The ArrayExpress gene expression database: a software engineering and implementation perspective

MOTIVATION: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for microarray data ArrayExpress we had to find novel solutions to many non-trivial software engineering problems. Our experience will be both relevant and useful for most bioinformaticians involved in developing information systems for a wide range of high-throughput technologies. RESULTS: ArrayExpress has been online since February 2002, growing exponentially to well over 10,000 hybridizations (as of September 2004). It has been demonstrated that our chosen design and implementation works for databases aimed at storage, access and sharing of high-throughput data. AVAILABILITY: The ArrayExpress database is available at http://www.ebi.ac.uk/arrayexpress/. The software is open source. CONTACT: ugis@ebi.ac.uk.     

Multiple arrhythmogenic substrate for tachycardia in a patient with frequent palpitations

We report a 26-year-old woman with frequent episodes of palpitation and dizziness. Resting electrocardiography showed no evidence of ventricular preexcitation. During electrophysiologic study, a concealed right posteroseptal accessory pathway was detected and orthodromic atrioventricular reentrant tachycardia incorporating this pathway as a retrograde limb was reproducibly induced. After successful ablation of right posteroseptal accessory pathway, another tachycardia was induced using a concealed right posterolateral accessory pathway in tachycardia circuit. After loss of retrograde conduction of second accessory pathway with radiofrequency ablation, dual atrioventricular nodal physiology was detected and typical atrioventricular nodal reentrant tachycardia was repeatedly induced. Slow pathway ablation was done successfully. Finally sustained self-terminating atrial tachycardia was induced under isoproterenol infusion but no attempt was made for ablation. During 8-month follow-up, no recurrence of symptoms attributable to tachycardia was observed.     

Coexistence of atrioventricular nodal reentrant tachycardia and idiopathic left ventricular outflow-tract tachycardia

Double tachycardia is a relatively rare condition. We describe a 21 year old woman with history of frequent palpitations. In one of these episodes, she had wide complex tachycardia with right bundle branch and inferior axis morphology. A typical atrioventricular nodal tachycardia was induced during electrophysiologic study, aimed at induction of clinically documented tachycardia. Initially no ventricular tachycardia was inducible. After successful ablation of slow pathway, a wide complex tachycardia was induced by programmed stimulation from right ventricular outflow tract. Mapping localized the focus of tachycardia in left ventricular outflow tract and successfully ablated via retrograde aortic approach. During 7 month's follow-up, she has been symptom free with no recurrence. This work describes successful ablation of rare combination of typical atrioventricular nodal tachycardia and left ventricular outflow tract tachycardia in the same patient during one session.     

Metabolic and endocrinologic complications in beta-thalassemia major: a multicenter study in Tehran

ABSTRACT : BACKGROUND : The combination of transfusion and chelation therapy has dramatically extended the life expectancy of thalassemic patients. The main objective of this study is to determine the prevalence of prominent thalassemia complications. METHODS : Two hundred twenty patients entered the study. Physicians collected demographic and anthropometric data and the history of therapies as well as menstrual histories. Patients have been examined to determine their pubertal status. Serum levels of 25(OH) D, calcium, phosphate, iPTH were measured. Thyroid function was assessed by T3, T4 and TSH. Zinc and copper in serum were determined by flame atomic absorption spectrophotometry. Bone mineral density (BMD) measurements at lumbar and femoral regions have been done using dual x-ray absorptiometry. The dietary calcium, zinc and copper intakes were estimated by food-frequency questionnaires. RESULTS : Short stature was seen in 39.3% of our patients. Hypogonadism was seen in 22.9% of boys and 12.2% of girls. Hypoparathyroidism and primary hypothyroidism was present in 7.6% and 7.7% of the patients. About 13 % of patients had more than one endocrine complication with mean serum ferritin of 1678 +/- 955 micrograms/lit. Prevalence of lumbar osteoporosis and osteopenia were 50.7% and 39.4%. Femoral osteoporosis and osteopenia were present in 10.8% and 36.9% of the patients. Lumbar BMD abnormalities were associated with duration of chelation therapy. Low serum zinc and copper was observed in 79.6% and 68% of the study population respectively. Serum zinc showed significant association with lumbar but not femoral BMD. In 37.2% of patients serum levels of 25(OH) D below 23 nmol/l were detected. CONCLUSION : High prevalence of complications among our thalassemics signifies the importance of more detailed studies along with therapeutic interventions.     

ArrayExpress--a public repository for microarray gene expression data at the EBI

ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses the annotation standard Minimum Information About a Microarray Experiment (MIAME) and the associated XML data exchange format Microarray Gene Expression Markup Language (MAGE-ML) and it is designed to store well annotated data in a structured way. The ArrayExpress infrastructure consists of the database itself, data submissions in MAGE-ML format or via an online submission tool MIAMExpress, online database query interface, and the Expression Profiler online analysis tool. ArrayExpress accepts three types of submission, arrays, experiments and protocols, each of these is assigned an accession number. Help on data submission and annotation is provided by the curation team. The database can be queried on parameters such as author, laboratory, organism, experiment or array types. With an increasing number of organisations adopting MAGE-ML standard, the volume of submissions to ArrayExpress is increasing rapidly. The database can be accessed at http://www.ebi.ac.uk/arrayexpress.     

Simultaneous determination of clobazam and its major metabolite in human plasma by a rapid HPLC method

A rapid and specific HPLC method has been developed and validated for simultaneous determination of clobazam, the anticonvulsant agent, and its major metabolite in human plasma. The sample preparation was a liquid-liquid extraction with tuloene yielding almost near 100% recoveries of two compounds. Chromatographic separation was achieved with a Chromolith Performance RP-18e 100 mm x 4.6mm column, using a mixture of a phosphate buffer (pH 3.5; 10mM)-acetonitrile (70:30, v/v), in isocratic mode at 2 ml/min at a detection wave-length of 228 nm. The calibration curves were linear (r(2)>0.998) in the concentration range of 5-450 ng ml(-1). The lower limit of quantification was 5 ng ml(-1) for two compounds studied. The within- and between-day precisions in the measurement of QC samples at four tested concentrations were in the range of 0.89-9.1% and 2.1-10.1% R.S.D., respectively. The developed procedure was applied to assess the pharmacokinetics of clobazam and its major metabolite following administration of a single 10mg oral dose of clobazam to healthy volunteers.     

On a Poorly Known Rookery of Green Turtles (<Emphasis Type="Italic">Chelonia mydas</Emphasis>) Nesting at the Chabahar Beach,Northeastern Gulf of Oman

There is a poorly known rookery of green turtles (Chelonia mydas) nesting in sandy beaches of Chabahar town, northeastern Gulf of Oman, Iran.This study has been carried out to evaluate nesting activity of this small rookery in 2014 nesting season (June to October). In this study, total clutches were collected and transferred to an artificial hatchery. The peak of nesting occurred from the third parts of August to the end of September. Mean CCL was 106.3 ± 6 cm and mean CCW was 94.5 ± 5 cm. Females laid on average of 99.42 ± 47.8 eggs per clutch. The mean inter-nesting interval was 18.5 days. The observed clutch frequency was 3.4. Mean hatching success was 36.63 ± 4.1%. The incubation period was 61.07 ± 5.4 days. Nest status evaluation represented that major causes for the failure was unhatched egg with no obvious embryo followed by unhatched eggs with obvious but undeveloped embryos > unhatched eggs with developed embryos > hatched eggs but dead embryos. The results achieved in this study are a valuable contribution to cognition of the reproductive ecology of the green turtle population globally and regionally.     

Mitochondrial DNA Polymorphism in Populations of the Caspian Region and Southeastern Europe

Mitochondrial DNA (mtDNA) restriction polymorphism was examined in Turkmens, Eastern Iranians, and Ukrainians. The gene pools of all populations studied were characterized by the presence of European mtDNA lineages. Mongoloid component observed in Turkmen and Iranian populations with the frequencies of about 20% was represented by groups C, D, and E/G in Turkmens, and by M*, D, A, and B in Iranians. The relative positions of the populations studied, of populations from the Caucasus, Western Iran, and Russian populations from the Krasnodar krai and Belgorod oblast in the space of principal components revealed a geographically specific pattern of the population clustering. The data on mtDNA polymorphism indicated pronounced differentiation of Eastern and Western Iranians. The latter were characterized by a mtDNA group composition similar to that in Eastern Slavs. The historical role of the Caspian populations in the formation of the population of Southeastern Europe is discussed.