Cytoscape.js 2023 update: a graph theory library for visualization and analysis.

SUMMARY: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. This update describes new features and enhancements introduced over many new versions from 2015 to 2022. AVAILABILITY AND IMPLEMENTATION: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cytoscape.js: a graph theory library for visualisation and analysis.

UNLABELLED: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. AVAILABILITY AND IMPLEMENTATION: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. CONTACT: gary.bader@utoronto.ca.

Using biological pathway data with paxtools.

A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial connections between cellular processes, identifying significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine. Due to its complexity and fragmented nature, however, working with pathway data is still difficult. We present Paxtools, a Java library that contains algorithms, software components and converters for biological pathways represented in the standard BioPAX language. Paxtools allows scientists to focus on their scientific problem by removing technical barriers to access and analyse pathway information. Paxtools can run on any platform that has a Java Runtime Environment and was tested on most modern operating systems. Paxtools is open source and is available under the Lesser GNU public license (LGPL), which allows users to freely use the code in their software systems with a requirement for attribution. Source code for the current release (4.2.0) can be found in Software S1. A detailed manual for obtaining and using Paxtools can be found in Protocol S1. The latest sources and release bundles can be obtained from biopax.org/paxtools.

The evolution of RET inhibitor resistance in RET-driven lung and thyroid cancers.

The efficacy of the highly selective RET inhibitor selpercatinib is now established in RET-driven cancers, and we sought to characterize the molecular determinants of response and resistance. We find that the pre-treatment genomic landscape does not shape the variability of treatment response except for rare instances of RAS-mediated primary resistance. By contrast, acquired selpercatinib resistance is driven by MAPK pathway reactivation by one of two distinct routes. In some patients, on- and off-target pathway reactivation via secondary RET solvent front mutations or MET amplifications are evident. In other patients, rare RET-wildtype tumor cell populations driven by an alternative mitogenic driver are selected for by treatment. Multiple distinct mechanisms are often observed in the same patient, suggesting polyclonal resistance may be common. Consequently, sequential RET-directed therapy may require combination treatment with inhibitors targeting alternative MAPK effectors, emphasizing the need for prospective characterization of selpercatinib-treated tumors at the time of monotherapy progression.

Effect of Tacrolimus on Peripheral Nerve Regeneration in Allograft Transplantation: A Light and Electron Microscopic Study.

OBJECTIVES: Peripheral nerve injuries are common in Europe; however, the treatment techniques may lead to disabilities. This study aimed to evaluate the effect of tacrolimus use on the capacity of the epineural sheath graft to improve its regeneration quality in rat sciatic nerves as a treatment option for nerve injuries. MATERIALS AND METHODS: In the experimental process, 30 male Sprague Dawley were used as recipients and 10 Wistar rats were used as donors. Under anesthesia, all rats were operated on to resect the sciatic nerve. The nerve tissue of Wistar rats was used as allograft. In the autograft group, the resected nerve was reversed and sutured, resulting in an epineural sheath graft. For the allograft groups, rats were randomly divided into 2 groups as the tacrolimus-treated group and the nontreated group after allograft transplant. Tacrolimus was administered intramuscularly at 0.1 mg/kg daily for 12 weeks. After the treatment period, rats were killed and evaluated histomorphologically with light and electron microscopy. RESULTS: Histological examination showed no remarkable differences between different regions of the sciatic nerves (distal, middle, and proximal). The axonal density was decreased in the allograft groups compared with the autograft group (P < .001). Results showed that the number of mast cells was increased in the allograft group without tacrolimus treatment (P < .05). Similarly, there was a mild increase in mast cell count in the tacrolimus-treated allograft group. CONCLUSIONS: Our results showed that tacrolimus use in rats with implanted epineural nerve sheath supported recovery in terms of morphological and physiological regeneration of the nerve.

Single-stage ala nasi reconstruction: lateral nasal artery perforator flap.

Since its first description, the nasolabial flap is one of the most preferred methods for the ala nasi reconstruction. Because of its similarity in skin color and texture to the nose, completely concealed scar in the nasolabial sulcus makes it a better choice. The major drawback of this flap is that it necessitates a 2-stage procedure. To gain more freedom in the reconstruction of alar defects, we planned to harvest a perforator flap around the nasolabial fold, which was the one of fixed areas, and included perforators from the lateral nasal artery that is a branch of the facial artery. Lateral nasal artery perforator flap was obtained from 8 patients who have them in the perialar region. Mean age was 64 years. Mean follow-up time was 18 months. In all patients, defects occurred after excision of basal cell carcinoma. All of them were verified histopathologically. In all patients, we identified a suitable lateral nasal artery perforator to meet our reconstructive demand. All defects that occurred were not suitable for primary closure, and sizes of all flaps were bigger than 1.5 cm in width and 1.5 cm in length. All of the flaps survived, and venous congestion was seen in the first 24 hours after operation, but this resolved without any partial or complete necrosis in 3 flaps. As another perforator flap, lateral nasal artery perforator flap can be adopted for defects in any fashion without any mobilizing restrictions. The lateral nasal artery perforator flap can be rotated 90 and 180 degrees as a propeller flap or can be transposed or advanced.

Reconstruction of complicated scalp defect via skin traction.

Management of an open wound is a problem frequently faced, with skin defects that cannot be closed primarily. Functional and aesthetic outcome could be improved if primary approximation of skin in these large defects were possible. Primary closure may be assisted using the viscoelastic properties of the skin. The viscoelastic properties of mechanical creep and stress relaxation in the skin were described more than 40 years ago. If skin is stretched with a constant force, it will expand with time as long as it is kept under tension, a phenomenon known as mechanical creep. In contrast, if the skin is stretched to a constant distance, it will expand and lead to a decrease in the force or tension on the skin with time, a phenomenon known as stress relaxation. We have recently applied these stretching properties to close the scalp because of a defect, which previously would have undergone pericranial flap and split-thickness graft. Because of the partial necrosis of the pericranial flap, skin grafting failed. In the second stage, we inserted only the wrist part of elastic latex gloves to the wound edges in full thickness. The skin margins were advanced slowly and gently.