Biomedical informatics publications: a global perspective: part I: conferences

BACKGROUND

In the past decade, Medical Informatics (MI) and Bioinformatics (BI) have converged towards a new discipline, called Biomedical Informatics (BMI) bridging informatics methods across the spectrum from genomic research to personalized medicine and global healthcare. This convergence still raises challenging research questions which are being addressed by researchers internationally, which in turn raises the question of how biomedical informatics publications reflect the contributions from around the world in documenting the research.

OBJECTIVES

To analyse the worldwide participation of biomedical informatics researchers from professional groups and societies in the best-known scientific conferences in the field. The analysis is focused on their geographical affiliation, but also includes other features, such as the impact and recognition of the conferences.

METHODS

We manually collected data about authors of papers presented at three major MI conferences: Medinfo, MIE and the AMIA symposium. In addition, we collected data from a BI conference, ISMB, as a comparison. Finally, we analyzed the impact and recognition of these conferences within their scientific contexts.

RESULTS

Data indicate a predominance of local authors at the regional conferences (AMIA and MIE), whereas other conferences with a world-wide scope (Medinfo and ISMB) had broader participation. Our analysis shows that the influence of these conferences beyond the discipline remains somewhat limited.

CONCLUSIONS

Our results suggest that for BMI to be recognized as a broad discipline, both in the geographical and scientific sense, it will need to extend the scope of collaborations and their interdisciplinary impacts worldwide.

Food anaphylaxis in antiphospholipid syndrome and thrombosis

BACKGROUND

We have observed that some cases of food anaphylaxis were followed by severe thrombosis associated to anticardiolipin antibodies. Food anaphylaxis associated with antiphospholipid syndrome has seldom been published.

OBJECTIVE

The aims were: 1) to test anticardiolipin antibodies in an important number of patients with anaphylaxis due to vegetal foods and their relationship with possible thrombosis; and 2) to study seed and fruit hypersensitivity in patients with previous thrombotic events associated with antiphospholipid antibodies (aCL).

METHODS

We included 30 patients diagnosed of thrombosis associated with aCL, 52 patients who suffered from anaphylaxis due to seeds or fruits, and 120 control patients. Haematological, cardiopulmonary vascular and rheumatologic studies had been performed as needed. In vivo and in vitro allergy tests with a large battery of vegetal allergens were carried out in all the patients. Measurement of IgG aCL antibodies and specific IgE to vegetal food was done by ELISA and CAP-FEIA (Phadia). Immunodetection and inhibitions with lipoproteins belonging to seeds were performed.

RESULTS

Seventy-five percent of the patients diagnosed as having antiphospholipid primary syndrome had specific IgE against different proteins from different vegetable allergens, most of them seeds, and clearly against lipoproteins that were also recognised by the patients with food anaphylaxis but not by the control cases. Among the patients with anaphylaxis, 28% had anticardiolipin antibodies and 17.3% thrombosis.

CONCLUSION

Our study suggests that seed lipoproteins which cause severe food anaphylaxis might have a potential role in the antiphospholipid syndrome and related thrombosis.

Ambulatory blood pressure monitoring in renal transplant patients: should it be routinely performed?

INTRODUCTION

Arterial hypertension is common among kidney transplant patients. It increases cardiovascular risk and is a factor for progression of renal failure. Our objective was to perform ambulatory blood pressure monitoring (ABPM) in renal transplant patients with office hypertension.

METHODS

Patients were divided into 2 groups according to their mean ABPM blood pressures with treatment: well-controlled hypertension (blood pressure [BP] <130/85 mmHg), and poorly controlled hypertension (BP>130/85 mmHg). A "nondipper pattern" was defined as a decrease of <10% or an increase, and a "raiser pattern," in which mean blood pressure was greater during the nocturnal than the diurnal period. "White coat effect" was considered when the mean of 3 BP measurements in the clinic was >140/90 mmHg among well-controlled hypertensive patients as documented by ABPM.

RESULTS

ABPM was performed in 53 patients: 25 (47%) "well-controlled hypertensives" and 28 (53%) "poorly controlled hypertensives." Of the latter, 24 (85%) showed a nondipper or raiser pattern with only 4 revealing dipper patterns. We compared well-controlled with poorly controlled hypertensives. The latter cohort were older (54.4±9.3 vs 45.5±13.8 years; P=.009), received grafts from older donors (56.7±15.0 vs 45.8±17 years; P=.02); had worse renal function measured by serum creatinine (1.7±0.5 vs 1.4±0.4 mg/dL, P=.03) or the Modification of Diet in Renal Disease (MDRD)=4 formula (41.8±14.0 vs 55.4±20.5 mL/min/1.73 m2; P=.009), and displayed more proteinuria (0.30±0.33 vs 0.18±0.10 g/d, P=.08). Nondipper or raiser patients showed a higher mean body mass index (27.1 vs 21.7 kg/m2; P=.04). Among 25 well-controlled patients, 11 presented "white coat phenomenon."

CONCLUSION

We observed an important "white coat" effect, a large prevalence of uncontrolled nocturnal hypertension, and a small but important incident of "masked hypertension." Factors related to hypertension control were patient age, donor age, renal function, induction use, and proteinuria.

Biomedical ontologies: toward scientific debate

OBJECTIVES

Biomedical ontologies have been very successful in structuring knowledge for many different applications, receiving widespread praise for their utility and potential. Yet, the role of computational ontologies in scientific research, as opposed to knowledge management applications, has not been extensively discussed. We aim to stimulate further discussion on the advantages and challenges presented by biomedical ontologies from a scientific perspective.

METHODS

We review various aspects of biomedical ontologies going beyond their practical successes, and focus on some key scientific questions in two ways. First, we analyze and discuss current approaches to improve biomedical ontologies that are based largely on classical, Aristotelian ontological models of reality. Second, we raise various open questions about biomedical ontologies that require further research, analyzing in more detail those related to visual reasoning and spatial ontologies.

RESULTS

We outline significant scientific issues that biomedical ontologies should consider, beyond current efforts of building practical consensus between them. For spatial ontologies, we suggest an approach for building "morphospatial" taxonomies, as an example that could stimulate research on fundamental open issues for biomedical ontologies.

CONCLUSIONS

Analysis of a large number of problems with biomedical ontologies suggests that the field is very much open to alternative interpretations of current work, and in need of scientific debate and discussion that can lead to new ideas and research directions.

International efforts in nanoinformatics research applied to nanomedicine

BACKGROUND

Nanomedicine and nanoinformatics are novel disciplines facing substantial challenges. Since nanomedicine involves complex and massive data analysis and management, a new discipline named nanoinformatics is now emerging to provide the vision and the informatics methods and tools needed for such purposes. Methods from biomedi-cal informatics may prove applicable with some adaptation despite nanomedicine involving different biophysical and biochemical characteristics of nanomaterials and corresponding differences in information complexity.

OBJECTIVES

We analyze recent initiatives and opportunities for research in nanomedicine and nanoinformatics as well as the previous experience of the authors, particularly in the context of a European project named ACTION-Grid. In this project the authors aimed to create a collaborative environment in biomedical and nanomedical research among countries in Europe, Western Balkans, Latin America, North Africa and the USA.

METHODS

We review and analyze the rationale and scientific issues behind the new fields of nanomedicine and nanoinformatics. Such a review is linked to actual research projects and achievements of the authors within their groups.

RESULTS

The work of the authors at the intersection between these two areas is presented. We also analyze several research initiatives that have recently emerged in the EU and USA context and highlight some ideas for future action at the international level.

CONCLUSIONS

Nanoinformatics aims to build new bridges between medicine, nanotechnology and informatics, allowing the application of computational methods in the nano-related areas. Opportunities for world-wide collaboration are already emerging and will be influential in advancing the field.

Impact of fugitive emissions in ambient PM levels and composition: a case study in Southeast Spain

The results of this study show the high impact that anthropogenic fugitive emissions of mineral dust have on air quality (levels of PM(10), PM(2.5) and some metals) in a region in SE Spain named L'Alacantí. This could be extensive to other areas of Europe with similar characteristics. Fugitive emissions, such as those arising from large public construction works, cement and ceramic manufacturing, mining, heavy industries, handling and transport of powdered raw materials and road dust, are very often left out of emission monitoring and inspections in Europe. The comparative study of daily PM(10) series in the area shows how the increase of annual average PM(10) concentrations over 40 microg/m(3) is due to extreme episodes occurring in 2006 and 2007, at a regional scale, given the simultaneous recording of PM episodes at distant monitoring sites. The annual average values of the PM(10) concentrations were close to or slightly higher than 40 microg/m(3) (limit value of Directive 2008/50/CE) during 2006-2007 (Alicante-University 39-41, Agost 40-42, Sant Vicent 42-46, Alicante-El Plà 40-42 microg/m(3)). The main PM(10) sources in the zone were identified with the assistance of the PMF receptor model. Six common factors were determined, mineral as a main source (37% at Agost and 32% at Sant Vicent), road traffic, secondary sulfate, petroleum coke, sea spray and industry. Mineralogical studies, with XRD and SEM-EDX techniques, support the hypothesis that the highest PM episodes are associated to fugitive emissions of mineral matter. Despite the fact that L'Alacantí region is a heavily industrialized area with two cement plants and a significant number of ceramic manufacturing plants, the fugitive emissions may have accounted for the exceedances of the PM limit values during these two years, part of them caused by the construction of a highway. These results may contribute to the interpretation of prior studies on source apportionment carried out in Southern Europe, with very high loads of anthropogenic dust in PM(10) and PM(2.5).

Integration of relational and textual biomedical sources. A pilot experiment using a semi-automated method for logical schema acquisition

OBJECTIVES

Bringing together structured and text-based sources is an exciting challenge for biomedical informaticians, since most relevant biomedical sources belong to one of these categories. In this paper we evaluate the feasibility of integrating relational and text-based biomedical sources using: i) an original logical schema acquisition method for textual databases developed by the authors, and ii) OntoFusion, a system originally designed by the authors for the integration of relational sources.

METHODS

We conducted an integration experiment involving a test set of seven differently structured sources covering the domain of genetic diseases. We used our logical schema acquisition method to generate schemas for all textual sources. The sources were integrated using the methods and tools provided by OntoFusion. The integration was validated using a test set of 500 queries.

RESULTS

A panel of experts answered a questionnaire to evaluate i) the quality of the extracted schemas, ii) the query processing performance of the integrated set of sources, and iii) the relevance of the retrieved results. The results of the survey show that our method extracts coherent and representative logical schemas. Experts' feedback on the performance of the integrated system and the relevance of the retrieved results was also positive. Regarding the validation of the integration, the system successfully provided correct results for all queries in the test set.

CONCLUSIONS

The results of the experiment suggest that text-based sources including a logical schema can be regarded as equivalent to structured databases. Using our method, previous research and existing tools designed for the integration of structured databases can be reused - possibly subject to minor modifications - to integrate differently structured sources.

Vitrification: an effective new approach to oocyte banking and preserving fertility in cancer patients

INTRODUCTION

Oocyte cryopreservation is a useful tool for preserving the fertility of cancer patients at risk of losing ovarian function due to undergoing potentially sterilising therapies. Results obtained with different cryopreservation protocols have been disappointing, particularly those obtained with slow cooling procedures. The efficacy of vitrification as an application in clinical practice has recently been demonstrated. The aim of this study is to report results obtained with the Cryotop method of oocyte vitrification in a population of healthy women and to point out its potential usefulness for fertility preservation in oncological patients.

MATERIALS AND METHODS

The study population consisting of non-oncological patients included 47 oocyte donors and 57 recipients undergoing an oocyte donation cycle of assisted reproductive technology (ART). A total of 693 mature metaphase II oocytes were collected following ovarian stimulation using long protocol down-regulation plus gonadotropin administration. Vitrification was carried out by means of the Cryotop method. Oocytes were donated to a compatible recipient after endometrial preparation.

RESULTS

Of the 693 oocytes, 666 (96.1%) survived. A total of 487 (73.1%) were fertilised successfully. One hundred and seventeen embryos were transferred to 57 recipients. Pregnancy rate per transfer and implantation rates were 63.2% and 38.5% respectively. Twenty-eight healthy babies were later born.

CONCLUSIONS

Oocyte cryo-banking by means of the Cryotop vitrification method represents a viable option for healthy women, producing excellent survival rates and a clinical outcome similar to that obtained with fresh oocytes. This approach could potentially be used in cancer patients who want to safeguard their fertility. Cancer patients could potentially benefit from this approach by storing their oocytes before the onset of the oncological therapy.

Treatment of renal transplant failure

INTRODUCTION

Among graft failures beyond months, we performed progressive reduction and complete withdrawal of immunosuppressive drugs and steroids over a period of 6 months.

PATIENTS AND METHODS

We analyzed the treatment and complications associated with all late allograft failures in 34 patients (8.19%) out of 415 patients transplanted from November 1996 to November 2006.

RESULTS

In 21 patients (61.8%), the progressive reduction of immunosuppressive treatment was effective and well tolerated; however, in 13 patients (38.2%) there was rejection of the allograft at 10.74 +/- 8.95 months (0.77-34.80) after the failure. With the reintroduction of these drugs, the rejection was controlled in seven patients, but in the other six we had to embolize the allograft, which had to be repeated in one case. Embolization was well tolerated, but in one case there was migration of one coil to the femoral artery. One patient treated with drug withdrawal experienced emphysematous pyelonephritis after repeated urinary infections, requiring a nephrectomy. Thirteen (38.2%) of the patients with late failures have been admitted for a second transplant; five of them showed HLA sensitization.

CONCLUSIONS

Conservative treatment with progressive withdrawal of immunosuppression was effective and well tolerated in two-thirds of the patients with late renal allograft failure, but one-third of the patients rejected the graft and needed allograft embolization. Infection of the graft and HLA sensitization can complicate the course of these patients.

[Gene expression in obese patients with non-alcoholic steatohepatitis]

Although the molecular basis for the pathophysiology of non-alcoholic steatohepatitis (NASH) is poorly understood, we evaluate the hepatic gene expression of cytokines, chemokines, cell receptors, growth factors, intracellular transducers and extracellular communication proteins in liver tissue of obese patients (with and without NASH), and we determine the specific intrahepatic gene expression profiles associated with histological severe NASH.Thirty-eight obese patients with BMI > 35 were analyzed, who underwent bariatric surgery. Biopsy specimen samples were snap-frozen in liquid nitrogen. Hepatic gene expression was determined in liver biopsy specimens from 3 groups: a) obese patients without NASH (n = 12); b) patients with NASH without fibrosis (n = 13); and c) patients with NASH and fibrosis (n = 13). Genes were considered to be expressed differentially in NASH only if there was a greater than 2-fold difference in abundance of mRNA when compared with each of the control group. These results were confirmed by real-time PCR. Fourteen genes were differentially expressed (10 overexpressed and 4 underexpressed) in patients with NASH. Genes that were significantly overexpressed included prohibitin, TNF, TNF RI (p55), MCSF, R2-TRAIL, b1-CTGF, FGF, VEGF, and BIGH3OBR. Insulin growth factor-1, insulin growth factor-2, interleukin-2 and tyrosine-receptor were underexpressed in NASH patients.

IN CONCLUSION

1. The obese patients with NASH without fibrosis show an overexpression of proinflammatory and proapoptotic genes. Also, the NASH patients with fibrosis show an overexpression of fibrogenic genes, including the leptin receptor Ob-Rb.2. The up-regulated gene expression of prohibitin suggests mitochondrial dysfunction in NASH patients.

Clinical trial: pharmacodynamics and pharmacokinetics of re-treatment with fixed-dose induction of peginterferon alpha-2a in hepatitis C virus genotype 1 true non-responder patients

BACKGROUND

Patients infected with hepatitis C virus genotype 1 who are true non-responders to previous therapy suffer from a very difficult-to-cure disease. New approaches to treatment are necessary.

AIM

To explore the efficacy, pharmacokinetics and safety of fixed-dose induction with peginterferon alpha-2a and ribavirin in this difficult-to-cure population.

METHODS

Seventy-five hepatitis C virus genotype 1 true non-responder patients to a previous interferon-based combination regimen were randomised to receive peginterferon alpha-2a 360, 270 or 180 microg/week for 12 weeks, followed by 180 microg/week for 36 weeks, in combination with ribavirin (1000/1200 mg/day). Peginterferon alpha-2a concentration was measured throughout the study.

RESULTS

Sustained virological response rates were 38%, 30% and 18%, in the 360, 270 and 180 microg/week groups, respectively (relapse rates: 25%, 50% and 64%, respectively). The area under the serum concentration-time curve of peginterferon alpha-2a from 0-12 weeks increased in a dose-dependent manner (P < 0.0001) and was associated with the sustained virological response (odds ratio: 1.35; 95% CI: 0.89, 2.06). The three regimens were equally well tolerated.

CONCLUSION

Fixed-dose induction of peginterferon alpha-2a resulted in increased drug exposure and improved the likelihood of achieving a cure, without compromising safety in hepatitis C virus genotype 1 true non-responder patients.

Neuron-derived orphan receptor-1 (NOR-1) is induced by thrombin and mediates vascular endothelial cell growth

BACKGROUND AND AIM

Neuron-derived orphan receptor-1 (NOR-1) is a transcription factor overexpressed in human atherosclerotic plaques that is involved in vascular smooth muscle cell (VSMC) proliferation. The aim of this study was to analyze the role of NOR-1 in thrombin-induced endothelial cell growth.

RESULTS

Thrombin induced an early and transient up-regulation of NOR-1 in human umbilical vein endothelial cells (HUVEC). NOR-1 up-regulation by thrombin is dependent on multiple pathways, including cytosolic Ca(2+), activation of protein kinase C (PKC), mitogen-activated protein kinase (MAPK) pathways [both extracellular-regulated kinase (ERK) and p38 MAPK], and downstream activation of cAMP response element binding protein (CREB). The critical role of CREB in the induction of NOR-1 by thrombin was demonstrated using a dominant-negative of CREB. By site-direct mutagenesis we identified two CRE sites present at -79 and -53 bp in the NOR-1 promoter involved in the up-regulation of NOR-1 by thrombin. Inhibition of thrombin receptor PAR-1 abolished CREB activation, NOR-1 up-regulation and DNA synthesis (used as an index of cell proliferation). TRAP-6 mimicked both NOR-1 up-regulation and CREB activation induced by thrombin, while PPACK (an irreversible thrombin inhibitor) prevented such an effect. Direct inhibition of thrombin-induced NOR-1 up-regulation, using antisense oligonucleotides or siRNA against NOR-1, reduced DNA synthesis and endothelial cell re-growth after injury in an in vitro model of wound repair.

CONCLUSIONS

These results indicate that NOR-1 up-regulation plays a key role in thrombin-induced endothelial cell growth. Strategies aimed to block NOR-1 could be useful to prevent vascular effects triggered by thrombin.