GOGrapher: A Python library for GO graph representation and analysis

Background

The Gene Ontology is the most commonly used controlled vocabulary for annotating proteins. The concepts in the ontology are organized as a directed acyclic graph, in which a node corresponds to a biological concept and a directed edge denotes the parent-child semantic relationship between a pair of terms. A large number of protein annotations further create links between proteins and their functional annotations, reflecting the contemporary knowledge about proteins and their functional relationships. This leads to a complex graph consisting of interleaved biological concepts and their associated proteins. What is needed is a simple, open source library that provides tools to not only create and view the Gene Ontology graph, but to analyze and manipulate it as well. Here we describe the development and use of GOGrapher, a Python library that can be used for the creation, analysis, manipulation, and visualization of Gene Ontology related graphs.

Findings

An object-oriented approach was adopted to organize the hierarchy of the graphs types and associated classes. An Application Programming Interface is provided through which different types of graphs can be pragmatically created, manipulated, and visualized. GOGrapher has been successfully utilized in multiple research projects, e.g., a graph-based multi-label text classifier for protein annotation.

Conclusion

The GOGrapher project provides a reusable programming library designed for the manipulation and analysis of Gene Ontology graphs. The library is freely available for the scientific community to use and improve.

Nasal endothelial interleukin-10 expression is negatively correlated with nasal symptoms after allergen provocation

BACKGROUND

Despite major efforts, factors that predict or correspond to the level of allergic symptoms remain elusive. Given our previous observations of mucosal interleukin-10 (IL-10) expression by local tissue cells and its described role as immune modulator, we hypothesized that, in allergic rhinitis, nasal mucosal IL-10 expression could influence the severity of symptoms.

METHODS

In this study, we investigated endothelial IL-10 expression in nasal mucosa of healthy- and house dust mite allergic patients, both before and after provocation, and under nasal steroid therapy. Nasal turbinate biopsies were taken from healthy individuals as well as from house dust mite allergic patients, both before and after provocation. Allergic patients received fluticasone proprionate aqueous nasal spray or control treatment. In the allergic patients, endothelial IL-10 scores based on immunohistochemical stainings were correlated with allergic symptoms, measured by visual analog scores.

RESULTS

At baseline, variable levels of endothelial IL-10 were detected in nasal biopsies. After nasal provocation, but not at baseline, endothelial IL-10 expression corresponded very closely to the allergic symptoms after allergen provocation. Low symptom scores were correlated with high endothelial IL-10 scores. This correlation disappeared after fluticason propionate treatment.

CONCLUSIONS

There is a large variation in the level of endothelial IL-10 expression both in healthy individuals and in house dust mite allergic patients. Endothelial IL-10 expression may affect local immune reactions resulting in reduced levels of allergic symptoms.

Multi-label literature classification based on the Gene Ontology graph

BACKGROUND

The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of text mining approaches to facilitate the process by automatically extracting the Gene Ontology annotation from literature. The task is usually cast as a text classification problem, and contemporary methods are confronted with unbalanced training data and the difficulties associated with multi-label classification.

RESULTS

In this research, we investigated the methods of enhancing automatic multi-label classification of biomedical literature by utilizing the structure of the Gene Ontology graph. We have studied three graph-based multi-label classification algorithms, including a novel stochastic algorithm and two top-down hierarchical classification methods for multi-label literature classification. We systematically evaluated and compared these graph-based classification algorithms to a conventional flat multi-label algorithm. The results indicate that, through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods can significantly improve predictions of the Gene Ontology terms implied by the analyzed text. Furthermore, the graph-based multi-label classifiers are capable of suggesting Gene Ontology annotations (to curators) that are closely related to the true annotations even if they fail to predict the true ones directly. A software package implementing the studied algorithms is available for the research community.

CONCLUSION

Through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods have better potential than the conventional flat multi-label classification approach to facilitate protein annotation based on the literature.

Nasal epithelial cells express IL-10 at levels that negatively correlate with clinical symptoms in patients with house dust mite allergy

BACKGROUND

Despite constant exposure to micro-organisms and other immunogenic environmental factors, relatively very few immunological responses are initiated in the nasal mucosa. Although several mechanisms could play a role in maintaining this immune suppressive milieu, none of them have been validated. Previous data from our group suggested that locally produced interleukin (IL)-10 could be involved in maintaining local homeostasis.

METHODS

To investigate the role of epithelial IL-10 expression in the manifestation of allergic symptoms, we used immunohistochemistry to study the expression of IL-10 in the nasal epithelium of healthy individuals and house dust mite allergic patients. In the allergic patients, we determined potential correlations of epithelial expression with allergic symptoms, both at baseline and after allergen provocation.

RESULTS

IL-10 is expressed in the basal and differentiated epithelial cells of both healthy individuals and allergic rhinitis patients. In the allergic individuals, there is a strong negative correlation at baseline between the epithelial expression level of IL-10 and rhinorrhoea and sneezing, but not between that expression level and nasal blockage or peak nasal inspiratory flow (PNIF). This correlation disappears with steroid treatment or after allergen provocation, although the expression at baseline seems to predict PNIF scores after provocation.

CONCLUSIONS

Our data not only reveals IL-10 expression by human nasal epithelial cells, but also suggests that nasal epithelial IL-10 regulates allergic symptoms. Targeting the regulation mechanisms affecting IL-10 or targeting the regulation mechanism affected by IL-10 could constitute new options for the treatment of allergic disease.

Long-term safety of fluticasone furoate nasal spray in adults and adolescents with perennial allergic rhinitis

BACKGROUND

Fluticasone furoate is a novel-enhanced affinity glucocorticoid and its long-term safety must be assessed. This study was designed to assess the safety and tolerability of 12-month intranasal administration of fluticasone furoate in adult and adolescent patients with perennial allergic rhinitis (PAR).

METHODS

In this randomized, double-blind, placebo-controlled, parallel-group study, 806 patients with PAR were randomized to once daily (od) fluticasone furoate nasal spray 110 microg (n = 605) or vehicle placebo nasal spray (n = 201) for 12 months, following a 7- to 14-day screening period. Safety was assessed by monitoring adverse events (AEs), 24-h urinary cortisol excretion, nasal and ophthalmic examinations, electrocardiograms and clinical laboratory tests. Plasma concentrations of fluticasone furoate were determined from blood samples.

RESULTS

Fluticasone furoate was well tolerated. The incidence of most AEs was similar to that observed with placebo, with the exception of epistaxis, which was more frequently reported on active treatment. There were no clinically meaningful differences between fluticasone furoate and placebo in terms of safety assessments, including mean changes in ophthalmic parameters and 24-h urine cortisol excretion. Plasma concentrations of fluticasone furoate were not quantifiable in the majority of patients following intranasal administration.

CONCLUSIONS

Long-term (12-month) administration of fluticasone furoate 110 microg od revealed an AE profile typical of the intranasal corticosteroid class in both adult and adolescent patients with PAR, with no evidence of clinically relevant systemic corticosteroid exposure.

Synovitis score: discrimination between chronic low-grade and high-grade synovitis

AIMS

To standardize the histopathological assessment of synovial membrane specimens in order to contribute to the diagnostics of rheumatic and non-rheumatic joint diseases.

METHODS AND RESULTS

Three features of chronic synovitis (enlargement of lining cell layer, cellular density of synovial stroma, leukocytic infiltrate) were semiquantitatively evaluated (from 0, absent to 3, strong) and each feature was graded separately. The sum provided the synovitis score, which was interpreted as follows: 0-1, no synovitis; 2-4, low-grade synovitis; 5-9, high-grade synovitis. Five hundred and fifty-nine synovectomy specimens were graded by two independent observers. Clinical diagnoses were osteoarthrosis (n=212), post-traumatic arthritis (n=21), rheumatoid arthritis (n=246), psoriatic arthritis (n=22), reactive arthritis (n=9), as well as controls (n=49) from autopsies of patients without joint damage. Median synovitis scores when correlated with clinical diagnoses were: controls 1.0, osteoarthritis 2.0, post-traumatic arthritis 2.0, psoriatic arthritis 3.5, reactive arthritis 5.0 and rheumatoid arthritis 5.0. The scores differed significantly between most disease groups, especially between degenerative and rheumatic diseases. A high-grade synovitis was strongly associated with rheumatic joint diseases (P<0.001, sensitivity 61.7%, specificity 96.1%). The correlation between the two observers was high (r=0.941).

CONCLUSION

The proposed synovitis score is based on well-defined, reproducible histopathological criteria and may contribute to diagnosis in rheumatic and non-rheumatic joint diseases.

Mycobacterium avium intracellulare otomastoiditis: case report and literature review

Otomastoiditis caused by Mycobacterium avium intracellulare (MAI) is rare. Sub-optimal management of this condition can lead to significant morbidity and serious damage to the middle ear. Diagnosis is difficult, especially since most physicians are not familiar with the mode of presentation and symptoms. Presented here is a new case, followed by a review of the literature on MAI mastoiditis.

The 'best method' of topical nasal drug delivery: comparison of seven techniques

OBJECTIVE

To determine whether there is a 'best' technique for delivering drugs to the middle meatus.

DESIGN

Single-blind cross-over study in healthy individuals using endoscopic video-imaging.

PARTICIPANTS

A dyed test formulation was administered intranasally on seven non-sequential days to ten healthy individuals with no 'nasal' history. The participants were recruited through advertisement.

MAIN OUTCOME MEASURES

Comparison of seven different techniques, 20 nostrils and 140 endoscopic videos for the deposition patterns of dyed test formulation. Analysis was possible in 90% of all endoscopic videos. Three head positions were tested for both nasal drops and nasal sprays.

RESULTS

Deposition of dyed test formulation near the middle meatus was observed in 43% of all observations. No significant differences were observed in terms of delivery between any of the seven techniques.

CONCLUSIONS

Our study suggests there may not be a single 'best' technique for topical nasal drug delivery. A more individual approach to topical nasal drug treatment, taking anatomy and head position into account would seem to be more appropriate.

Diaphorase can metabolize some vasorelaxants to NO and eliminate NO scavenging effect of 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl-3-oxide (PTIO)

Diaphorase was studied as a possible oxidoreductase participating in NO production from some vasorelaxants. In the presence of NADH or NADPH, diaphorase can convert selected NO donors, glycerol trinitrate (GTN) and formaldoxime (FAL) to nitrites and nitrates with NO as an intermediate. This activity of diaphorase was inhibited by diphenyleneiodonium (DPI) (inhibitor of some NADPH-dependent flavoprotein oxidoreductases), while it remained uninhibited by NG-nitro-L-arginine methyl ester (inhibitor of NO synthase) 7-Ethoxyresorufin (inhibitor of cytochrome P-450 1A1 and cytochrome P-450 NADPH-dependent reductase) inhibited the conversion of GTN only. Existence of NO as an intermediate of the reaction was supported by results of electron paramagnetic resonance spectroscopy. In addition to its ability to affect the above mentioned NO donors, diaphorase was able to reduce 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl-3-oxide (PTIO) and thus to eliminate its NO scavenging effect. This activity of diaphorase could also be inhibited by DPI. The reaction of diaphorase with GTN and PTIO was not affected by superoxide dismutase (SOD) or catalase. Reaction of FAL with diaphorase was lowered with SOD by 38 % indicating the partial participation of superoxide anion probably generated by the reaction of diaphorase with NADH or NADPH. Catalase had no effect. Diaphorase could apparently be one of the enzymes participating in the metabolism of studied NO donors to NO. The easy reduction and consequent elimination of PTIO by diaphorase could affect its use as an NO scavenger in biological tissues.

Usage of troponin in the real world: a lesson for the introduction of biochemical assays

BACKGROUND

Studies have demonstrated economic and clinical effectiveness using troponin as a risk stratification tool in chest pain patients. Those with a positive result are investigated invasively, whilst those with a negative result and ECG are promptly mobilized, facilitating discharge.

AIM

To determine whether our use of troponin I (cTnI) in routine clinical practice conforms to ideal standards.

DESIGN

Audit study.

METHODS

Data were collected from 93 laboratory request forms for cTnI measurement on 72 patients with matched available patient records.

RESULTS

Eighty requests had no information regarding timing of blood sample in relation to the clinical event; 39% gave no clinical indication. Only 71% of results were available within 12 h. An admission diagnosis of acute coronary syndrome (ACS) was made in 25%. Fifteen had typical cardiac chest pain with a negative cTnI: 6 of these had an exercise treadmill test before discharge. Nine had a positive cTnI, but only two had coronary angiography. Of patients with negative cTnI and possible ACS, 84% were in hospital for >4 days.

DISCUSSION

The introduction of troponin assays into widespread use requires careful assessment. cTnI requests and subsequent patient management remain below expected standards. Ideally, the laboratory should provide an accurate result within a reasonable time frame, while physicians need to request cTnI at a suitable time-point and use the result appropriately. Lessons from the introduction of cTnI measurement may be useful for the introduction of future new tests in other areas of cardiology and medicine.