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Biomedical subjects

J F Wang

Publications and source records attributed to J F Wang.

At least 19 recordsLinked to original sources
PubMed2006

Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation.

BACKGROUND AND PURPOSE: Traditional Chinese Medicine (TCM) is widely practised and is viewed as an attractive alternative to conventional medicine. Quantitative information about TCM prescriptions, constituent herbs and herbal ingredients is necessary for studying and exploring TCM. EXPERIMENTAL APPROACH: We manually collected information on TCM in books and other printed sources in Medline. The Traditional Chinese Medicine Information Database TCM-ID, at http://tcm.cz3.nus.edu.sg/group/tcm-id/tcmid.asp, was introduced for providing comprehensive information about all aspects of TCM including prescriptions, constituent herbs, herbal ingredients, molecular structure and functional properties of active ingredients, therapeutic and side effects, clinical indication and application and related matters. RESULTS: TCM-ID currently contains information for 1,588 prescriptions, 1,313 herbs, 5,669 herbal ingredients, and the 3D structure of 3,725 herbal ingredients. The value of the data in TCM-ID was illustrated by using some of the data for an in-silico study of molecular mechanism of the therapeutic effects of herbal ingredients and for developing a computer program to validate TCM multi-herb preparations. CONCLUSIONS AND IMPLICATIONS: The development of systems biology has led to a new design principle for therapeutic intervention strategy, the concept of 'magic shrapnel' (rather than the 'magic bullet'), involving many drugs against multiple targets, administered in a single treatment. TCM offers an extensive source of examples of this concept in which several active ingredients in one prescription are aimed at numerous targets and work together to provide therapeutic benefit. The database and its mining applications described here represent early efforts toward exploring TCM for new theories in drug discovery.

Artificial Intelligence↗
PubMed2006

Usefulness of traditionally defined herbal properties for distinguishing prescriptions of traditional Chinese medicine from non-prescription recipes.

Traditional Chinese medicine (TCM) has been widely practiced and is considered as an attractive to conventional medicine. Multi-herb recipes have been routinely used in TCM. These have been formulated by using TCM-defined herbal properties (TCM-HPs), the scientific basis of which is unclear. The usefulness of TCM-HPs was evaluated by analyzing the distribution pattern of TCM-HPs of the constituent herbs in 1161 classical TCM prescriptions, which shows patterns of multi-herb correlation. Two artificial intelligence (AI) methods were used to examine whether TCM-HPs are capable of distinguishing TCM prescriptions from non-TCM recipes. Two AI systems were trained and tested by using 1161 TCM prescriptions, 11,202 non-TCM recipes, and two separate evaluation methods. These systems correctly classified 83.1-97.3% of the TCM prescriptions, 90.8-92.3% of the non-TCM recipes. These results suggest that TCM-HPs are capable of separating TCM prescriptions from non-TCM recipes, which are useful for formulating TCM prescriptions and consistent with the expected correlation between TCM-HPs and the physicochemical properties of herbal ingredients responsible for producing the collective pharmacological and other effects of specific TCM prescriptions.

Algorithms↗
PubMed2006

Percutaneous intravascular stents for treatment of portal venous stenosis after liver transplantation: midterm results.

Portal vein stenosis after liver transplantation is a relatively uncommon vascular complication that may result in graft loss if not promptly treated. The purpose of this study was to evaluate the midterm result of the use of intravascular stents for portal vein stenosis after liver transplantation. From April 2004 to September 2005, percutaneous transhepatic balloon dilation with stent deployment was performed in nine cases. Varices were embolized with stainless steel coils in two cases. No procedure-related complication occurred. Portal venous patency was maintained in all nine patients from 6 to 19 months (mean 10 months). In conclusion, an intravascular stent is an effective treatment for the portal vein stenosis after liver transplantation with excellent midterm patency.

Angioplasty, Balloon, Coronary↗
PubMed2006

The influence of intramammary lipopolysaccharide infusion on serum Ca, P, vitamin D, cytokines and cortisol concentrations in lactating sows.

Ten multiparous lactating sows were used to investigate whether intramammary infusion of lipopolysaccharides (LPS; Escherichia coli 0111:B4; 2.0 microg/kg of body weight) would affect the circulating concentrations of Ca, P, 25-hydroxyvitamin D (25-OHD), tumour necrosis factor-alpha (TNF-alpha), interleukin-6 (IL-6) and cortisol. The sows were randomly allotted to either control group (control) or LPS-treated group with five individuals per group and were infused with either physiological saline solution or LPS solution. The rectal temperature and udder quarter appearance were recorded at 0 (just before infusion), 1, 3, 7, 12 or 24 h after infusion. Blood samples were taken at 0, 1, 3, 7, 12 or 24 h after infusion. Before infusion, the rectal temperatures of all sows were below 39.2 degrees C. At 3 and 7 h after infusion, the sows in the LPS group had a rectal temperature over 39.4 degrees C. At 24 h after infusion, the rectal temperatures returned to pre-infusion levels. Serum Ca and P concentrations in the LPS group decreased (P < 0.05) after LPS infusion compared with the control group at 1 h after infusion. No significant differences (P > 0.05) in the concentrations of 25-OHD were observed between groups control and LPS at any sampling time. Increased (P < 0.01) concentrations of serum TNF-alpha, IL-6 and cortisol were observed in the LPS group compared with the control group at 3 and 7 h after infusion respectively. In conclusion, the elevation of serum concentrations of TNF-alpha, IL-6 and cortisol and the alterations of circulating concentrations of Ca and P following LPS infusion indicate that the immune system has been activated and immune activation may affect macromineral homeostatic regulation, which might have important implications for metabolic health of lactating sows. Lowered serum Ca and P following immune activation also shows a causative mechanism whereby immune activation increases the risk of secondary disorders such as mastitis-metritis-agalactia syndrome. However, immune activation did not affect circulating concentrations of vitamin D metabolites.

Animals↗
PubMed2006

Anaerobic uptake of phosphate in an anaerobic-aerobic granular sludge sequencing batch reactor.

An unusual phenomenon of anaerobic phosphate uptake under alternating anaerobic/aerobic condition was observed in a granular sludge sequencing batch reactor, fed with acetate as sole organic substrate. Anaerobic phosphate uptake efficiencies remained at 50-70% as the influent P/COD was increased from 2/100 to 4/100, and results showed that anaerobic uptake of phosphate was correlated with anaerobic absorption of acetate. Excluding the main possibility of chemical phosphate removal, it appeared that phosphate uptake during the anaerobic phase was associated with organisms enriched in the reactor. Moreover, results indicated that intracellular glycogen was used as the main energy source of organics anaerobic absorption and intracellular polymers storage. Measuring and analysing the variation of phosphate, organic substrate, intracellular glycogen and pH in the anaerobic phase, a preliminary explanation was developed that anaerobic uptake of phosphate was the demand of intracellular glycogen degradation, and extracellular phosphate was transported to intracellular by pH gradient-sensitive phosphate carrier protein.

Aerobiosis↗
PubMed2005

Assessment of approximate string matching in a biomedical text retrieval problem.

Text-based search is widely used for biomedical data mining and knowledge discovery. Character errors in literatures affect the accuracy of data mining. Methods for solving this problem are being explored. This work tests the usefulness of the Smith-Waterman algorithm with affine gap penalty as a method for biomedical literature retrieval. Names of medicinal herbs collected from herbal medicine literatures are matched with those from medicinal chemistry literatures by using this algorithm at different string identity levels (80-100%). The optimum performance is at string identity of 88%, at which the recall and precision are 96.9% and 97.3%, respectively. Our study suggests that the Smith-Waterman algorithm is useful for improving the success rate of biomedical text retrieval.

Algorithms↗
PubMed2005

A computer method for validating traditional Chinese medicine herbal prescriptions.

Traditional Chinese medicine (TCM) has been widely practiced and is considered as an alternative to conventional medicine. TCM herbal prescriptions contain a mixture of herbs that collectively exert therapeutic actions and modulating effects. Traditionally defined herbal properties, related to the pharmacodynamic, pharmacokinetic and toxicological, as well as physicochemical properties of their principal ingredients, have been used as the basis for formulating TCM multi-herb prescriptions. These properties are used in this work to develop a computer program for predicting whether a multi-herb recipe is a valid TCM prescription. This program is based on a statistical learning method, support vector machine (SVM), and it is trained by using 575 well-known TCM prescriptions and 1961 non-TCM recipes generated by random combination of TCM herbs. Testing results by using 72 well-known TCM prescriptions and 5039 non-TCM recipes showed that 73.6% of the TCM prescriptions and 99.9% of non-TCM recipes are correctly classified by this system. A further test by using 48 TCM prescriptions published in recent years found that 68.7% of these are correctly classified. These accuracies are comparable to those of SVM classification of other biological systems. Our study indicates the potential of SVM for facilitating the analysis of TCM prescriptions.

Chemistry, Pharmaceutical↗
PubMed2005

Effects of dietary zinc levels on the activities of enzymes, weights of organs, and the concentrations of zinc and copper in growing rats.

Zinc (Zn) is an essential nutrient that is required in humans and animals for many physiological functions, including immune and antioxidant function, growth, and reproduction. The present study was performed to investigate the effects of three Zn levels, including Zn adequate (35.94 mg/kg, as a control), Zn deficiency (3.15 mg/kg), and Zn overload (347.50 mg/kg) in growing male rats for 6 wk. This allowed for evaluation of the effects that these Zn levels might have on body weight, organ weight, enzymes activities, and tissues concentrations of Zn and Cu. The results showed that Zn deficiency has negative effects on growth, organ weight, and biological parameters such as alkaline phosphatase (ALP) and Cu-Zn superoxide dismutase (Cu-Zn SOD) activities, whereas Zn overload played an effective role in promoting growth, improving the developments of organs and enhancing immune system. Hepatic metallothionein (MT) concentration showed an identical increase tendency in rats fed both Zn-deficient and Zn-overload diets. The actual mechanism of reduction of Cu concentration of jejunum in rats fed a Zn-overload diet might involve the modulation or inhibition of a Cu transporter protein by Zn and not by the induction of MT.

Alkaline Phosphatase↗
PubMed2004

Treatment planning for scanned ion beams.

Since 1997 a radiotherapy unit using fast carbon ions is operational at GSI. An intensity-controlled magnetic raster scanner together with a synchrotron allowing fast energy variation enable a unique method of purely active dose shaping in three dimensions. This contribution describes the necessary steps to establish a treatment planning system for this novel modality. We discuss the requirements for the physical beam model and the radiobiological model. Based on these we chose to implement a home-grown pencil beam model to describe the ion-tissue interaction and the Local Effect Model to calculate the RBE voxel-by-voxel. Given the large number of degrees of freedom biological dose optimization must be achieved by means of inverse treatment planning. All ion-related aspects are collected in our TRiP98 software. Biological dosimetry measuring cell survival in two dimensions turns out to be a good way to verify the model predictions as well as the actual irradiation procedure. We show a patient example and outline the future steps towards a dedicated clinic facility for all light ions.

Carbon↗
PubMed2004

In vitro fermentation of various fiber and starch sources by pig fecal inocula.

Freeze-dried ileal effluent (1% wt/vol) from cannulated pigs fed rice-based diets with the inclusion of either animal protein (CON), animal protein plus potato starch (PS), animal protein plus sugar beet pulp (SBP), or animal protein plus wheat bran (WB) was incubated anaerobically at pH 6.0 in fermenters containing 5% (wt/vol) fecal slurry comprising mineral salts medium and 50 g/L of fresh feces from pigs fed the same diets as the cannulated pigs. Samples were collected from the fermenters at 0, 2, 4, 12, 24, and 48 h during in vitro fermentation for measuring nonstarch polysaccharides (NSP), starch, and short-chain fatty acids (SCFA). Results showed that the major SCFA produced were acetate, propionate, and butyrate. The inclusion of soluble dietary fiber (diet SBP) caused the highest concentrations of acetate, propionate, butyrate, and total SCFA, whereas the increase in the production of propionate resulting from the addition of insoluble dietary fiber (diet WB) only occurred at the initial stages during 48 h in vitro fermentation. At all sampling occasions (except for 4 h), the levels of butyrate were increased (P < 0.01) by resistant starch compared with fiber sources, showing that a higher level of butyrate can be achieved through microbial fermentation by potato starch. Lowered (P < 0.05) butyrate concentrations were observed with diet WB during in vitro fermentation. With the inclusion of fiber sources, the energy originating from SCFA was similar to that from NSP disappearance, whereas the values were lower (P < 0.05) from NSP disappearance than for SCFA generated without fiber sources supplemented. We conclude that more substrate is available in ileal effluent with the addition of soluble dietary fiber, and an increased level of butyrate could be achieved through microbial fermentation by resistant starch.

Animals↗
PubMed2003

Exact representation of crossover of transitions from first order to second order in the Potts model for rumor transmission.

The L-state Potts model for rumor is the N-spin chain describing how a simple rumor transmitted by N recreant rumormongers is aggrandized. The studied rumor is represented mathematically by a simple proposition with the universal quantifier, which again is represented geometrically by a point in a proposition space. During the transmission, such a proposition is changed with the change of the rumor, which has individual number N0 at the beginning of the transmission. Correspondingly, the point expressing the proposition may start from an arbitrary site at the proposition space, and then it shifts in the space. Thus, a spin sum of the Potts model corresponds to a walk of a point in the proposition space and spin configuration's numbers is given by enumerating the corresponding walks. The concept of the lattice path in combinatorial mathematics is introduced and the exact series representation of the configuration's numbers is given. The partition function exhibits the transition of the chain and critical equivalent inverse temperature beta(c) is determined. Moreover, there is a crossover value of the individual number, N00. The model has a first-order transition when N0 N00.

Journal Article↗
PubMed2003

Biological dosimetry of complex ion radiation fields.

We report on a set of cell survival experiments performed in complex field combinations of therapeutic 12C ion beams. CHO cells were exposed to the superposition of two or three fields of 12C ions arranged in a similar way to real patient treatments. Two-dimensional survival distributions were measured and compared with the predictions of the TRiP98 treatment planning system. Good agreement was found in general. In particular the method of tissue sparing using dose ramps could be verified.

Animals↗
PubMed2003

Valproate inhibits oxidative damage to lipid and protein in primary cultured rat cerebrocortical cells.

Valproate is often prescribed as a long-term therapeutic mood stabilizing agent for individuals with bipolar disorder. Although research suggests that this drug may produce a neuroprotective effect, its neuroprotective mechanism is not yet clear. The purpose of this study was to determine if valproate provides a neuroprotective effect against damage caused by oxidative stress in primary cultured rat cerebral cortical cells. We found that chronic treatment with valproate at therapeutically relevant concentrations for 7 days inhibited lipid peroxidation and protein oxidation induced by treatment with 0.25 mM oxidant FeCl(3) for 90 min, indicating that valproate inhibits oxidative damage to lipid and protein. Our results suggest that chronic treatment with valproate may protect neuronal cells from damage caused by oxidative stress and that neuroprotection from oxidative damages may be involved in the mechanism of action of valproate. Supporting this possibility are recent findings that chronic treatment with valproate increased the expression of endoplasmic reticulum stress protein GRP78 and antiapoptotic factor bcl-2 in rat cerebral cortex. Since GRP78 binds Ca(2+) and folds damaged protein, bcl-2 stabilizes mitochondrial transmembrane potential and inhibits cytochrome C release, and both GRP78 and bcl-2 have been shown to inhibit oxyradical accumulation, together these findings indicate that valproate may target one or more of these processes in order to produce neuroprotective effects.

Animals↗
PubMed2003

Attenuation of N-methyl-D-aspartate-mediated cytoplasmic vacuolization in primary rat hippocampal neurons by mood stabilizers.

Recent post-mortem and brain imaging studies suggest that decreased neuronal and glial densities may account for cell loss in vulnerable brain regions such as the hippocampus and the frontal cortex in patients with bipolar disorder. Investigations into the mechanisms of action of mood stabilizers suggest that these drugs may regulate the expression of neuroprotective genes and protect against excitotoxicity. In this study, we characterized the ultrastructural appearance of rat hippocampal neurons pretreated with mood stabilizers and then exposed to the glutamate receptor agonist N-methyl-D-aspartate. Using transmission electron microscopy we found that rat hippocampal neurons exposed to 0.5 mM N-methyl-D-aspartate for 10 min produced more cytoplasmic vacuolization than in control neurons. Chronic treatment with mood stabilizers, lithium, valproate or carbamazepine for 7 days at therapeutically relevant concentrations fully attenuated N-methyl-D-aspartate-mediated cytoplasmic vacuolization. These results suggest that inhibition of neurotoxicity may be involved in the action of mood stabilizers.

Animals↗
PubMed2003

Structural genomics efforts at the Chinese Academy of Sciences and Peking University.

Structural genomics efforts at the Chinese Academy of Sciences and Peking University are reported in this article. The major targets for the structural genomics project are targeted proteins expressed in human hematopoietic stem/progenitor cells, proteins related to blood diseases and other human proteins. Up to now 328 target genes have been constructed in expression vectors. Among them, more than 50% genes have been expressed in Escherichia coli, approximately 25% of the resulting proteins are soluble, and 35 proteins have been purified. Crystallization, data collection and structure determination are continuing. Experiences accumulated during this initial stage are useful for designing and applying high-throughput approaches in structural genomics.

Academies and Institutes↗
PubMed2002

ADME-AP: a database of ADME associated proteins.

Drug absorption, distribution, metabolism and excretion (ADME) often involve interaction of a drug with specific proteins. Knowledge about these ADME-associated proteins is important in facilitating the study of the molecular mechanism of disposition and individual response as well as therapeutic action of drugs. It is also useful in the development and testing of pharmacokinetics prediction tools. Several databases describing specific classes of ADME-associated proteins have appeared. A new database, ADME-associated proteins (ADME-AP), is introduced to provide comprehensive information about all classes of ADME-associated proteins described in the literature including physiological function of each protein, pharmacokinetic effect, ADME classification, direction and driving force of disposition, location and tissue distribution, substrates, synonyms, gene name and protein availability in other species. Cross-links to other databases are also provided to facilitate the access of information about the sequence, 3D structure, function, polymorphisms, genetic disorders, nomenclature, ligand binding properties and related literatures of each protein. ADME-AP currently contains entries for 321 proteins and 964 substrates.

Databases, Protein↗