BioC interoperability track overview

BioC is a new simple XML format for sharing biomedical text and annotations and libraries to read and write that format. This promotes the development of interoperable tools for natural language processing (NLP) of biomedical text. The interoperability track at the BioCreative IV workshop featured contributions using or highlighting the BioC format. These contributions included additional implementations of BioC, many new corpora in the format, biomedical NLP tools consuming and producing the format and online services using the format. The ease of use, broad support and rapidly growing number of tools demonstrate the need for and value of the BioC format.

Database URL:http://bioc.sourceforge.net/

An analysis on the entity annotations in biological corpora

Collection of documents annotated with semantic entities and relationships are crucial resources to support development and evaluation of text mining solutions for the biomedical domain. Here I present an overview of 36 corpora and show an analysis on the semantic annotations they contain. Annotations for entity types were classified into six semantic groups and an overview on the semantic entities which can be found in each corpus is shown. Results show that while some semantic entities, such as genes, proteins and chemicals are consistently annotated in many collections, corpora available for diseases, variations and mutations are still few, in spite of their importance in the biological domain.

CellFinder: a cell data repository

CellFinder (http://www.cellfinder.org) is a comprehensive one-stop resource for molecular data characterizing mammalian cells in different tissues and in different development stages. It is built from carefully selected data sets stemming from other curated databases and the biomedical literature. To date, CellFinder describes 3394 cell types and 50 951 cell lines. The database currently contains 3055 microscopic and anatomical images, 205 whole-genome expression profiles of 194 cell/tissue types from RNA-seq and microarrays and 553 905 protein expressions for 535 cells/tissues. Text mining of a corpus of >2000 publications followed by manual curation confirmed expression information on ∼900 proteins and genes. CellFinder’s data model is capable to seamlessly represent entities from single cells to the organ level, to incorporate mappings between homologous entities in different species and to describe processes of cell development and differentiation. Its ontological backbone currently consists of 204 741 ontology terms incorporated from 10 different ontologies unified under the novel CELDA ontology. CellFinder’s web portal allows searching, browsing and comparing the stored data, interactive construction of developmental trees and navigating the partonomic hierarchy of cells and tissues through a unique body browser designed for life scientists and clinicians.

New-onset diabetes after transplantation: assessment of risk factors and clinical outcomes

BACKGROUND

New-onset diabetes after transplantation (NODAT) is a serious complicatin of kidney transplantation (KT) with adverse impacts on graft and patient survivals. This study aims assess potential risk factors for development of NODAT and compare clinical outcomes of KT recipients with versus without NODAT.

METHODS

We retrospectively evaluated 648 patients who underwent KT between 2005 and 2009. From the 83 (12.8%) subjects who developed NODAT, we selected 47 for comparison with controls free of diabetes.

RESULTS

The diagnosis of NODAT was made at 4.3 ± 8.5 months after transplantation in 47 patients, including 76.6% males, with an overall mean age of 54.5 ± 10.8 years. Patients with NODAT presented higher pretransplantation fasting plasma glucose levels (P < .001) as well as cyclosporine and tacrolimus trough levels (P = .003 and P < .001, respectively). On multivariate analysis, higher pretransplantation fasting plasma glucose and higher tacrolimus, but not cyclosporine concentrations were independent predictors of NODAT. No differences were found for other potential risk factors. Upon follow-up at 6, 12, 24, 36, 48, and 60 months, renal function (estimated Glomerular Filtration Rate using Modification of Diet in Renal Disease), 24 hour proteinuria and proportions of patients with hypertension were similar between groups. Patients with NODAT showed comparable numbers of hospitalizations and infections, as well as acute rejection episodes and acute cardiovascular events as their counterparts. Event-free survival (loss of graft function/death with functioning graft) was similar between the groups (P = .418; K-M).

DISCUSSION

In our population, higher pretransplantation fasting plasma glucose levels and higher tacrolimus concentrations were independent predictors of NODAT. During a mean follow-up of 3 years, NODAT was not associated with worse clinical outcomes.

Conversion to everolimus in kidney transplant recipients: to believe or not believe?

INTRODUCTION

Immunosuppression with calcineurin inhibitors (CNI) in renal transplantation is associated with chronic graft dysfunction, increased cardiovascular risk, and malignancies. Everolimus (EVR) appears to permit a CNI-sparing regimen among stable kidney recipients.

AIM

The aim of this study was to analyze the efficacy and safety of conversion from CNI to EVR.

MATERIAL AND METHODS

This was a retrospective registry-based study of all kidney transplant recipients converted from CNI to EVR between 2006 and 2010. One hundred fifty-one patients, including 69.5% males and with an overall mean age of 50.2 ± 12.7 years, underwent conversion to EVR at 37.0 ± 49.8 (16) months after transplantation with 33.7% during the first 6 months. Reasons for conversion included: CNI nephrotoxicity prevention (54.3%), chronic graft dysfunction (25.8%), malignant tumors (10.6%), CNI-adverse reactions (6.6%), and biopsy-proven CNI nephrotoxicity (2.6%). During a follow-up of 17.9 ± 9.9 months (range, 6-58.5), 18 patients (11.9%) were reconverted to CNI, 2 died with functioning grafts, and 2 lost kidney function.

RESULTS

We observed a significant (P < .001) increase in estimated glomerular filtration rate-Modification of Diet in Renal Disease (eGFR-MDRD) by 11.3% within 6 months: 56.7 ± 22.1 to 64.1 ± 23.4 mL/min/1.73 m(2). At final evaluation it was 13.7%, namely, to 65.5 ± 23.0 mL/min/1.73 m(2). At the end of follow-up the proportion of patients with >300 mg/d proteinuria increased from 7.9% to 23.3% (P = .001). Dyslipidemia prevalence increased from 69.5% to 77.5% (P = not significant [NS]) and arterial hypertension increased from 49% to 65.9% (P < .001) at the end of follow-up. Other reported side effects included oral ulcers (2.6%), edema (5.3%), interstitial pneumonitis (1.3%), and toxic hepatitis (1.3%), some of them leading to EVR discontinuation.

CONCLUSION

In our population, renal function improved significantly after conversion from CNI to EVR. Although side effects were common, most were mild, withdrawal of EVR was necessary in a low percentage of cases. EVR appears to be an effective, safe alternative to CNI for maintenance therapy in selected kidney transplant recipients.

Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts

Biomedical literature curation is the process of automatically and/or manually deriving knowledge from scientific publications and recording it into specialized databases for structured delivery to users. It is a slow, error-prone, complex, costly and, yet, highly important task. Previous experiences have proven that text mining can assist in its many phases, especially, in triage of relevant documents and extraction of named entities and biological events. Here, we present the curation pipeline of the CellFinder database, a repository of cell research, which includes data derived from literature curation and microarrays to identify cell types, cell lines, organs and so forth, and especially patterns in gene expression. The curation pipeline is based on freely available tools in all text mining steps, as well as the manual validation of extracted data. Preliminary results are presented for a data set of 2376 full texts from which >4500 gene expression events in cell or anatomical part have been extracted. Validation of half of this data resulted in a precision of ∼50% of the extracted data, which indicates that we are on the right track with our pipeline for the proposed task. However, evaluation of the methods shows that there is still room for improvement in the named-entity recognition and that a larger and more robust corpus is needed to achieve a better performance for event extraction.

Database URL: http://www.cellfinder.org/

Uncommon cause of chest pain in a renal transplantation patient with autosomal dominant polycystic kidney disease: a case report

Autosomal dominant polycystic kidney disease (ADPKD) is a common cause of end-stage renal disease (ESRD) and, because of its intrinsic systemic involvement, its treatment can be a medical and surgical challenge. This condition is often associated with the presence of hepatic cysts and their prevalence generally increases with age. Most patients remain asymptomatic, but some of these will develop complications associated with enlargement and infection of their cysts. Chest pain is a rare manifestation of these complications and, after exclusion of more common cardiovascular and pulmonary causes, should raise the suspicion of an infected hepatic cyst in these patients. We report the case of a 62-year-old male who underwent a kidney transplantation from a cadaveric donor in 1997 (etiology of the ESRD was ADPKD), and was admitted to the emergency department with complaints of chest pain radiating to both shoulders and the interscapular region. An echocardiogram was showed compression of the right atrium by a large liver cyst without associated ventricular dysfunction. Computer tomography-guided drainage of the cyst was performed and an Enterobacter aerogenes sensitive to carbamapenemes was isolated from respective cultures. The patient presented a favorable clinical outcome with prolonged administration of antibiotic therapy according to the antibiotic susceptibility testing. There was no need for surgical intervention.

Multidisciplinary approach to an asymmetric traumatic occlusion: a case report

The case of a 47-year-old female patient with an asymmetric traumatic occlusion, great alveolar destruction in the mandibular left central incisor, gingival recession with attachment loss and lack o fkeratinized tissue more accentuated in the crossbite teeth is described. This situation was caused by the traumatic position of the teeth, aggravated by a forced asymmetric anterior position of the mandible and aggravated by mandibular movements. After the extraction of the left central mandibular incisor, keratinized tissue reconstruction and alveolar bone regeneration were performed to obtain enough bone to move the adjacent teeth in this direction and allow the correct placement of an implant at the end of orthodontic treatment. The orthodontic treatment achieved general stable occlusal contacts and esthetic results that were finalized with a definitive prosthetic treatment. This interdisciplinary management was important to solve in the present case the seriously compromised function and esthetics that would never be achieved without this combination.

A survey on annotation tools for the biomedical literature

New approaches to biomedical text mining crucially depend on the existence of comprehensive annotated corpora. Such corpora, commonly called gold standards, are important for learning patterns or models during the training phase, for evaluating and comparing the performance of algorithms and also for better understanding the information sought for by means of examples. Gold standards depend on human understanding and manual annotation of natural language text. This process is very time-consuming and expensive because it requires high intellectual effort from domain experts. Accordingly, the lack of gold standards is considered as one of the main bottlenecks for developing novel text mining methods. This situation led the development of tools that support humans in annotating texts. Such tools should be intuitive to use, should support a range of different input formats, should include visualization of annotated texts and should generate an easy-to-parse output format. Today, a range of tools which implement some of these functionalities are available. In this survey, we present a comprehensive survey of tools for supporting annotation of biomedical texts. Altogether, we considered almost 30 tools, 13 of which were selected for an in-depth comparison. The comparison was performed using predefined criteria and was accompanied by hands-on experiences whenever possible. Our survey shows that current tools can support many of the tasks in biomedical text annotation in a satisfying manner, but also that no tool can be considered as a true comprehensive solution.

Molecular adaptations to concurrent training

This study investigated the chronic effects of concurrent training (CT) on morphological and molecular adaptations. 37 men (age=23.7±5.5 year) were divided into 4 groups: interval (IT), strength (ST) and concurrent (CT) training and a control group (C) and underwent 8 weeks of training. Maximum strength (1RM) and muscle cross-sectional area (CSA) were evaluated before and after training. Muscle samples were obtained before the training program and 48 h after the last training session. VO2max improved in 5±0.95% and 15±1.3% (pre- to post-test) in groups CT and IT, respectively, when compared to C. Time to exhaustion (TE) improved from pre- to post-test when compared to C (CT=6.1±0.58%; IT=8.3±0.88%; ST=3.2±0.66%). 1RM increased from pre-to post-test only in ST and CT groups (ST=18.5±3.16%; CT=17.6±3.01%). Similarly, ST and CT groups increased quadriceps CSA from pre-to post-test (6.2±1.4%; 7.8±1.66%). The p70S6K1 total protein content increased after CT. The ST group showed increased Akt phosphorylation at Ser473 (45.0±3.3%) whereas AMPK phosphorylation at Thr172 increased only in IT group, (100±17.6%). In summary, our data suggest that despite the differences in molecular adaptations between training regimens, CT did not blunt muscle strength and hypertrophy increments when compared with ST.

C4d deposits in acute "cell-mediated" rejection: a marker for renal prognosis?

BACKGROUND

Accumulation of C4d along peritubular capillaries (PTC) of renal allografts is normally attributed to antibody-mediated rejection. The prognostic implication of these deposits associated with "cell-mediated" rejection on graft survival remains uncertain. Our study aims to evaluate the impact of C4d deposits along PTC of patients with acute cell- mediated rejection on graft function and survival.

METHODS

We retrospectively analyzed patients transplanted between 2005 and 2010 with histopathologic diagnosis of acute rejection (AR). Eleven patients with "pure" antibody-mediated rejection were excluded. The remaining 79 patients were divided into two groups according to type of AR by Banff 2003 criteria: type I (69.6%) versus type II (30.4%). In each group, comparisons were made between C4d-negative (-) and C4d-positive (+) biopsies.

RESULTS

Fifty-five patients presented with type I AR: 35 (63.6%) C4d- and 20 (36.4%) C4d+. Twenty-four patients presented with type II AR: 13 (54.2%) C4d- and 11 (45.8%) C4d+. In the type I AR group, graft survival at the first and second years was similar in C4d- and C4d+ patients (94% and 91% versus 75% and 75%, respectively, log-rank P = .26). No differences were encountered in estimated glomerular filtration rate (eGFR) between subgroups at the first, second, and final years of follow-up. Graft loss occurred in 14.7% of C4d- patients versus 25% in C4d+ patients (P = NS). In the type II AR group, graft survival at the first and second years was similar in C4d- and C4d+ patients (85% and 85% versus 72% and 61%, respectively, log-rank P = .50). No differences were encountered in eGFR between subgroups at the first, second, and final years of follow-up. Graft loss occurred in 30.8% of C4d- patients versus 45.5% in C4d+ patients (P = NS).

CONCLUSION

Our results suggest that detection of C4d staining in acute "cell-mediated" rejection does not imply a worse renal prognosis.