were transfected into rMC-1 cells to investigate its effect on inflammation induced by high glucose. Incubation with IL-1β or IL-6 was performed to test their effect on AQP4 expression in rMC-1 cells. In the current work, it was found that AQP4 expression was enhanced in the retina of diabetic rats. AQP4 knockdown led to exacerbation of retinopathy including enhancing retinal vascular permeability, retinal thickness, pro-inflammatory factors expression, and VEGF and GFAP expression in retinas of diabetic rats. AQP4 knockdown enhanced the expression of pro-inflammatory cytokines induced by high glucose in rMC-1 cells. In addition, AQP4 knockdown enhanced the release of IL-6 and VEGF from rMC-1 cells into the medium. Moreover, it was found that incubation with IL-1β or IL-6 suppressed AQP4 expression in rMC-1 cells. These results suggested that streptozotocin injection induced diabetes resulted in compensatory increases of AQP4 expression, and downregulation of AQP4 exacerbated diabetic retinopathy through aggravating inflammatory response, at last in part. Therefore, regulation of retinal function by AQP4 may attenuate diabetic retinopathy, offering a promising therapeutic strategy for diabetic retinopathy.
Experimental Eye Research 03/2012; 98:37-43. · 3.26 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: To explore the pathogenesis, influencing factors, ways of medical intervention and evaluation indicators of cataract by observing changes in serum biochemical indices in mice with targeted disruption of βB2-crystallin.
Nine 6-week-old male mice with targeted knockout of βB2-crystallin were used as the study group, and nine age- and sex-matched normal wild-type mice as the control group. The genetype of the modeled mice was identified by PCR technique. Tropicamide and phenylephrine eye drops were used as the cycloplegic agents to observe changes in lens opacity with a slit-lamp. The lens was then removed and blood was collected for biochemical evaluation in the serum.
Two genotypes were successfully identified by PCR technique. Slit-lamp observation showed that the lens cortex was opaque and GSH level in the lens cortex was remarkably decreased in mice with βB2-crystallin deficiency compared with the control group (P<0.01). Serum Na(+), Cl(-), Ca(2+), Mg(2+) and Fe(2+) levels, ALT and AST activities, and TP, ALP, Cr, TC, GLU content were decreased significantly compared with the control group (P<0.05). There was no difference in LDH, P, Cu(2+), K(+) levels between the two groups (P>0.05).
Compared with the wild-type mice, serum biochemical indices underwent significant changes in mice with targeted disruption of βB2-crystallin gene, especially with abnormal distribution of Na(+)&Ca(2+), which induced the formation of cataract.
International journal of ophthalmology. 01/2012; 5(1):55-8.
-
[show abstract]
[hide abstract]
ABSTRACT: MOTIVATION: MicroRNAs (miRNAs) are small non-coding RNAs that cause mRNA degradation and translational inhibition. They are important regulators of development and cellular homeostasis through their control of diverse processes. Recently, great efforts have been made to elucidate their regulatory mechanism, but the functions of most miRNAs and their precise regulatory mechanisms remain elusive. With more and more matched expression profiles of miRNAs and mRNAs having been made available, it is of great interest to utilize both expression profiles to discover the functional regulatory networks of miRNAs and their target mRNAs for potential biological processes that they may participate in. RESULTS: We present a probabilistic graphical model to discover functional miRNA regulatory modules at potential biological levels by integrating heterogeneous datasets, including expression profiles of miRNAs and mRNAs, with or without the prior target binding information. We applied this model to a mouse mammary dataset. It effectively captured several biological process specific modules involving miRNAs and their target mRNAs. Furthermore, without using prior target binding information, the identified miRNAs and mRNAs in each module show a large proportion of overlap with predicted miRNA target relationships, suggesting that expression profiles are crucial for both target identification and discovery of regulatory modules.
Bioinformatics 10/2010; 26(24):3105-11. · 5.47 Impact Factor
-
Fifth International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2010, University of Hunan, Liverpool Hope University, Liverpool, United Kingdom / Changsha, China, September 8-10 and September 23-26, 2010; 01/2010
-
Bioinformatics. 01/2010; 26:3105-3111.
-
[show abstract]
[hide abstract]
ABSTRACT: Different biological labs conduct similar experiments on same diseases. It is highly desirable to have a better model based on more experimental results than that on a single result. In this paper, we propose a method for integrating microarray data from multiple sources for building classification models. To test the method, we use three real world microarray data sets from different labs with different experimental devices and environments. Although microarray data is well known for its inconsistencies across labs, we demonstrate that it is possible to build consistent models using data sets from multiple labs. We report our method, experimental results and observations in the paper.
Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 01/2010; 2010:1503-6.
