A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference

A central strategy of synthetic biology is to understand the basic processes of living creatures through engineering organisms using the same building blocks. Biological machines described in terms of parts can be studied by computer simulation in any of several languages or robotically assembled in vitro. In this paper we present a language, the Genetic Circuit Description Language (GCDL) and a compiler, the Genetic Circuit Compiler (GCC). This language describes genetic circuits at a level of granularity appropriate both for automated assembly in the laboratory and deriving simulation code. The GCDL follows Semantic Web practice, and the compiler makes novel use of the logical inference facilities that are therefore available. We present the GCDL and compiler structure as a study of a tool for generating κ-language simulations from semantic descriptions of genetic circuits.

Cholesteatoma vs granulation tissue: a differential diagnosis by DWI-MRI apparent diffusion coefficient

PURPOSE

To diagnose cholesteatoma when it is not visible through tympanic perforation, imaging techniques are necessary. Recently, the combination of computed tomography and magnetic resonance imaging has proven effective to diagnose middle ear cholesteatoma. In particular, diffusion weighted images have integrated the conventional imaging for the qualitative assessment of cholesteatoma. Accordingly, the aim of this study was to obtain a quantitative analysis of cholesteatoma calculating the apparent diffusion coefficient value. So, we investigated whether it could differentiate cholesteatoma from other inflammatory tissues both in a preoperative and in a postoperative study.

METHODS

This study included 109 patients with clinical suspicion of primary or residual/recurrent cholesteatoma. All patients underwent preoperative computed tomography and magnetic resonance imaging with diffusion sequences before primary or second-look surgery to calculate the apparent diffusion coefficient value.

RESULTS

We found that the apparent diffusion coefficient values of cholesteatoma were significantly lower than those of non cholesteatoma. In particular, the apparent diffusion coefficient median value of the cholesteatoma group (0.84 × 10^- 3 mm²/s) differed from the inflammatory granulation tissue (2.21 × 10^- 3 mm²/s) group (p < 2.2 × 10^- 16). Furthermore, we modeled the probability of cholesteatoma by means of a logistic regression and we determined an optimal cut-off probability value of ~ 0.86 (specificity = 1.0, sensitivity = 0.97), corresponding to an apparent diffusion coefficient cut-off value of 1.37 × 10^- 3 mm²/s.

CONCLUSIONS

Our study has demonstrated that apparent diffusion coefficient values constitute a valuable quantitative parameter for preoperative differentiation of cholesteatomas from other middle ear inflammatory diseases and for postoperative diagnosis of recurrent/residual cholesteatomas.

Cooperation in microbial communities and their biotechnological applications

Microbial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross-feeding, which can be understood in the general framework of ecological and evolutionary (eco-evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of 'cheating' cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications.

Endoscopic tympanoplasty in the treatment of chronic otitis media: our experience

CONCLUSION

The endoscopy ensures good surgical exposure of hidden areas, frequently sites of residual cholesteatoma. Also, the minimally invasive endoscopic approach is more respectful of anatomy and functionality of the middle ear, restoring and preserving mastoid mucosa, with faster healing time.

OBJECTIVES

To investigate the benefits that the systematic use of endoscopy in middle ear surgery has made.

STUDY DESIGN

Retrospective cohort studies.

METHOD

Two groups of patients were surgically treated for inflammatory diseases of the middle ear. The first group refers to the Pre-Endoscopic period, the second one to the Endoscopic Period. This study analyzed the type of surgical approach (Transcanalar vs Retroauricolar) in all cases treated and the differences in incidence of residual disease in the cases treated for cholesteatoma.

RESULTS

The oto-endoscopy led to a significant increase (p < .01) of the transcanalar approach and to a significant reduction (p < .05) of residual cholesteatoma at the second look surgery.

Detecting the Collapse of Cooperation in Evolving Networks

The sustainability of biological, social, economic and ecological communities is often determined by the outcome of social conflicts between cooperative and selfish individuals (cheaters). Cheaters avoid the cost of contributing to the community and can occasionally spread in the population leading to the complete collapse of cooperation. Although such collapse often unfolds unexpectedly, it is unclear whether one can detect the risk of cheater’s invasions and loss of cooperation in an evolving community. Here, we combine dynamical networks and evolutionary game theory to study the abrupt loss of cooperation with tools for studying critical transitions. We estimate the risk of cooperation collapse following the introduction of a single cheater under gradually changing conditions. We observe an increase in the average time it takes for cheaters to be eliminated from the community as the risk of collapse increases. We argue that such slow system response resembles slowing down in recovery rates prior to a critical transition. In addition, we show how changes in community structure reflect the risk of cooperation collapse. We find that these changes strongly depend on the mechanism that governs how cheaters evolve in the community. Our results highlight novel directions for detecting abrupt transitions in evolving networks.

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization

MOTIVATION

Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model.

RESULTS

We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualization of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general.

AVAILABILITY AND IMPLEMENTATION

The annotation ontology for rule-based models can be found at http://purl.org/rbm/rbmo The krdf tool and associated executable examples are available at http://purl.org/rbm/rbmo/krdf

CONTACT

anil.wipat@newcastle.ac.uk or vdanos@inf.ed.ac.uk.

Hyperbaric oxygen for idiopathic sudden hearing loss: is the routine application helpful?

CONCLUSION

We recommend the routine application of hyperbaric oxygen (HBO) in conjunction with intravenous steroid (IVS) for all patients with idiopathic sudden sensorineural hearing loss (ISSNHL). For best results, this therapy must be started within 14 days.

OBJECTIVE

To investigate the necessity of routine application of HBO therapy for ISSNHL.

METHODS

This was a retrospective cohort study. A total of 300 patients (300 diseased ears) were divided into 3 groups according to the therapy received: IVS (group A), HBO (group B), or IVS + HBO (group C). Patients in each treatment group were subdivided into subgroups according to the time of therapy initiation. The outcomes of their hearing recovery were classified into three recovery grades: good, fair, and poor.

RESULTS

The proportion of patients responding to therapy and those with complete recovery was the highest in the combined treatment group, 84% and 58%, respectively, regardless of the initial hearing levels. In all the groups, mean gains of cases in whom therapy was started in the first 2 weeks were significantly higher (p < 0.05) and hypercholesterolemia (>240 mg/dl) caused significantly worse responses (p < 0.05).

Recurrent epistaxis following stabbing headache responsive to acetazolamide

The co-occurrence of epistaxis and headache is not uncommon in migraine patients, although only few case reports have been published. A trigeminovascular activation may be causally involved although the exact mechanisms linking epistaxis and migraine remain unclear. Significant dural sinus stenosis may sustain or worsen an increased cerebral venous pressure and is considered a radiological predictor of idiopathic intracranial hypertension. We report a 49-year-old female patient with chronic migraine associated to stabbing headache-like attacks followed by epistaxis and by the resolution or the significant improvement of pain. As she also reported adjunctive symptoms suggestive of raised intracranial pressure and showed a bilateral narrowing of transverse sinuses at MR-venography, a possible intracranial hypertension was hypothesized despite the lack of papilledema. Acetazolamide 250 mg twice/day was added to therapy and the patient reported sudden reduction of headache severity and frequency and complete resolution of both the stabbing pain and the recurrent epistaxis, maintained for 5 months. At treatment discontinuation she complained the worsening of migraine headache and the reoccurrence of the superimposed stabbing pain followed by epistaxis. The mechanism linking the sequential occurrence of painful stabs, epistaxis and relief from pain with raised intracranial pressure in our patients remains unclear. We speculate that the sudden reopening of collapsed collateral veins of the anterior venous circle, possibly prompted by periodic waves of central venous hypertension coupled with intracranial hypertensive peaks, could explain the unusual strict time succession of painful stabs, epistaxis, and subsequent resolution of pain.

Hyaluronan in the Treatment of Chronic Rhinosinusitis with Nasal Polyposis

Chronic rhinosinusitis (CRS) is a common condition and affects the quality of life of approximately 16 % of adults in US and 10.9 % in Europe. Hyaluronan (HA) is a nonsulphate glycosaminoglycan found in the extracellular matrix of connective tissues, and plays an important role in the healing process and repair of mucosal surfaces. We aim to evaluate the effect of HA on nasal symptoms and endoscopic appearance in patients with CRS and nasal polyps (NP) who have not undergone sinus surgery. Eighty patients older than 18 years old were randomized to receive either open-label nebulized saline solution (NS) or intranasal corticosteroid spray (ICS) 200 µg bid or nebulized sodium hyaluronate (NHA, YABRO(®)) or both ICS and NHA. Results were collected at 1 month, 3 months and 3 months after treatment. Significant improvements in nasal symptoms scores, endoscopic appearance scores, radiologic scores, rhinomanometry and saccharine clearance test were observed in the NHA, ICS and ICS + NHA groups after 1 month and 3 months of treatment compared with baseline (all p ≤ 0.005). The use of oral steroids was significantly reduced after 3 months of therapy in the same groups versus baseline (all p < 0.05). The incidence of adverse events at 3 months was similar between the 4 groups (all p > 0.05). Throat irritation, nasal burning and drug-related epistaxis were not reported in the group NHA. HA, as a nebulized nasal douche preparation, improved nasal symptoms and endoscopic appearances in patients with CRS and NP who have not undergone sinus surgery.

Tragal cartilage shield tympanoplasty: our technique and results in 612 cases

CONCLUSION

This study reveals that tragal cartilage tympanoplasty is a reliable technique, it has a high degree of graft take, and the tympanic re-aeration and hearing results are satisfactory.

OBJECTIVE

Cartilage is the grafting material of choice in advanced pathologies of the middle ear while the indications for its routine use remain controversial. The purpose of this study was to report our long-term experience with the 'tragal cartilage shield' tympanoplasty.

METHODS

This was a retrospective case series. The study was conducted on 612 adult patients from January 2003 until January 2012. We evaluated graft take, pure-tone average air-bone gap (PTA-ABG), postoperative aeration, and complications. The mean postoperative follow-up was 68 months.

RESULTS

Sex, age, and tobacco smoke did not have any impact on postoperative results. Graft take was achieved in 99.35% of patients; there were no immediate postoperative complications. The overall average preoperative PTA-ABG was 44.95 ± 7.77 dB, whereas 1 year after surgery it was 10.66 ± 5.41 dB (p < 0.0001). Statistically significant improvement was observed up to 10 years after surgery. Moreover, we obtained a good tympanic ventilation (1 year after surgery, the average aeration score was 9.09 ± 1.93), which was stable up to 10 years.

Cooperation and competition in the dynamics of tissue architecture during homeostasis and tumorigenesis

The construction of a network of cell-to-cell contacts makes it possible to characterize the patterns and spatial organization of tissues. Such networks are highly dynamic, depending on the changes of the tissue architecture caused by cell division, death and migration. Local competitive and cooperative cell-to-cell interactions influence the choices cells make. We review the literature on quantitative data of epithelial tissue topology and present a dynamical network model that can be used to explore the evolutionary dynamics of a two dimensional tissue architecture with arbitrary cell-to-cell interactions. In particular, we show that various forms of experimentally observed types of interactions can be modelled using game theory. We discuss a model of cooperative and non-cooperative cell-to-cell communication that can capture the interplay between cellular competition and tissue dynamics. We conclude with an outlook on the possible uses of this approach in modelling tumorigenesis and tissue homeostasis.

Plasticity facilitates sustainable growth in the commons

In the commons, communities whose growth depends on public good, individuals often rely on surprisingly simple strategies, or heuristics, to decide whether to contribute to the shared resource (at risk of exploitation by free-riders). Although this appears a limitation, we show here how four heuristics lead to sustainable growth when coupled to specific ecological constraints. The two simplest ones—contribute permanently or switch stochastically between contributing or not—are first shown to bring sustainability when the public good efficiently promotes growth. If efficiency declines and the commons is structured in small groups, the most effective strategy resides in contributing only when a majority of individuals are also contributors. In contrast, when group size becomes large, the most effective behaviour follows a minimal-effort rule: contribute only when it is strictly necessary. Both plastic strategies are observed in natural scenarios across scales that present them as relevant social motifs for the sustainable management of public goods.

Prosperity is associated with instability in dynamical networks

Social, biological and economic networks grow and decline with occasional fragmentation and re-formation, often explained in terms of external perturbations. We show that these phenomena can be a direct consequence of simple imitation and internal conflicts between 'cooperators' and 'defectors'. We employ a game-theoretic model of dynamic network formation where successful individuals are more likely to be imitated by newcomers who adopt their strategies and copy their social network. We find that, despite using the same mechanism, cooperators promote well-connected highly prosperous networks and defectors cause the network to fragment and lose its prosperity; defectors are unable to maintain the highly connected networks they invade. Once the network is fragmented it can be reconstructed by a new invasion of cooperators, leading to the cycle of formation and fragmentation seen, for example, in bacterial communities and socio-economic networks. In this endless struggle between cooperators and defectors we observe that cooperation leads to prosperity, but prosperity is associated with instability. Cooperation is prosperous when the network has frequent formation and fragmentation.

Notes on the microbiology of cholesteatoma: clinical findings and treatment

Anomalous proliferation of the cholesteatoma epithelium is caused by extrinsic factors such as toxins or bacterial antigens combined with lytic enzymes, lymphokines and cytokines released from the inflammatory infiltrate. This could explain the close relationship between the aggressiveness of cholesteatoma and repeated bacterial superinfection, therefore it is very important to know the bacteria involved in order to control the regrowth of skin following surgery, reduce the aggressive potential of the cholesteatoma and limit the incidence of complications. This study focused on 70 females and 80 males aged between 15 and 65 years, affected by cholesteatomatous otitis media; all underwent bacteriological examination of the auricular secretion. The floral bacteria which proved to play the most important role (60.3%) were the aerobic type and the highest levels were those of Pseudomonas aeruginosa (31.1%) followed by Staphylococcus aureus (19.1%), Proteus mirabilis (7.7%), Escherichia coli (1.4%) and Klebsiella pneumoniae (1%). Anaerobic floral bacteria were found in a fairly high percentage of cases (38.2%); in particular, anaerobic gram-positive cocci (Peptococcus 12.4% and Peptostreptococcus in 4.8% of cases), Bacteroides (12.4%), Clostridium (3.8%), Fusobacterium (2.9%) and Propionobacterium (1.9%) were isolated. In 3 cases of mycetes (1.4%) only Aspergillus, in association with Pseudomonas and Staphylococcus, was identified. The study showed, then, how effective second generation fluoroquinolones and third generation cephalosporins are (the latter being used in pre-adolescent children), the reason being that these antibiotics work not only on Pseudomonas and Staphylococcus, but also on the anaerobic bacteria.

Tragal cartilage in tympanoplasty: anatomic and functional results in 306 cases

Cartilage is the grafting material of choice in advanced disorders of the middle ear while the indications for its routine use remain controversial due to the possible detrimental effect on post-operative hearing. Aim of the present study was to report personal experience with "tragal cartilage shield" tympanoplasty. The study focused on 306 adult patients (236 primary procedures and 70 revisions from January 2003 to June 2007). Mean post-operative follow-up was 37 months (range 1-66). The following parameters were evaluated: graft take, change between the pre- and post-operative pure-tone average air-bone gap (PTA-ABG), post-operative complications. Graft take was achieved in 304 patients (99.35%) and there were no immediate post-operative complications. The overall average pre-operative pure-tone average air-bone gap was 43.79 +/- 7.07 dB, whereas the post-operative (1 year after surgery) pure-tone average air-bone gap was 10.43 +/- 5.25 dB (p < 0.0001). Statistically significant improvement was observed up to 5 years after surgery. This study reveals that tragal cartilage shield tympanoplasty is a reliable technique, in fact it has a high degree of graft take and hearing results are satisfactory. Furthermore, the cartilage is a satisfactory grafting material because it is easily accessible, easy to adapt, resistant to negative middle ear pressures, stable, elastic, well tolerated by the middle ear, resistant to resorption. Therefore, we also recommend its use in less severe middle ear disorders, in which the functional outcome is more essential.

Osteosarcoma of the larynx: a case report

BACKGROUND

We add a new rare illustrative case of osteosarcoma of the larynx to the literature.

CASE PRESENTATION

The patient (man; 56 years old) first underwent several biopsies, followed in the end by a total laryngectomy. Diagnosis was histological. The patient developed regional and distant metastases and died of disease after 3 months from surgery.

CONCLUSION

Osteosarcoma of the larynx is a rare and aggressive tumour with a poor long-term prognosis. The preferred treatment for this tumour is aggressive surgery.To perform a diagnosis we must be in presence of osteoid or of neoplastic osseous tissue directly produced by the neoplastic cells.

Monopolar and bipolar radiofrequency thermal ablation of inferior turbinates: 20-month follow-up

OBJECTIVE

We prospectively evaluated the efficacy and morbidity of monopolar and bipolar radiofrequency volumetric tissue reduction (RFVTR) of inferior turbinates during a 20-month follow-up.

METHODS

The study was conducted on 150 patients randomly assigned into two groups of 75 each. In group A, we used the bipolar device "Coblator II ENT" (Arthrocare Corp, Sunnyvale, CA) and in group B the monopolar device Somnoplasty (Somnus Medical Technologies, Inc, Sunnyvale, CA). Nasal endoscopy, visual analog scale, anterior active rhinomanometry, acoustic rhinometry, and saccharin tests were used to assess the outcomes of the treatments.

RESULTS

Turbinate edema and nasal obstruction decreased significantly (P < 0.0001) in group A seven days after surgery and in group B from month 1. The nasal symptoms were significantly reduced in both groups from the first month (P < 0.0001). A significant increase (P < 0.0001) in nasal volume and decrease in nasal resistance were detected in the first month. No difference was found from three to 20 months after surgery (P > 0.5).

CONCLUSION

We have shown that both methods of RFVTR can produce a long-term improvement on symptoms and on maintenance of nasal function.

Oncocytic cyst of the larynx: an unusual occurrence

Oncocytic cysts of the larynx are rare benign, slow growing lesions that are lined predominantly or exclusively by oncocytes, the cytoplasm of which contains a considerable number of hypertrophied mitochondria, which accounts for their eosinophilia and swollen appearance. The oncocytic change is a phenomenon of metaplasia which occurs frequently in epithelial endocrine cells with high metabolic activity and it is also associated with inflammation, degenerative process or cellular ageing. In the larynx, oncocytic metaplasia is very uncommon, but it is occasionally seen in the lining of laryngeal cysts, which are found most commonly in the ventricles or in the false vocal cords, where seromucinous glands are more abundant. Oncocytic cysts typically occur in the elderly and are usually solitary, with involvement of an isolated site, whereas diffuse involvement with multiple cysts is extremely rare. Hoarseness is the most common presenting symptom, while pain, stridor or laryngeal obstruction are unusual complaints. Management of these lesions is conservative and consists of local excision, endoscopic removal being the treatment of choice. Although oncocytic cysts are benign lesions, follow-up is recommended, as recurrence is possible, especially in the case of patients with multiple involvement, since they may show a tendency to develop new cysts. To date, approximately 150 cases of laryngeal oncocytic cysts have been published. Herein, a very unusual case is presented occurring in a 43-year-old male patient, therefore, "epidemiologically" atypical for developing oncocytic lesions. Causes of oncocytic changes and pathogenesis of laryngeal cysts are discussed.

Otorhinolaryngology-related tuberculosis

Data from personal case histories, from 1984 to 2000 inclusive, are reported in order to contribute to a better understanding of some of the clinical and epidemiological ENT associated TB aspects. Analysis of these data shows that: (1) Like the pulmonary form, ENT localizations are increasing due to the traditional risk factors (immigration, poverty, immunodeficiency, drug addiction). (2) They are generally clinically primitive forms (which are found in extrapulmonary regions as the first expression of tubercular disease) and typically affect young people with a slight prevalence among females. Lymph gland localizations are the most frequent.