Yuan-Hu Zhi Tong Prescription Mitigates Tau Pathology and Alleviates Memory Deficiency in the Preclinical Models of Alzheimer's Disease

Alzheimer's disease (AD) is characterized by memory dysfunction, Aβ plaques together with phosphorylated tau-associated neurofibrillary tangles. Unfortunately, the present existing drugs for AD only offer mild symptomatic cure and have more side effects. As such, developments of effective, nontoxic drugs are immediately required for AD therapy. Present study demonstrates a novel role of Chinese medicine prescription Yuan-Hu Zhi Tong (YZT) in treating AD, and it has substantiated the in vivo effectiveness of YZT in two different transgenic mice models of AD, namely P301S tau and 3XTg-AD mice. Oral treatment of YZT significantly ameliorates motor dysfunction as well as promotes the clearance of aggregated tau in P301S tau mice. YZT improves the cognitive function and reduces the insoluble tau aggregates in 3XTg-AD mice model. Furthermore, YZT decreases the insoluble AT8 positive neuron load in both P301S tau and 3XTg-AD mice. Using microarray and the "Connectivity Map" analysis, we determined the YZT-induced changes in expression of signaling molecules and revealed the potential mechanism of action of YZT. YZT might regulate ubiquitin proteasomal system for the degradation of tau aggregates. The research results show that YZT is a potential drug candidate for the therapy of tau pathogenesis and memory decline in AD.

A Case of Unintentional Methadone Overdose Followed by Hypoglycaemia

Methadone overdose is expected to result in intoxication simulating the other opioids. We report a case of hypoglycaemia following accidental methadone ingestion. A 21-year-old woman presented to a local accident and emergency department 10 hours after ingestion of 800 mg of methadone. She was found to have coma, respiratory suppression, hypotension, prolonged QTc and hypoglycaemia. The hypoglycaemia was reversed by dextrose replacement. The patient required intubation and inotropic support because of cardio-respiratory instability. She eventually recovered without consequence. To date, this is the first reported case of methadone overdose induced hypoglycaemia.

Outcome and Prognostic Factors of Patients in Out-Of-Hospital Cardiac Arrests Presenting with Non-Shockable Rhythm in Hong Kong

Objective

To obtain the recent local epidemiological data and evaluate factors associated with outcomes of adult patients in non-traumatic non-shockable out-of-hospital-cardiac-arrest (OHCA) in Hong Kong.

Methods

It was a cross-sectional study lasting for nine months (from July 2009 to March 2010) in two emergency departments (ED) which served a population of 1.1 million. All non-traumatic OHCA patients aged equal or greater than 18 years presented with non-shockable cardiac rhythms to ED without postmortem changes were included. The pre-hospital factors, managements and outcomes were recorded in a standardised data entry form at the time of patient consultation. Logistic regression was used to evaluate the relationship between survival to admission (STA) and various prognostic factors.

Results

A total of 348 patients fulfilled the inclusion criteria. The mean age was 75.9 years old. Overall, there were 61 patients (17.5%) with restoration of spontaneous circulation and 58 patients (16.7%) had STA. The survival to hospital discharge (STD) rate was 0.86% (3 patients). Factors independently associated with better prognosis in terms of STA were initial pulseless electrical activity arrest (PEA) rhythm in ED (OR=4.72, 95% CI 2.30-9.69), witnessed arrest (OR=8.00, 95% CI 3.38-18.96) and non-cardiac cause of arrest (OR=2.17, 95% CI 1.00-4.67).

Conclusion

STA for adults presenting with non-traumatic non-shockable OHCA in our centre is 16.7%. Witnessed non-shockable OHCA patients presenting with initial PEA arrest rhythm and with a presumed non-cardiac in etiology are significantly associated with higher STA rate.

Treatment of Acute Diarrhoea in Adults with Dioctahedral Smectite (Smecta): A Prospective Randomised Study

Background

Acute diarrhoea is a common presenting problem to the accident and emergency department. This study aimed to assess the efficacy of dioctahedral smectite (Smecta) in altering the duration and frequency of acute diarrhoea in the adult population in Hong Kong.

Material and methods

This was a prospective, randomised controlled study carried out in the Accident and Emergency Department of Caritas Medical Centre from July 2005 to October 2005. One hundred and ninety eligible adult patients with acute diarrhoea lasting not more than 14 days were randomly assigned either (1) oral rehydration solution (ORS) one sachet three times daily and Smecta one sachet three times daily for two days; or (2) ORS one sachet three times daily for two days. The duration of diarrhoea, daily frequency of diarrhoea, presence of vomiting and fever following treatment were obtained by telephone interviews and mailed questionnaires.

Results

For patients treated with or without Smecta, there was no statistically significant difference in the mean duration and daily frequency of diarrhoea in the first three days.

Conclusion

The use of Smecta did not change the duration or frequency of acute diarrhoea in the adults in this study.

Outcome Predictors of Patients in Out-Of-Hospital Cardiac Arrests with Pre-Hospital Defibrillation in Hong Kong

Objective

To report the epidemiology, outcomes and the predictors of survival in patients with out-of-hospital cardiac arrest (OHCA) with pre-hospital shockable cardiac rhythms in Hong Kong.

Methods

It was a prospective study based on data from the cardiac arrest registry of emergency departments (ED) in two regional hospitals in Hong Kong from 1st August 2010 to 31st January 2012. All non-traumatic patients aged 18 years or above presented with OHCA with shockable pre-hospital cardiac rhythm and received pre-hospital defibrillation were included. The characteristics of patients, pre-hospital data, management and outcomes were recorded in a standardised form compatible with Utstein template at the time of patient consultation. Binominal logistic regression was applied to evaluate the relationship between survival to admission (STA) and patients' variables.

Results

A total of 135 patients fulfilled the inclusion criteria. The mean age was 67.0 years old. The STA rate was 34.8% and the survival to discharge (STD) rate was 6.7%. Factors independently associated with better prognosis in terms of STA were presence of bystander cardiopulmonary resuscitation (CPR) (OR 5.76, 95% CI=1.08-30.5), restoration of spontaneous circulation (ROSC) before arrival to ED (OR 43.94, 95% CI= 4.19-460.43) and short time from calling emergency medical services (EMS) to first defibrillation (OR 0.82, 95% CI=0.70-0.96).

Conclusion

STA rate for adults presenting with shockable OHCA in our study was 34.8%. Patients with shockable OHCA with bystander CPR, short call-to-shock time and achieved ROSC before arrival to ED are significantly associated with higher STA rate.

An Unusual Case of Dizziness Presenting to Emergency Department: Acute Cerebellitis

Acute cerebellitis is an uncommon and potentially fatal disease which usually presents initially with non-specific symptoms. There is scarce report on local cases of isolated acute cerebellitis. We report a patient with isolated acute cerebellitis attending emergency department with predominant symptom of dizziness. Diagnosis was made by magnetic resonance imaging assisted by lumbar puncture. He received timely medical treatment and the clinical course was benign. The clinical feature, diagnosis, and managements of acute cerebellitis are discussed.

Adrenomedullin increases the short-circuit current in the rat prostate: Receptors, chloride channels, the effects of cAMP and calcium ions and implications on fluid secretion

In this study, we have investigated the effects of adrenomedullin on chloride and fluid secretion in the rat prostate. The presence of adrenomedullin (ADM) in rat prostate was confirmed using immunostaining, and the molecular species was determined using gel filtration chromatography coupled with an enzyme-linked assay for ADM. The effects of ADM on fluid secretion were studied by short-circuit current technique in a whole mount preparation of the prostate in an Ussing chamber. The results indicated that the ADM level was higher in the ventral than the dorso-lateral prostate and the major molecular species was the active peptide. ADM increased the short-circuit current through both the cAMP- and calcium-activated chloride channels in the ventral lobe, but only through the calcium-activated channels in the dorso-lateral lobe. These stimulatory effects were blocked by the calcitonin gene-related peptide (CGRP) receptor antagonist, hCGRP8-37. We conclude that ADM may regulate prostatic fluid secretion through the chloride channels, which may affect the composition of the seminal plasma bathing the spermatozoa and hence fertility.

Adrenomedullin increased the short-circuit current in the pig oviduct through chloride channels via the CGRP receptor: mediation by cAMP and calcium ions but not by nitric oxide

The oviduct serves as a site for the fertilization of the ovum and the transport of the conceptus down to the uterus for implantation. In this study, we investigated the presence of adrenomedullin (ADM) and its receptor component proteins in the pig oviduct. The effect of ADM on oviductal secretion, the specific receptor, and the mechanisms involved were also investigated. The presence of ADM and its receptor component proteins in the pig oviduct were confirmed using immunostaining. Short-circuit current (I(sc)) technique was employed to study chloride ion secretion in the oviductal epithelium. ADM increased I(sc) through cAMP- and calcium-activated chloride channels, and this effect could be inhibited by the CGRP receptor antagonist, hCGRP8-37. In contrast, the nitric oxide synthase inhibitor, L-NG-nitroarginine methyl ester (L-NAME), could not block the effect of ADM on I(sc). In summary, ADM may increase oviductal fluid secretion via chloride secretion independent of the nitric oxide pathway for the transport of sperm and the conceptus.

What are the ten new commandments in severe polytrauma management?

This review aims to provide a concise overview of the trauma management evolution in the past decade. 1) Trauma care priorities have incorporated staff protection against infection and early decision making in addition to the conventional ABCDE. 2) Five stratified levels for DAM have replaced the non-specific conventional Plans A & B. 3) CT scanning can be the tunnel to death for the hemodynamically unstable patient. 4) DPL has virtually been replaced by the FAST USG. 5) Direct whole-body MDCT provides rapid imaging diagnosis & expedites the definitive treatment but carries high radiation hazards. 6) The dynamic shock assessment by fluid resuscitation response provides more outcome-specific evaluation than the static blood volume loss model. 7) DCR comprising of permissive hypotension, hemostatic resuscitation & DCS aims to overcome the lethal triad of trauma. Early transfusion of blood components of FFP & platelet concentrates improves the outcome in massive blood transfusion. 8) DCS aims to rectify the deranged physiology and not to fully restore the damaged anatomy. 9) A pre-defined protocol for major pelvic fracture can be life-saving and the novel Pre-PPP (pre-peritoneal pelvic packing) may further reduce mortality coupled with the necessary TCAE. 10) Injury prevention is equally important if not more than the trauma resuscitation & operation.

Secretin Controls Anion Secretion in the Rat Epididymis in an Autocrine/Paracrine Fashion1

There is growing evidence that secretin, the first hormone discovered in our history, has functions in the brain other than in the gastrointestinal tract. This article reports for the first time that secretin and its receptor mRNAs are produced in distinct cell types within the epididymis. To test if secretin affects electrolyte transport in the epididymis, we measured short-circuit current (Isc) in cultured epididymal epithelia and found secretin dose-dependently stimulated Isc. Ion substitution experiments and use of pharmacological agents inferred that the stimulated Isc is a result of concurrent electrogenic chloride and bicarbonate secretion. It is further shown that secretin and pituitary adenylate cyclase-activating polypeptide (PACAP) function via totally different mechanisms: 1) PACAP works only from the apical side of the epithelium to stimulate chloride and not bicarbonate secretion, while secretin acts on the apical and basolateral sides to stimulate chloride and bicarbonate secretion. 2) the stimulation by PACAP but not secretin requires local prostaglandin synthesis. By immunocytochemical staining, secretin is localized in the principal cells of the initial segment and caput epididymidis, whereas secretin receptor is present in the principal cells of the proximal as well as the distal part of the epididymis. This pattern of distribution appears to be consistent with the idea that secretin is secreted by the proximal epididymis and acts on the proximal and distal epididymis in an autocrine and paracrine fashion. Its function is to control secretion of electrolytes and water.

Regulation of epididymal principal cell functions by basal cells: role of transient receptor potential (Trp) proteins and cyclooxygenase-1 (COX-1)

The epithelia lining the epididymides of many species including the human are known to consist of several cell types. Among them, the principal cells are the most abundant and their functions most extensively studied. There are other cell types such as the narrow cells, clear cells, halo cells and basal cells which are scattered along the duct in lesser number. Although these minority cell types have not been studied to the same extent as the principal cells, it is conceivable that their presence are essential to the integrated functions of the epididymis. In the intact epididymis, basal cells can be seen adhering to the basement membrane forming close contact with the principal cells above them. Work in our laboratory has provided evidence that through local formation of prostaglandins, basal cells may regulate electrolyte and water transport by the principal cells. This regulatory process involves two proteins which are exclusively expressed by the basal cells. They are the transient receptor potential (Trp) proteins, which serve as transmembrane pathways for Ca(2+) influx, and cyclooxygenase 1 (COX-1), a key enzyme in the formation of prostaglandins. The role of the two proteins in the integrated functions of the basal cells as humoral regulators of principal cells is discussed.

Twin births in Singapore: a population-based study using the National Birth Registry

INTRODUCTION

Twin studies are a most effective method to analyse gene and environment interactions. Using data from the Singapore National Registry of Births and Deaths (SNRBD), this paper describes the number of twin and multiple births among different ethnic populations in Singapore.

MATERIALS AND METHODS

All births recorded in the SNRBD from 1 January 1986 to 31 December 2001 were analysed. Outcomes measured were twin and triple birth rates (per 1000 maternities) of the 3 main ethnic groups in Singapore (Chinese, Malays and Asian Indians). Further outcomes were calculated using Weinberg's differential rule to estimate the number of monozygotic and dizygotic twins.

RESULTS

Overall twin birth rates have steadily increased across all ethnic groups (7 to 9/1000). The largest increase in multiple births among the ethnic groups were twins born to Asian Indian fathers (6.9 to 9.9/1000) and Malay mothers (5.9 to 9.8/1000). A significant difference in birth rates between the ethnic groups was found during the years 1994 to 1997, where Chinese parents had the lowest multiple birth rates and Asian Indians the highest. Estimation and ratios of monozygotic and dizygotic twin births differed among the ethnic groups: Asian Indians had the highest ratios, followed by the Chinese and, lastly, the Malays.

CONCLUSION

The SNRBD has provided an overview of multiple births in Singapore, although the establishment of a national twin register would enable more detailed analysis of genetic and environmental effects in multiple births.

Reduction of chromate (CrO4(2-)) by an enrichment consortium and an isolate of marine sulfate-reducing bacteria

An enrichment consortium and an isolate (isolate TKW) of sulfate-reducing bacteria (SRB) have been obtained from metal-contaminated marine sediments of Tokwawan, Hong Kong SAR. These bacteria are capable of reducing highly toxic and soluble hexavalent chromium (Cr6+) enzymatically into less toxic and insoluble trivalent chromium (Cr3+) under anaerobic conditions. The enrichment consortium almost completely (98.5%) reduced 0.6 mM Cr6+ in 168 h and the rate of reduction was 0.5 g (Cr6+) g(protein)(-1)h(-1). In comparison, with Cr6+ as the sole electron acceptor (as a surrogate for SO4(2-)), isolate TKW reduced 94.5% of the initially added Cr6+ (0.36 mM) in 288 h, with the rate of 0.26 g (Cr6+) g(protein)(-1)h(-1). Adsorption by these bacteria was not the major mechanism contributing to the transformation or removal of Cr6+. The biomass and Cr3+ in the cultures increased simultaneously with the reduction of Cr6+. These indigenous SRB might have potential application in bioremediation of metal contaminated sediments.

Synergistic effects of cystic fibrosis transmembrane conductance regulator and aquaporin-9 in the rat epididymis

The cystic fibrosis transmembrane conductance regulator (CFTR) and aquaporin-9 (AQP-9) are present in the luminal membrane of the epididymis, where they play an important role in formation of the epididymal fluid. Evidence is accumulating that CFTR regulates other membrane transport proteins besides functioning as a cAMP-activated chloride channel. We have explored the possible interaction between epididymal CFTR and AQP-9 by cloning them from the rat epididymis and expressing them in Xenopus oocytes. The effects of the expressed proteins on oocyte water permeability were studied by immersing oocytes in a hypo-osmotic solution, and the ensuing water flow was measured using a gravimetric method. The results show that AQP-9 alone caused an increase in oocyte water permeability, which could be further potentiated by CFTR. This potentiation was markedly reduced by phloretin and lonidamine (inhibitors of AQP-9 and CFTR, respectively). The regulation of water permeability by CFTR was also demonstrated in intact rat epididymis luminally perfused with a hypo-osmotic solution. Osmotic water reabsorption across the epididymal tubule was reduced by phloretin and lonidamine. Elevation of intracellular cAMP with 3-isobutyl-1-methylxanthine increased osmotic water permeability, whereas inhibiting protein kinase A with H-89 (N-(2-[p-bromocinnamylamino]ethyl)-5-isoquinoline sulfonamide hydrochloride) reduced it. These results are consistent with a role for CFTR in controlling water permeability in the epididymis in vivo. We conclude that this additional role of CFTR in controlling water permeability may have an impact on the genetic disease cystic fibrosis, in which men with a mutated CFTR gene have abnormal epididymis and infertility.

Indazole inhibition of cystic fibrosis transmembrane conductance regulator Cl(-) channels in rat epididymal epithelial cells

Previous studies have shown that two indazole compounds, lonidamine [1-(2,4-dichlorobenzyl)-indazole-3-carboxylic acid] and its analogue AF2785 [(1-(2,4-dichlorobenzyl)-indazol-3-acrylic acid], suppress fertility in male rats. We also found that these compounds inhibit the cystic fibrosis transmembrane conductance regulator chloride (CFTR-Cl(-)) current in epididymal epithelial cells. To further investigate how lonidamine and AF2785 inhibit the current, we used a spectral analysis protocol to study whole-cell CFTR current variance. Application of lonidamine or AF2785 to the extracellular membrane of rat epididymal epithelial cells introduced a new component to the whole-cell current variance. Spectral analysis of this variance suggested a block at a rate of 3.68 micro mol(-1)/sec(-1) and an off rate of 69.01 sec(-1) for lonidamine, and an on rate of 3.27 micro mol(-1)/sec(-1) and an off rate of 108 sec(-1) for AF2785. Single CFTR-Cl(-) channel activity using excised inside-out membrane patches from rat epididymal epithelial cells revealed that addition of lonidamine to the intracellular solution caused a flickery block (a reduction in channel-open time) at lower concentration (10 micro M) without any effect on open channel probability or single-channel current amplitude. At higher concentrations (50 and 100 micro M), lonidamine showed a flickery block and a decrease in open-channel probability. The flickery block by lonidamine was both voltage-dependent and concentration-dependent. These results suggest that lonidamine and AF2785, which are open-channel blockers of CFTR at low concentrations, also affect CFTR gating at high concentrations. We conclude that these indazole compounds provide new pharmacological tools for the investigation of CFTR. By virtue of their interference with reproductive processes, these drugs have the potential for being developed into novel male contraceptives.

A BK(Ca) to K(v) switch during spermatogenesis in the rat seminiferous tubules

Spermatogenesis is a complex cellular event during which the diploid germ cells differentiate and divide by mitosis and meiosis at specific time points along the spermatogenic cycle to generate the haploid spermatozoa. For this complex event to go in an orderly manner, cell differentiation and division must be precisely controlled by signals arising from within and outside the seminiferous tubules. Changes in the membrane potential of the germ cells are likely to be an important part of the signaling mechanism. We have applied the whole-cell patch clamp technique to identify and characterize ion channels in different spermatogenic cells from immature and mature rat testes fractionated by discontinuous Percoll gradient. A voltage- and Ca(2+)- dependent, outwardly rectifying current with gating and pharmacologic properties resembling the large conductance K(+) channels (BK(Ca)) was recorded from the spermatogonia and primary spermatocytes. Another voltage-dependent, outwardly rectifying current that was sensitive to 4-aminopyridine, a K(v) channel blocker, was detected in spermatocytes and early spermatids. This current is likely caused by the smaller conductance, voltage-sensitive K(+) channels (K(v)). In some spermatogonia, both the BK(Ca) channels and the K(v) channels could be simultaneously detected in the same cell. It appears that during the course of spermatogenesis, there is up-regulation of K(v) but down-regulation of BK(Ca). Reverse transcription-polymerase chain reaction, Western blot analysis, and immunohistochemistry further confirmed the differential expression of the ion channels in different spermatogenic cells. We conclude that these ion channels may play an important role in the control of spermatogenesis.

Expression of the cystic fibrosis transmembrane conductance regulator in rat spermatids: implication for the site of action of antispermatogenic agents

To establish whether cystic fibrosis transmembrane conductance regulator (CFTR) is functionally expressed in the testis, we subjected spermatogenic cells from rat testes to analysis of CFTR mRNA, protein and channel activity. CFTR mRNA was detected in the testes of mature but not immature rats using reverse transcription-polymerase chain reaction analysis. Western blot analysis performed with a CFTR specific antibody revealed immunoreactivity in the membrane extract of spermatogenic cells. Immunohistochemical studies localized CFTR in round and elongated spermatids, but not in the fully developed spermatozoa. Using a whole-cell patch clamp technique, we recorded an inward current activated by intracellular cAMP (100 micromol/l) in round spermatids. The current displayed a linear I / V relationship and was inhibited by diphenylamine-2-carboxylate (DPC), a chloride channel blocker. Transfection of the rat germ cell CFTR cDNA into human embryonic kidney (HEK) 293 cells caused the expression of a cAMP-activated chloride current with CFTR characteristics. The current was completely blocked by the antispermatogenic agents 1-(2,4-dichlorobenzyl)-indazole-3-carboxylic acid, lonidamine (500 micromol/l) and 1-(2,4-dichlorobenzyl)-indazole-3-acrylic acid, AF2785 (250 micromol/l). These results taken together provide evidence that CFTR is differentially expressed in spermatids during spermiogenesis. We speculate that CFTR may interact with aquaporin to bring about cytoplasmic volume contraction which is an essential feature of spermiogenesis.

Expression of cystic fibrosis transmembrane conductance regulator in rat efferent duct epithelium

The expression of cystic fibrosis transmembrane conductance regulator (CFTR) was studied in rat efferent ducts. Under whole-cell patch-clamp condition, efferent duct cells responded to intracellular cAMP with a rise in inward current. The cAMP-activated current exhibited a linear I-V relationship and time- and voltage-independent characteristics. The current was inhibited by the Cl(-) channel blocker diphenylamine 2,2'-dicarboxylic acid (DPC) in a voltage-dependent manner and reversed at 24 +/- 0.5 mV, close to the equilibrium potential for Cl(-) (30 mV), suggesting that the current was Cl(-) selective. The cAMP-activated current displayed a permeability sequence of Br(-) > Cl(-) > I(-). Short-circuit current measurement in cultured rat efferent duct epithelia also revealed a cAMP-activated inward current inhibitable by DPC. These electrophysiological properties of the cAMP-activated Cl(-) conductance in the efferent duct were consistent with those reported for CFTR. In support of the functional studies, reverse transcription polymerase chain reaction revealed the presence of CFTR message in cultured efferent duct epithelium. Immunohistochemical studies in intact rats also demonstrated CFTR protein at the apical membrane of the principal cells of efferent duct. CFTR may play a role in modulating fluid transport in the efferent duct.

Na+ reabsorption in cultured rat epididymal epithelium via the Na+/nucleoside cotransporter

The effect of nucleoside on Na+ reabsorption via Na+/nucleoside cotransporter in cultured rat epididymal epithelia was studied by short-circuit current (Isc) technique. Guanosine added apically stimulated Isc in a dose-dependent manner, with a median effective concentration (EC50) of 7 +/- 2 microM (mean +/- SEM). Removal of Na+ from the apical bathing solution or pretreatment with a nonspecific Na+/nucleoside cotransporter inhibitor, phloridzin, completely blocked the Isc response to guanosine. Moreover, the guanosine response was abolished by pretreatment of the tissue with ouabain, a Na+/K+-ATPase inhibitor, suggesting the involvement of Na+/nucleoside cotransporter on the apical side and Na+/K+-ATPase on the basolateral side in Na+ reabsorption. In contrast, the Isc response to guanosine was not affected after desensitization of purinoceptors by ATP. Addition of the Na+/K+/2Cl- symport inhibitor bumetanide to the basolateral side or the nonspecific Cl- channel blocker diphenylamine-2-carboxylate to the apical side showed no effect on the Isc response to guanosine, excluding stimulation of Cl- secretion by guanosine as the cause of the guanosine-induced Isc. The Isc response to purine nucleoside (guanosine and inosine) was much higher than that to pyrimidine nucleoside (thymidine and cytidine). Consistent with substrate specificity, results of reverse transcription-polymerase chain reaction revealed mRNA for concentrative nucleoside transporter (CNT2), which is a purine nucleoside-selective Na+/nucleoside cotransporter in the epididymis, but not for CNT1. It is suggested that the Na+/nucleoside cotransporter (i.e., CNT2) may be one of the elements involved in Na+ and fluid reabsorption in the epididymis, thereby providing an optimal microenvironment for the maturation and storage of spermatozoa.

A metadata framework for interoperating heterogeneous genome data using XML

The rapid advances in the Human Genome Project and genomic technologies have produced massive amounts of data populated in a large number of network-accessible databases. These technological advances and the associated data can have a great impact on biomedicine and healthcare. To answer many of the biologically or medically important questions, researchers often need to integrate data from a number of independent but related genome databases. One common practice is to download data sets (text files) from various genome Web sites and process them by some local programs. One main problem with this approach is that these programs are written on a case-by-case basis because the data sets involved are heterogeneous in structure. To address this problem, we define metadata that maps these heterogeneously structured files into a common eXtensible Markup Language (XML) structure to facilitate data interoperation. We illustrate this approach by interoperating two sets of essential yeast genes that are stored in two yeast genome databases (MIPS and YPD).

ALFRED: an allele frequency database for diverse populations and DNA polymorphisms--an update

ALFRED (the ALelle FREquency Database) is designed to store and disseminate frequencies of alleles at human polymorphic sites for multiple populations, primarily for the population genetics and molecular anthropology communities. Currently ALFRED has information on over 180 polymorphic sites for more than 70 populations. Since our initial release of the database we have focussed on increasing the quantity and quality of data, making reciprocal links between ALFRED and other related databases, and providing useful tools to make the data more comprehensible to the end user. ALFRED is accessible from the Kidd Lab home page (http://info.med.yale. edu/genetics/kkidd/) or from ALFRED directly (http://alfred.med.yale. edu/alfred/index.asp).

ALFRED: a Web-accessible allele frequency database

We present a Web-accessible database (ALFRED) that allows public access to gene frequency data for a diverse set of population samples and genetic systems. The data in ALFRED are modeled based on the experience and needs of a single laboratory, but with the expectation that the database will meet the needs of a much broader scientific community that needs population-specific gene frequency estimates. Our database currently contains data on more than 40 populations representing most major regions of the world and data on more than 150 genetic systems including SNPs, STRPs, and insertion-deletion polymorphisms. While data are not available for all population-genetic system combinations, over 2000 allele frequency tables already exist. In this paper, we enumerate the broad needs in the scientific domain, describe their significance, and describe how we have designed the database to meet those needs. We compare our database with dbSNP, the NCBI database that has a broader but overlapping purpose.

An integrated web interface for large-scale characterization of sequence data

Large-scale genome projects require the analysis of large amounts of raw data. This analysis often involves the application of a chain of biology-based programs. Many of these programs are difficult to operate because they are non-integrated, command-line driven, and platform-dependent. The problem is compounded when the number of data files involved is large, making navigation and status-tracking difficult. To demonstrate how this problem can be addressed, we have created a platform-independent Web front end that integrates a set of programs used in a genomic project analyzing gene function by transposon mutagenesis in Saccharomyces cerevisiae. In particular, these programs help define a large number of transposon insertion events within the yeast genome, identifying both the precise site of transposon insertion as well as potential open reading frames disrupted by this insertion event. Our Web interface facilitates this analysis by performing the following tasks. Firstly, it allows each of the analysis programs to be launched against multiple directories of data files. Secondly, it allows the user to view, download, and upload files generated by the programs. Thirdly, it indicates which sets of data directories have been processed by each program. Although designed specifically to aid in this project, our interface exemplifies a general approach by which independent software programs may be integrated into an efficient protocol for large-scale genomic data processing.

Graphically-enabled integration of bioinformatics tools allowing parallel execution

Rapid analysis of large amounts of genomic data is of great biological as well as medical interest. This type of analysis will greatly benefit from the ability to rapidly assemble a set of related analysis programs and to exploit the power of parallel computing. TurboGenomics, which is a software package currently in its alpha-testing phase, allows integration of heterogeneous software components to be done graphically. In addition, the tool is capable of making the integrated components run in parallel. To demonstrate these abilities, we use the tool to develop a Web-based application that allows integrated access to a set of large-scale sequence data analysis programs used by a transposon-insertion based yeast genome project. We also contrast the differences in building such an application with and without using the TurboGenomics software.

ALFRED: an allele frequency database for diverse populations and DNA polymorphisms

We have developed a publicly accessible database (ALFRED, the ALlele FREquency Database) that catalogues allele frequency data for a wide range of population samples and DNA polymorphisms. This database is web-accessible through our laboratory (Kidd Lab) Web site: http://info.med.yale.edu/genetics/kkidd. ALFRED currently contains data on 60 populations and 156 genetic systems including single nucleotide polymorphisms (SNPs), short tandem repeat polymorphisms (STRPs), variable number of tandem repeats (VNTRs) and insertion-deletion polymorphisms. While data are not available for all population-DNA polymorphism combinations, over 2000 allele frequency tables have been entered. Our database is designed (i) to address our specific research requirements as well as broader scientific objectives; (ii) to allow researchers and interested educators to easily navigate and retrieve data of interest to them; and (iii) to integrate links to other related public databases such as dbSNP, GenBank and PubMed.

TRIPLES: a database of gene function in Saccharomyces cerevisiae

Using a novel multipurpose mini-transposon, we have generated a collection of defined mutant alleles for the analysis of disruption phenotypes, protein localization, and gene expression in Saccharomyces cerevisiae. To catalog this unique data set, we have developed TRIPLES, a Web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces. Encompassing over 250 000 data points, TRIPLES provides convenient access to information from nearly 7800 transposon-mutagenized yeast strains; within TRIPLES, complete data reports of each strain may be viewed in table format, or if desired, downloaded as tab-delimited text files. Each report contains external links to corresponding entries within the Saccharomyces Genome Database and International Nucleic Acid Sequence Data Library (GenBank). Unlike other yeast databases, TRIPLES also provides on-line order forms linked to each clone report; users may immediately request any desired strain free-of-charge by submitting a completed form. In addition to presenting a wealth of information for over 2300 open reading frames, TRIPLES constitutes an important medium for the distribution of useful reagents throughout the yeast scientific community. Maintained by the Yale Genome Analysis Center, TRIPLES may be accessed at http://ycmi.med.yale.edu/ygac/triples.htm

Large-scale analysis of the yeast genome by transposon tagging and gene disruption

Economical methods by which gene function may be analysed on a genomic scale are relatively scarce. To fill this need, we have developed a transposon-tagging strategy for the genome-wide analysis of disruption phenotypes, gene expression and protein localization, and have applied this method to the large-scale analysis of gene function in the budding yeast Saccharomyces cerevisiae. Here we present the largest collection of defined yeast mutants ever generated within a single genetic background--a collection of over 11,000 strains, each carrying a transposon inserted within a region of the genome expressed during vegetative growth and/or sporulation. These insertions affect nearly 2,000 annotated genes, representing about one-third of the 6,200 predicted genes in the yeast genome. We have used this collection to determine disruption phenotypes for nearly 8,000 strains using 20 different growth conditions; the resulting data sets were clustered to identify groups of functionally related genes. We have also identified over 300 previously non-annotated open reading frames and analysed by indirect immunofluorescence over 1,300 transposon-tagged proteins. In total, our study encompasses over 260,000 data points, constituting the largest functional analysis of the yeast genome ever undertaken.

A metadata approach to query interoperation between molecular biology databases

MOTIVATION

Molecular biology databases have been proliferating rapidly. Their heterogeneity and complexity pose a great challenge to efforts in database interoperation. To minimize the efforts of interoperating heterogeneous databases, it is useful to develop a system that lets a user of a particular genomic database access another related database as if the latter is structurally similar to the former.

RESULTS

We extend a structurally simple model-the entity-attribute-value (EAV) model-to describe uniformly metadata relating to individual databases. Such metadata, which are necessary for performing database comparisons, include descriptions of primitive database objects (including entities, attributes, domain values and entity relationships) and specification of correspondences among the database objects. We show how to decompose SQL queries and map them from one database to another based on the EAV representation of the basic database objects. A prototype system is implemented to demonstrate query interoperation between two chromosome map databases.

AVAILABILITY

Freely available (Cold Fusion source code and an Access database containing the mapping knowledge) upon request from the author.

CONTACT

kei.cheung@yale.edu

Automatic query mapping among genomic databases: a pilot exploration

As databases in the human genome project proliferate, it is important for users of one genomic database to identify similar or inconsistent data in other autonomously developed genomic databases. To do so, the user needs to issue the same query across multiple databases. We describe an approach that allows a query issued against one database to be automatically mapped to an equivalent query against another structurally different database. Our approach features two components: 1) a database designed to capture knowledge (metadata) that describes the correspondences among individual database components and 2) a module that utilizes the metadata to perform query mappings. As a demonstration, we apply our query mapping approach to two chromosome map databases (DB/12 and GDB).

PhenoDB: an integrated client/server database for linkage and population genetics

In this paper we describe PhenoDB, an Internet-accessible client/server database application for population and linkage genetics. PhenoDB stores genetic marker data on pedigrees and populations. A database for population and linkage genetics requires two core functions: data management tasks, such as interactive validation during data entry and editing, and data analysis tasks, such as generating summary population statistics and performing linkage analyses. In PhenoDB we attempt to make these tasks as easy as possible. The client/server architecture allows efficient management and manipulation of large datasets via an easy-to-use graphical interface. PhenoDB data (73 populations, 34 pedigrees, approximately 4200 individuals, and close to 80,000 typings) are stored in a generic format that can be readily exported to (or imported from) the file formats required by various existing analysis programs such as LIPED and Lathrop and Lalouel's Multipoint Linkage. PhenoDB allows performance of complex ad-hoc queries and can generate reports for use in project management. Finally, PhenoDB can produce statistical summaries such as allele frequencies, phenotype frequencies, and Chi-square tests of Hardy-Weinberg ratios of population/pedigree data.

DNA workbench: a database package to manage regional physical mapping

DNA Workbench (DW) is a client-server database to manage physical mapping data that will form the basis for sequencing and efforts in biologically interesting regions of a chromosome. DW draws maps at different levels of resolution in either of two modes: proportional, when the sizes of objects and the physical distances between them are known accurately or approximately, and nonproportional, when most physical distance information in a region is not available, but order information is. DW interacts with the user primarily through the map graphic. Selection of individual objects on the graphic lets the user inspect and modify the underlying data. DW also manages dependency tracking between map objects and has a rudimentary form of version control. It is currently used to manage information on the DRD2 region on chromosome 11, and on the HOX region of chromosome 17.

SQLGEN: a framework for rapid client-server database application development

SQLGEN is a framework for rapid client-server relational database application development. It relies on an active data dictionary on the client machine that stores metadata on one or more database servers to which the client may be connected. The dictionary generates dynamic Structured Query Language (SQL) to perform common database operations; it also stores information about the access rights of the user at log-in time, which is used to partially self-configure the behavior of the client to disable inappropriate user actions. SQLGEN uses a microcomputer database as the client to store metadata in relational form, to transiently capture server data in tables, and to allow rapid application prototyping followed by porting to client-server mode with modest effort. SQLGEN is currently used in several production biomedical databases.

Fuzzy classification of hemodynamic trends and artifacts: experiments with the heart rate

Fuzzy set theory allows one to map inexact data, concepts, and events to fuzzy sets via user-defined membership functions. This paper describes a method for (1) robustly estimating the mean and slope of an arbitrary number of data points, (2) developing a set of fuzzy membership functions to classify various properties of heart rate trends, and (3) finding the longest consecutive sequence of heart rate data that fit a particular fuzzy membership function. Preliminary results indicate that fuzzy set theory has significant potential in the development of a clinically robust method for classifying heart rate data, trends, and artifacts.

A parallel implementation of a multi-state Kalman filtering algorithm to detect ECG arrhythmias

Detecting arrhythmias from the electrocardiogram (ECG) is of great importance for the continued development of intelligent cardiovascular monitors (ICM). An ICM's main goal is to present to the clinician a 'high-level' analysis of the patient's condition (e.g., the patient is slightly hypovolemic) based upon 'low-level' physiologic signals (e.g., blood pressure, heart rate, etc.). This paper reports on a parallel implementation of a multi-state Kalman filtering algorithm, within a prototype ICM, to help detect ECG arrhythmias. Preliminary test results show that the parallel, multi-state implementation performed exactly as the original sequential version. Several different rhythm disturbances were correctly identified after 3-5 beats. We conclude that our parallel implementation of the multi-state Kalman filter provides a faster and still reliable means of accurately detecting ECG arrhythmias in real-time.

Online bibliographic information: integration into an emerging IAIMS environment

The Medical Library at Yale University has developed an online free-text database containing Current Contents citations. The database was designed to be integrated into an emerging campus-wide information environment. To this end Current Contents at Yale was designed with a user interface familiar to the Yale community, an alerting service based on electronic mail, and search expansion using the National Library of Medicine's Meta-1 metathesaurus.