The first mitochondrial genome of a South America parthenogenetic lizard (Squamata: Gymnophthalmidae)

The mitogenome of the South American parthenogenetic lizard Loxopholis percarinatum Müller, 1923 (Squamata: Gymnophthalmidae), a uni-bisexual species complex, was recovered for three individuals from Rio Negro region, Amazonas, Brazil. The content and order of genes are typical for vertebrate mitochondrial genomes, and we recovered 13 protein-coding genes, 22 tRNA, and two rRNA (12S and 16S), in addition to partial fragments of the Control Region. A maximum likelihood phylogenetic analysis with mitogenomes of selected lizard families recovered L. percarinatum with Iphisa elegans Gray, 1851, the only other Gymnophthalmidae species available in GenBank.

Implementation of an Execution Engine for SNOMED CT Expression Constraint Language

The need to achieve high levels of semantic interoperability in the health domain is regarded as a crucial issue. Nowadays, one of the weaknesses when working in this direction is the lack of a coordinated use of information and terminological models to define the meaning and content of clinical data. IHTSDO is aware of this problem and has recently developed the SNOMED CT Expression Constraint Language to specify subsets of concepts. In this paper, we describe an implementation of an execution engine of this language. Our final objective is to allow advanced terminological binding between archetypes and SNOMED CT as a fundamental pillar to get semantically interoperable systems. The execution engine is available at http://snquery.veratech.es.

Archetype-based data warehouse environment to enable the reuse of electronic health record data

BACKGROUND

The reuse of data captured during health care delivery is essential to satisfy the demands of clinical research and clinical decision support systems. A main barrier for the reuse is the existence of legacy formats of data and the high granularity of it when stored in an electronic health record (EHR) system. Thus, we need mechanisms to standardize, aggregate, and query data concealed in the EHRs, to allow their reuse whenever they are needed.

OBJECTIVE

To create a data warehouse infrastructure using archetype-based technologies, standards and query languages to enable the interoperability needed for data reuse.

MATERIALS AND METHODS

The work presented makes use of best of breed archetype-based data transformation and storage technologies to create a workflow for the modeling, extraction, transformation and load of EHR proprietary data into standardized data repositories. We converted legacy data and performed patient-centered aggregations via archetype-based transformations. Later, specific purpose aggregations were performed at a query level for particular use cases.

RESULTS

Laboratory test results of a population of 230,000 patients belonging to Troms and Finnmark counties in Norway requested between January 2013 and November 2014 have been standardized. Test records normalization has been performed by defining transformation and aggregation functions between the laboratory records and an archetype. These mappings were used to automatically generate open EHR compliant data. These data were loaded into an archetype-based data warehouse. Once loaded, we defined indicators linked to the data in the warehouse to monitor test activity of Salmonella and Pertussis using the archetype query language.

DISCUSSION

Archetype-based standards and technologies can be used to create a data warehouse environment that enables data from EHR systems to be reused in clinical research and decision support systems. With this approach, existing EHR data becomes available in a standardized and interoperable format, thus opening a world of possibilities toward semantic or concept-based reuse, query and communication of clinical data.

Using archetypes for defining CDA templates

While HL7 CDA is a widely adopted standard for the documentation of clinical information, the archetype approach proposed by CEN/ISO 13606 and openEHR is gaining recognition as a means of describing domain models and medical knowledge. This paper describes our efforts in combining both standards. Using archetypes as an alternative for defining CDA templates permit new possibilities all based on the formal nature of archetypes and their ability to merge into the same artifact medical knowledge and technical requirements for semantic interoperability of electronic health records. We describe the process followed for the normalization of existing legacy data in a hospital environment, from the importation of the HL7 CDA model into an archetype editor, the definition of CDA archetypes and the application of those archetypes to obtain normalized CDA data instances.

Premenstrual asthma and atopy markers

BACKGROUND

The frequency of atopy in women with premenstrual asthma (PMA) and its possible effect on the premenstrual exacerbation of asthma are unknown.

OBJECTIVE

To analyze the relation between atopy markers (total IgE, Phadiatop, and specific IgE) and PMA.

METHODS

Asthmatic women of reproductive age completed a questionnaire about respiratory symptoms and recorded peak flow during an entire menstrual cycle to be classified as asthmatic patients with or without PMA. Their asthma severity was graded according to the 2005 Global Initiative for Asthma scale. PMA was defined as a clinical or functional exacerbation (>or=20%) in the premenstrual phase compared with the preovulatory phase. Blood tests for several atopy markers were conducted for: total IgE and screening for aeroallergens (Phadiatop) and specific IgE.

RESULTS

Blood determinations were performed in 59 asthmatic women, of whom 31 (53%) had PMA. Twenty-six patients with PMA (84%) and 12 without PMA (43%) had total IgE values greater than 100 kU/L (P=.001). Twenty-one patients with PMA (68%) and 14 without PMA (50%) tested positive for Phadiatop (P=.17). Those who were positive for Phadiatop were also tested for specific IgE. No relation was found between specific IgE and PMA; values for ryegrass (63%), olive (60%), and Dermatophagoides pteronyssinus (54%) exceeded 0.35 kU/L.

CONCLUSIONS

PMA seems to be closely linked to total IgE levels but not to specific allergens. The atopy affects the clinical manifestations of PMA in women of reproductive age.

Premenstrual asthma and symptoms related to premenstrual syndrome

BACKGROUND

It is unclear whether premenstrual asthma is associated with premenstrual syndrome. The objective of this study is to compare premenstrual symptoms among asthmatic women according to whether they have premenstrual asthma or not.

METHODS

A questionnaire on respiratory symptoms during a single menstrual cycle was developed for asthmatics of fertile age, together with another on symptoms related to premenstrual syndrome. These included dysphoric-psychiatric symptoms (anxiety, depression, fatigue, irritability, and mood swings), edematous symptoms (abdominal and mammary tension, swelling, acne, and migraine), and other symptoms (leg pains, nausea, sweating, vomiting, and tiredness). Morning and evening peak flow scores were collected to evaluate lung function. Premenstrual asthma was determined to be a ≥ 20% objective exacerbation in the premenstrual phase over the preovulatory phase in terms of both respiratory symptoms and/or peak flow. The intensity of the change in symptoms was evaluated according to the effect size.

RESULTS

The study examined 103 patients of fertile age, 46 of whom (44.7%) presented with premenstrual asthma. Practically all of the monitored symptoms increased in the premenstrual phase with respect to the preovulatory phase. This increase was greater in women with premenstrual asthma, especially for abdominal tension (effect size .88 against .33; p = .009) and mammary tension (.95 against .49; p = .018).

CONCLUSIONS

A clear link was found between premenstrual asthma and the premenstrual exacerbation of dysphoric symptoms, and certain edematous symptoms such as abdominal and mammary tension as well as a swelling sensation.

CEN EN13606 normalisation framework implementation experiences

Since the approval of the CEN EN13606 norm for the electronic health record communication, a growing interest around the application of this specification has emerged. The main objective of the norm is to serve as a mechanism to achieve the semantic interoperability of clinical data. This will require an effort to use common terminologies, to normalise the clinical knowledge domain and to combine all these formalisations with the existing information systems. This paper presents a methodology and developed tools to reach the seamless semantic interoperability of health data in legacy systems and several study cases where the developed framework has been applied.

Association between modelled traffic-related air pollution and asthma score in the ECRHS

The aim of our analysis was to study the association between air pollution and asthma among adults. For this goal, a previously developed "asthma score" was used. Persons aged 25-44 yrs were randomly selected (1991-1993) and followed up (2000-2002) within the European Community Respiratory Health Survey (ECRHS I and II, respectively). The asthma score was defined from 0 to 5, based on the positive answers to the following symptoms reported for the last 12 months: wheeze/breathlessness, chest tightness, dyspnoea at rest, dyspnoea after exercise and woken by dyspnoea. Participants' home addresses were linked to outdoor modelled NO2 estimates for 2001. Negative binomial regression was used to model the asthma score. The score from ECRHS II was positively associated with NO2 (ratio of the mean asthma score (RMS) 1.23, 95% CI 1.09-1.38, for an increase of 10 microg x m(-3)). After excluding participants with asthma and symptoms at baseline, the association remained (RMS 1.25, 95% CI 1.05-1.51), and was particularly high among those reporting a high score in ECRHS II. The latter probably reflects incident cases of asthma. Our results suggest that traffic-related pollution causes asthma symptoms and possibly asthma incidence in adults. The asthma score offers an alternative with which to investigate the course and aetiology of asthma in adults.

Non-invasive lightweight integration engine for building EHR from autonomous distributed systems

In this paper we describe Pangea-LE, a message-oriented lightweight data integration engine that allows homogeneous and concurrent access to clinical information from disperse and heterogeneous data sources. The engine extracts the information and passes it to the requesting client applications in a flexible XML format. The XML response message can be formatted on demand by appropriate Extensible Stylesheet Language (XSL) transformations in order to meet the needs of client applications. We also present a real deployment in a hospital where Pangea-LE collects and generates an XML view of all the available patient clinical information. The information is presented to healthcare professionals in an Electronic Health Record (EHR) viewer Web application with patient search and EHR browsing capabilities. Implantation in a real setting has been a success due to the non-invasive nature of Pangea-LE which respects the existing information systems.

[Association between the forced midexpiratory flow/forced vital capacity ratio and bronchial hyperresponsiveness]

OBJECTIVE

A long-standing hypothesis is that a low ratio of airway caliber to lung size is associated with bronchial hyperresponsiveness (BHR). The aim of our study was to measure the association between airway caliber relative to lung size (expressed as the ratio between forced expiratory flow, midexpiratory phase, divided by forced vital capacity [FEF(25%-75%)/FVC]) and BHR measured by a methacholine challenge test, adjusting for age, height, sex, smoking history, geographic area, respiratory symptoms, and baseline forced expiratory volume in 1 second (FEV1).

MATERIAL AND METHODS

We carried out a multicenter cross-sectional study of the general Spanish population in 2647 subjects from the European Community Respiratory Health Survey (ECRHS I). The ECRHS questionnaire was administered, total and specific immunoglobulin E were measured, and skin tests, spirometry, and a methacholine challenge test were performed.

RESULTS

We show the relationship of the various clinical and sociodemographic variables with the 2 parameters indicative of a positive methacholine test. The lower the FEF(25%-75%)/FVC ratio was, the greater the risk of HRB, after adjustment for variables (odds ratio [OR]=0.09; 95% confidence interval [CI], 0.04-0.018 for the concentration provoking a 20% decrease in FEV1, and OR=0.06; 95% CI, 0.03-0.12 for the dose provoking a 20% decrease in FEV1).

CONCLUSIONS

There is a significant association between the FEF(25%-75%)/FVC ratio and BHR after adjustment for age, atopy, smoking, geographic area, respiratory symptoms, and initial FEV1.

Incidence of asthma and its determinants among adults in Spain

The objective was to measure the incidence of asthma and its determinants in Spain, where the prevalence of asthma is low to medium. A follow-up of subjects participating in the European Community Respiratory Health Survey (ECRHS) was conducted in 1998- 1999 (n = 1,640, 85% of those eligible). Subjects were randomly selected from the general population and were 20 to 44 yr old in 1991-1993. Time of follow-up was on average 6.75 yr (range, 5.3 to 7.9 yr). Asthma was defined as reporting ever having had asthma. The incidence of asthma was 5.53 (95% confidence interval, 4.28- 7.16) per 1,000 person-years (6.88 in females, 4.04 in males). Incidence was highest in subjects who at the baseline survey had bronchial hyperresponsiveness (incidence rate ratio [IRR], 3.85), in those with positive IgE against timothy grass (IRR, 3.16), and in females (IRR, 1.80). These results persisted after adjusting for respiratory symptoms at baseline. There was no significant association (p < 0.2) with high total serum IgE, atopy defined by reactivity to any allergen, smoking, occupational exposure, or maternal asthma. A sensitivity analysis using four definitions of population at risk yielded incidence rates varying from 5.53 to 1.50. In this population of subjects without self-reported asthma or asthma-type symptoms at baseline, bronchial hyperresponsiveness and IgE reactivity to grass appeared as the main determinants of new asthma.

[Factors associated with the development of atopy in young adults]

BACKGROUND

To determine the risk factors for the development of atopy in Spanish young adults.

SUBJECTS AND METHODS

Case-control study over prevalent cases. Carried out in general population between the ages of 20 to 44 years old. Spanish participants of the ECRHS, a random representative sample of Spanish young adults (n = 16,884), and a 20% randomised subsample made by those who answered to a short respiratory questionnaire and had atopy assessed, was studied. Atopy was defined as having serum specific IgE positivity to the following aeroallergnes: cat dander, Cladosporium herbarum, Dermatophagoides pteronyssinus, Parietaria judaica and Phleum pratense.

RESULTS

Several factors had a statistically significant effect. In addition to male gender and lower age, maternal allergy (OR = 1.63; 95% CI = 1.11-2.40), having allergic siblings (OR = 1.40; 95% CI = 1.06-1.90) and a higher educational level (OR = 1.69; 95% CI = 1.22-2.34) were associated with the presence of high levels of specific IgE in our sample. Moreover, having had older siblings, especially older brothers appears to be a protective factor to the development of atopy but not in a statistically significant way, while having had pet birds during childhood appears to enhance the risk.

CONCLUSIONS

In addition to the familial variables that indicates both environmental and genetic factors, educational level seems to have low degree of association with atopy; this feature shows that variables related with life style are involved in atopy development.

Relationship between bacterial flora in sputum and functional impairment in patients with acute exacerbations of COPD. Study Group of Bacterial Infection in COPD

STUDY OBJECTIVES

To investigate the possible relationship between functional respiratory impairment measured by FEV1 and isolation of diverse pathogens in the sputum of patients with exacerbations of COPD.

DESIGN

Multicenter, cross-sectional, epidemiologic study.

SETTING

Pneumology units in six secondary or tertiary hospitals in Spain.

PATIENTS

Ninety-one patients with acute exacerbation of COPD were included.

INTERVENTIONS

A quantitative sputum culture was performed, and bacterial growth was considered significant only when the germ was isolated at concentrations > 10(6) cfu (> 10(5) for Streptococcus pneumoniae) in samples with < 10 epithelial cells and > 25 leukocytes per low magnification field (x 100).

RESULTS

Germs isolated were the following: Haemophilus influenzae (20 cases; 22%), Pseudomonas aeruginosa (14 cases; 15%), S. pneumoniae (9 cases; 10%), Moraxella catarrhalis (8 cases; 9%), other gram-negative bacteria (7 cases; 7%), and non-potentially pathogenic microorganisms (non-PPMs; 33 cases; 36%). P. aeruginosa and H. influenzae were isolated more frequently among the patients with FEV1 < 50% than among those with FEV1 > 50% (p < 0.05). All patients with P. aeruginosa in sputum had FEV1 < 1,700 mL. FEV1 < 50% was associated with a very high risk of P. aeruginosa or H. influenzae isolation: the odds ratios (ORs) are 6.62 (95% confidence interval [CI], 1.2 to 123.6) and 6.85 (95% CI, 1.6 to 52.6), respectively. Furthermore, active tobacco smoking was associated with a high risk of H. influenzae isolation (OR, 8.1; 95% CI, 1.9 to 43.0).

CONCLUSIONS

Patients with the greatest degree of functional impairment, as measured by their FEV1, presented a higher probability of having an isolation of P. aeruginosa or H. influenzae in significant concentrations in sputum during an exacerbation. The diagnostic yield of sputum in patients with an FEV1 > 50% was low, with a predominance of non-PPMs. Low FEV1 and active tobacco smoking are data that should be considered when establishing an empiric antibiotic treatment for exacerbated COPD.

Pulmonary ventilatory defects and occupational exposures in a population-based study in Spain. Spanish Group of the European Community Respiratory Health Survey

We assessed the association between occupational exposures and symptoms of chronic bronchitis and pulmonary ventilatory defects in a general population-based study of five areas in Spain. This study forms part of the European Community Respiratory Health Study (ECRHS). Subjects (n = 1,735; age range, 20-44 yr; 52.4% of those initially selected) completed a respiratory questionnaire on symptoms and occupation and underwent baseline spirometry. Occupation was translated with an ad hoc developed job-exposure matrix (EM) into none, low, and high exposure to biological dust, mineral dust, and gases and fumes. Exposure to high levels of biological dust was associated with cough for more than 3 mo (odds ratio [OR], 1.9; p = 0.07), a reduction in FEF(25-27) to 478 ml/s (SD 178), and a reduction in FEV1 to 151 mL (SD 71). These associations remained after excluding subjects with asthma symptoms or bronchial responsiveness. Smokers tended to have a higher risk for respiratory symptoms, but smoking did not modify the association of occupation with pulmonary function. Exposure to mineral dust and gases/fumes was less consistently related to pulmonary function or to respiratory symptoms and this association further decreased after excluding subjects with asthma. In conclusion, exposure to high levels of biological dust in young adults is associated with symptoms of chronic bronchitis and pulmonary ventilatory defects, independently of asthma and smoking.

Risk factors for asthma in young adults. Spanish Group of the European Community Respiratory Health Survey

We assessed the association of asthma prevalence in young adults with susceptibility factors and environmental exposures, taking into account the age at asthma onset. A random sample of the general population, aged 20-44 yrs, in five areas of Spain (Albacete, Barcelona, Galdakao, Huelva, and Oviedo) was selected in the frame of the European Community Respiratory Health Survey (ECRHS). Overall, 2,646 subjects (response rate = 60.9%) responded to a respiratory questionnaire and 1,797 (41.4%) finalized a bronchial challenge. Atopy to perennial (odds ratio (OR) = 10.2, 95% confidence interval 4.2-25) and seasonal allergens (11.5, 4.6-28), parental asthma (4.5, 2.5-8.4), and birth order (OR for no older siblings in comparison to having more than two = 3.2, 1.2-9.1) were associated with current asthma whatever the age of asthma onset. Past asthma was associated to a lesser extent with atopy (OR around 3.5 to both perennial and seasonal allergens). Lower respiratory tract infections before the age of 5 yrs (LRTI), having had a pet in childhood, and being born in a younger cohort were associated with asthma starting before the age of 15 yrs, but not after. Male gender was more frequent in childhood asthma and female gender in adulthood. In addition to the known risk factors of asthma (atopy to perennial allergens, parental asthma) we provide evidence for an association of asthma (whatever the age of onset) with sensitization to seasonal allergens, and having less than three older siblings; and for an association of childhood asthma with lower respiratory tract infections.

Atopy and nonspecific bronchial responsiveness. A population-based assessment. Spanish Group of the European Community Respiratory Health Survey

The relative importance of specific immunoresponse in explaining nonspecific bronchial responsiveness (BR) has scarcely been examined. We provide quantitative estimates of the proportion of BR attributable to specific atopy to different common aeroallergens. We used data from a cross-sectional study on a random sample of the general population 20 to 44 yr of age from five Spanish areas. There were 1,816 participants who performed a methacholine challenge and had atopy assessed. BR was defined as a 20% or more fall in FEV1. Atopy was assessed by measuring serum-specific IgE or skin tests to cat, Dermatophagoides pteronyssinus, Cladosporium, Alternaria, timothy grass, olive, birch, Parietaria, or ragweed. The strongest associations between BR and specific IgE response were against timothy grass (prevalence rate ratio = 1.78; 95% confidence interval 1.2 to 2.6), Dermatophagoides pteronyssinus = 1.64 (1.2 to 2.2), and olive = 2.36 (1.5 to 3.7), all after adjustment by age, sex, area of residence, smoking, and a positive response to any of the other eight allergens measured. The population attributable risk of BR for a positive response to any of the nine allergens measured was 20.96% (10.2 to 43.2%) when adjusting for area of residence, age, sex, and smoking. Nonspecific bronchial responsiveness in the general population was found to be related to atopy against single specific allergens, but the population risk attributable to atopy may be lower than previously suggested.

Leishmaniasis eco-epidemiology in the Alpujarra region (Granada Province, southern Spain)

An eco-epidemiological study was carried out in the region of the Alpujarras (southern Spain, Granada province). Nine villages were chosen at random in 5 bioclimatic zones. A study of leishmaniasis in the canine and human populations, was carried out concentrating especially upon schoolchildren. A total of 615 dogs were screened, which represents almost 100% of the canine census. Of the screened dogs, 33 showed an antibody titer > or = 1/160 when tested by IFA (seroprevalence of 5.3%). Age, sex, activity, and clinical symptoms of each dog were taken into account. Among the human population, infection from Leishmania was studied using the Leishmanin skin test (LST). Of 1286 people who were tested, 568 (44.16%) were positive. Most of the subjects were schoolchildren (878; practically 100% of the pupils), of whom 288 (32.8%) tested positive. A close relation was seen to exist between the percentage of positive LST's and age. Finally, a close relationship was also observed between canine seroprevalence and percentage of schoolchildren who tested positive in the LST, in the 5 bioclimatic zones under consideration.

Valvular dysfunction due to the obstruction of the ventricular catheter caused by cysticercus cyst

Five patients were studied with the diagnosis of secondary hydrocephaly to neurocysticercosis. Valvular dysfunction was observed due to the obstruction of the ventricular catheter caused by cysticercus cysts. The Biomed System was used in four cases and the Hakim System in one. Valvular dysfunction was observed in patients within a period of 18 to 24 months after derivation, they also had a history of several valvular dysfunctions. The diagnosis was made upon extraction of the catheter where the cyst was found to be attached to the ventricular brush. Subsequent evolution has not been satisfactory. The reasons for this complication are of a hydrodynamic and pharmacological nature and are also due to the growth of the cyst. This complication is not often suspected, therefore we recommend that in cases of frequent valvular dysfunction and asymmetrical hydrocephaly, studies like iodine-tomography or magnetic resonance be carried out in order to rule out this factor.

[Management using nimodipine of cerebral vasospasm secondary to subarachnoid hemorrhage caused by rupture of an intracranial aneurysm]

The cerebral vasospasm secondary to subarachnoid hemorrhage due to the rupture of an intracranial aneurysm has a high morbidity/mortality. Its cause is still unknown, so we obtain controversial results after prevention and treatment. We studied two groups, of 29 patients each one, where the first was treated with systemic nimodipine, and the second was the control group. We did not observed any correlation between the clinic vasospasm or the symptomatic, and the radiographic one. There was no difference between the final results of both groups. No collateral effects were shown in other organs with the use of this agent.

Obstruction of the ventricular catheter of a CSF shunt system due to the own cyst of Taenia solium

Five patients were studied who suffered secondary hydrocephalus due to neurocysticercosis. Shunt dysfunction was due to the obstruction of the ventricular catheter caused by the own cysticercus cysts. The Biomed system was used in four cases and the Hakim system in one. Valvular dysfunction was observed in patients within a period of 18 to 24 months after surgery, they had a history of several valvular dysfunctions. The diagnosis was made upon of extracting the catheter where the cyst was found to be attached to the ventricular brush. Subsequent evolution has not been satisfactory. The reasons for this complication are of a hydrodynamic and pharmacological nature and are also due to the growth of the cyst. This complication is not often suspected, therefore we recommend that in case of frequent valvular dysfunctions and asymmetrical hydrocephalus, studies like iodinetomography or magnetic resonance imaging be carried out in order to discard this possibility.