Macrobenthic Community in Tolo Harbour, Hong Kong and its Relations with Heavy Metals

The present study investigated the macrobenthic community in Tolo Harbour, Hong Kong, aiming at linking heavy metal concentrations to differences in macrobenthic community. The stations investigated in Tolo Harbour have widely contrasting features, with some areas located in the Plove Cove displaying both high species richness and abundance while other areas displaying quite impoverished or even void of macrobenthos. High diversity and abundance of macrobenthos in areas with low heavy metal concentrations were recorded. Strong negative correlation between macrobenthic diversity and heavy metal concentrations was found, and this implicated the pollution-induced degradation of macrobenthos in some locations in Tolo Harbour. These results support the Pearson-Rosenberg model for succession along a pollution gradient. © 2010 Coastal and Estuarine Research Federation.published_or_final_versionSpringer Open Choice, 01 Dec 201

sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Background: Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures. Results: This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies. Conclusions: The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMapComment: 3 pages, 1 table, 1 eps figur

Does pathway analysis make it easier for common variants to tag rare ones?

Analyzing sequencing data is difficult because of the low frequency of rare variants, which may result in low power to detect associations. We consider pathway analysis to detect multiple common and rare variants jointly and to investigate whether analysis at the pathway level provides an alternative strategy for identifying susceptibility genes. Available pathway analysis methods for data from genome-wide association studies might not be efficient because these methods are designed to detect common variants. Here, we investigate the performance of several existing pathway analysis methods for sequencing data. In particular, we consider the global test, which does not consider linkage disequilibrium between the variants in a gene. We improve the performance of the global test by assigning larger weights to rare variants, as proposed in the weighted-sum approach. Our conclusion is that straightforward application of pathway analysis is not satisfactory; hence, when common and rare variants are jointly analyzed, larger weights should be assigned to rare variants

基于局部模糊方差的过渡区提取及图像分割

Author name used in this publication: 田岩Author name used in this publication: 刘继军Author name used in this publication: 谢玉波Author name used in this publication: SHI Wen-Zhong2007-2008 > Academic research: refereed > Publication in refereed journal202012 bcrcVersion of RecordPublishe

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties. The Connectivity Map was a novel concept and innovative tool first introduced by Lamb et al to connect small molecules, genes, and diseases using genomic signatures [Lamb et al (2006), Science 313, 1929-1935]. However, the Connectivity Map had some limitations, particularly there was no effective safeguard against false connections if the observed connections were considered on an individual-by-individual basis. Further when several connections to the same small-molecule compound were viewed as a set, the implicit null hypothesis tested was not the most relevant one for the discovery of real connections. Here we propose a simple and robust method for constructing the reference gene-expression profiles and a new connection scoring scheme, which importantly allows the valuation of statistical significance of all the connections observed. We tested the new method with the two example gene-signatures (HDAC inhibitors and Estrogens) used by Lamb et al and also a new gene signature of immunosuppressive drugs. Our testing with this new method shows that it achieves a higher level of specificity and sensitivity than the original method. For example, our method successfully identified raloxifene and tamoxifen as having significant anti-estrogen effects, while Lamb et al's Connectivity Map failed to identify these. With these properties our new method has potential use in drug development for the recognition of pharmacological and toxicological properties in new drug candidates.Comment: 8 pages, 2 figures, and 2 tables; supplementary data supplied as a ZIP fil

2 Novel deletions of the sterol 27-hydroxylase gene in a Chinese Family with Cerebrotendinous Xanthomatosis

<p>Abstract</p> <p>Background</p> <p>Cerebrotendinous xanthomatosis (CTX) is a rare lipid-storage disease. We investigated the clinic manifestation, histopathology and sterol 27-hydroxylase gene (CYP27A1) in a Chinese family with Cerebrotendinous Xanthomatosis (CTX).</p> <p>Case Presentation</p> <p>A 36-year-old female with typical CTX clinical manifestation had Spindle-shaped lipid crystal clefts in xanthomas and "onion-like demyelination" in sural nerve. The patient was compound heterozygote carrying two deletions in exon 1 (c.73delG) and exon 2 (c.369_375delGTACCCA). The family memebers were carriers.</p> <p>Conclusions</p> <p>A Chinese family with Cerebrotendinous Xanthomatosis had typical clinical manifestation. CYP27A1 mutations were found in the proband and all other family members.</p

Post-Lie Algebras, Factorization Theorems and Isospectral-Flows

In these notes we review and further explore the Lie enveloping algebra of a post-Lie algebra. From a Hopf algebra point of view, one of the central results, which will be recalled in detail, is the existence of a second Hopf algebra structure. By comparing group-like elements in suitable completions of these two Hopf algebras, we derive a particular map which we dub post-Lie Magnus expansion. These results are then considered in the case of Semenov-Tian-Shansky's double Lie algebra, where a post-Lie algebra is defined in terms of solutions of modified classical Yang-Baxter equation. In this context, we prove a factorization theorem for group-like elements. An explicit exponential solution of the corresponding Lie bracket flow is presented, which is based on the aforementioned post-Lie Magnus expansion.Comment: 49 pages, no-figures, review articl

Availability, formulation, labelling, and price of low-sodium salts worldwide

BACKGROUND: Regular salt is about 100% sodium chloride (NaCl). Low-sodium salts have reduced sodium chloride content, most commonly through substitution with potassium chloride (KCl). Low-sodium salts have a potential role in reducing population sodium intake level and blood pressure, but its availability in global market was unknown. OBJECTIVE: The aim of this study was to assess the availability, formulation, labelling, and price of low-sodium salts currently available to consumers around the world. METHODS: Low-sodium salts were identified through a systematic literature review, Google search, online shopping sites search, and inquiry of key informants. The keywords of "salt substitute", "low-sodium salt", "potassium salt", "mineral salt", and "sodium reduced salt" in six official languages of the United Nations were used for search. Information about the brand, formula, labelling, and price was extracted and analysed. RESULTS: Eighty-seven low-sodium salts were available in 47 out of 195 countries around the world (24%), including 28 high-income countries, 13 upper-middle-income countries, and six lower-middle-income countries. The proportion of sodium chloride varied from 0% (sodium-free) to 88% (as percent of weight, regular salt is 100% NaCl). Potassium chloride was the most frequent another component with levels ranging from 0% to 100% (potassium chloride salt). Forty-three (49%) had labels advising potential health risk, 33 (38%) labelling the advice of potential health benefits. The median price of low-sodium salts in high-income, upper-middle-income, lower-middle-income countries was USD 15.0/kg (IQR: 6.4 to 22.5), USD 2.7/kg (IQR: 1.7 to 5.5) and USD 2.9/kg (IQR: 0.50 to 22.2) respectively. The price of low-sodium salts was between 1.1 and 14.6 times that of regular salts. CONCLUSIONS: Low-sodium salts are not widely available and are commonly more expensive than regular salts. Policies that promote the availability, affordability and labelling of low-sodium salts should enhance appropriate uptake for blood pressure lowering and cardiovascular prevention. CLINICALTRIAL: INTERNATIONAL REGISTERED REPORT: RR2-10.1111/jch.14054