Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

Context-Specific Protein Network Miner – An Online System for Exploring Context-Specific Protein Interaction Networks from the Literature

Background: Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis. Results: We developed a literature-based online system, Context-specific Protein Network Miner (CPNM), which derives context-specific PINs in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system. CPNM reports enriched information on protein interactions (with type and directionality), their network topology with summary statistics (e.g. most densely connected proteins in the network; most densely connected protein-pairs; and proteins connected by most inbound/outbound links) that can be explored via a user-friendly interface. Some of the novel features of the CPNM system include PIN generation, ontology-based PubMed query enhancement, real-time, user-queried, up-to-date PubMed document processing, and prediction of PIN directionality. Conclusions: CPNM provides a tool for biologists to explore PINs. It is freely accessible at http://www.biotextminer.com/CPNM/.Statistic

Platinum drugs in the treatment of non-small-cell lung cancer

The use of chemotherapy is considered standard therapy in patients with locally advanced non-small-cell lung cancer that cannot be treated with radiotherapy and in those with metastatic non-small-cell lung cancer and good performance status. This approach is also accepted in patients with earlier stage disease, when combined with radiotherapy in those with non-resectable locally advanced disease, or in the preoperative setting. Randomised clinical studies and meta-analyses of the literature have confirmed the beneficial survival effect of platinum-based chemotherapy. Cisplatin and carboplatin have been successfully used with other drugs in a wide variety of well-established two-drug combinations while three-drug combinations are still under investigation. Cisplatin and carboplatin use is limited by toxicity and inherent resistance. These considerations have prompted research into new platinum agents, such as the trinuclear platinum agent BBR3464, the platinum complex ZD0473 and oxaliplatin. These compounds could be developed in combination with agents such as paclitaxel, gemcitabine or vinorelbine in patients with advanced and/or refractory solid tumours

2017 HRS/EHRA/ECAS/APHRS/SOLAECE expert consensus statement on catheter and surgical ablation of atrial fibrillation: executive summary.

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Tuning the material-cytoskeleton crosstalk via nanoconfinement of focal adhesions

Material features proved to exert a potent influence on cell behaviour in terms of adhesion, migration and differentiation. In particular, biophysical and biochemical signals on material surfaces are able to affect focal adhesion distribution and cytoskeletal assemblies, which are known to regulate signalling pathways that ultimately influence cell fate and functions. However, a general, unifying model that correlates cytoskeletal-generated forces with genetic events has yet to be developed. Therefore, it is crucial to gain a better insight into the material-cytoskeleton crosstalk in order to design and fabricate biomaterials able to govern cell fate more accurately. In this work, we demonstrate that confining focal adhesion distribution and growth dramatically alters the cytoskeleton's structures and dynamics, which in turn dictate cellular and nuclear shape and polarization. MC3T3 preosteoblasts were cultivated on nanograted polydimethylsiloxane substrates and a thorough quantification - in static and dynamic modes - of the morphological and structural features of focal adhesions and cytoskeleton was performed. Nanoengineered surfaces provided well-defined zones for focal adhesions to form and grow. Unique cytoskeletal structures spontaneously assembled when focal adhesions were confined and, in fact, they proved to be very effective in deforming the nuclei. The results here presented provide elements to engineer surfaces apt to guide and control cell behaviour through the material-cytoskeleton-nucleus axis

Controlling cell behaviour with nanopatterned substrates

The biologica1 and mechanical functions of in-vitro generated tissues largely depend on the spatial arrangement of their microcostituents. Previous works, focused on controlling tissue structure by confining cells within mirco-grooves or by mechanically stimulating cell-substrate constructs. Since cells invariably crawl on synthetic platforms, it is expected that ce11 motion affects matrix organization, but little is known on this interaction. We hypothesize that a dynamic and reciproca1 interplay between ce11 migration and tissue structure exists. In particular, spatial deposition of collagen is affected by the way cells move: randomly migrating cells produce a disordered tissue whereas a polarized migration produce an aligned tissue. To test this, we used nanograted silicone substrates. MC3T3 cells were seeded on pattemed or flat silicone substrate and kept in culture up to 4 weeks. Cell migration analysis was performed by time lapse microscopy in low density (0-24h) and high density (>lwk) conditions. Collagen was quantified by Sircol assay and its alignment was observed using polarized light on picrosirius stained tissues. Microstructural analyses were performed by means of TEM and SEM. In the early stage of culture, MC3T3 are oriented and migrate predominantly along the nanogrooves. After one week, cells reach a confluent state, they are still aligned although migrating more slowly. In contrast, no preferential direction of migrationlalignment is evident on flat substrates. At longer times, cells produce a dense multilayered structure, whose orientation is visible under polarized light. Fibres are coaligned with cells and the nanogrooves. Tissue grown on flat substrates shows local patches of celllcollagen coalignment although no macroscopic alignment is evident. These results suggest that collagen alignment can be controlled by guiding cells migration. The experimental setup might be a starting platform to explore different topographic pattems and to assess the optimal condition to generate tissues with predetermined orientations

Molding Micropatterns of Elasticity on PEG-Based Hydrogels to Control Cell Adhesion and Migration

We present an innovative and simple, soft UV lithographic method “FIll-Molding In Capillaries” (FIMIC) that combines soft lithography with capillary force driven filling of micro-channels to create smooth hydrogel substrates with a 2D micro-pattern on the surface. The lithographic procedure involves the molding of a polymer; in our case a bulk PEG-based hydrogel, via UV-curing from a microfabricated silicon master. The grooves of the created regular line pattern are consequently filled with a second hydrogel by capillary action. As a result, a smooth surface is obtained with a well-defined pattern design of the two different polymers on its surface. The FIMIC method is very versatile; the only prerequisite is that the second material is liquid before curing in order to enable the filling process. In this specific case we present the proof of principle of this method by applying two hydrogels which differ in their crosslinking density and therefore in their elasticity. Preliminary cell culture studies on the fabricated elasticity patterned hydrogels indicate the preferred adhesion of the cells to the stiffer regions of the substrates, which implies that the novel substrates are a very useful platform for systematic cell migration studies, e.g. more fundamental investigation of the concept of “durotaxis”