Ensembl 2025.

Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity.

GENCODE 2025: reference gene annotation for human and mouse.

GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result.

AVATAR 2.0: next level communication systems for radiotherapy through face-to-face video, biofeedback, translation, and audiovisual immersion.

Purpose: This paper discusses an advanced version of our audiovisual-assisted therapeutic ambience in radiotherapy (AVATAR) radiolucent display systems designed for pediatric radiotherapy, enabling anesthesia-free treatments, video communication, and biofeedback. The scope of the AVATAR system is expanded here in two major ways: (i) through alternative mounting systems to accommodate a broader range of radiotherapy machines (specifically to fit robotic-arm and toroidal geometry photon radiotherapy and proton radiotherapy systems) and (ii) through additional hardware to provide video-calling, optimized audio for clear communication, and combined video inputs for biofeedback, translation, and other advanced functionalities.

Methods And Materials: Because robustness requires strong parts and radio-transparency requires thin, light parts, three-dimensional printing was used to rapidly prototype hollow structures and to iteratively improve robustness.

Integrating Audiovisual Immersion Into Pediatric Radiation Therapy Across Multiple Centers: Methodology, Timeliness, and Cost of the Audiovisual-Assisted Therapeutic Ambience in Radiation Therapy Prospective Multi-Institutional Trial.

Purpose: The Audiovisual-Assisted Therapeutic Ambience in Radiotherapy (AVATAR) trial was a prospective multicenter study (NCT03991156) examining the combination of video immersion with radiation therapy and was successfully conducted through the collaboration of pediatric radiation oncology teams at 10 institutions independent of any pre-existing consortium. We sought to analyze and report the methodology of trial conception and development, process map, and cost.

Methods And Materials: The study enrolled patients aged 3 to 10 years preparing to undergo radiation therapy, integrated the combination of AVATAR-based video immersion with radiation therapy at each institution, and offered AVATAR use as an alternative to anesthesia, with rates of anesthesia use and outcomes of serial standardized anxiety and quality-of-life assessments assessed among the 81 children enrolled.

Skin in the game: The cost consequences of skin cancer diagnosis, treatment and care in Northern Ireland.

Background: Skin cancer is a prevalent cancer in the UK. Its rising incidence and mortality rates are expected to result in substantial financial implications, particularly on diagnostic and treatment services for skin cancer management in Northern Ireland (NI). Such anticipated disease increases underscore the need for prevention and control measures that should help guide policymaking and planning efforts.

Ensembl 2024.

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades.

Common queries in managing rhabdomyosarcoma in low- and middle-income countries: An Indo-North American collaboration.

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma among children and adolescents. The management of RMS involves risk stratification of the patients based on various clinicopathological characteristics. The multimodality treatment approach requires chemotherapy, surgery, and/or radiation.

Food cravings during the first week of concussion.

The brain utilizes glucose as its main source of energy. Traumatic brain injuries may alter the brain's ability to shuttle glucose effectively; therefore, the symptoms experienced may be a signal of the dysregulation. The objective of this cross-sectional study was to investigate the presence of any specific food cravings during the first week post-concussion and if the consumption of such a food decreased the symptoms of concussion.

Effect of Testicular Boost in Children With Leukemia Receiving Total Body Irradiation and Stem Cell Transplant: A Single-Institution Experience.

Purpose: Children with leukemia who receive fractionated total body irradiation (fTBI) with 12 to 13.2 Gy as part of conditioning for hematopoietic stem cell transplant are frequently treated with an additional 4 Gy testicular boost to reduce the risk of testicular relapse. While institutional practices vary, limited data exists regarding whether the 4-Gy testicular boost reduces the risk of relapse and whether it causes toxicity beyond that imparted by TBI.

Long-term Outcomes of Diffuse or Recurrent Tenosynovial Giant Cell Tumor Treated with Postoperative External Beam Radiation Therapy.

Purpose: Tenosynovial giant cell tumor (TGCT) is a rare proliferative disorder of synovial membrane that previously was known as pigmented villonodular synovitis. Primary treatment involves surgical resection; however, complete removal of all disease involvement is difficult to achieve. Radiation may be useful to reduce the risk of recurrence.

GENCODE: reference annotation for the human and mouse genomes in 2023.

GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function.

Ensembl 2023.

Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years.

Adherence to topical glaucoma therapy in patients attending virtual clinics.

Background/objectives: Poor adherence to medical therapy is a major challenge to the effective treatment of chronic diseases including glaucoma. Potential factors influencing adherence include treatment complexity and patient understanding of disease and health beliefs. An increasing number of patients are seen in virtual clinics, where there is no face-to-face consultation, potentially reducing opportunities for patient education and reinforcement of the importance of treatment.

Transformation of identity in substance use as a pathway to recovery and the potential of treatment for hepatitis C: a systematic review.

Background And Aim: People who inject drugs are at high risk of contracting hepatitis C (HCV). The introduction of direct acting antiviral (DAA) drugs to treat HCV has the potential to transform care; however, uptake of DAAs has been slower than anticipated. The strong link between HCV and injecting drug use frames HCV as a shameful, stigmatising disease, reinforcing an 'addict' identity.

Future destinations and social inclusion scoping review: how people cured of hepatitis C (HCV) using direct- acting antiviral drugs progress in a new HCV-free world.

Background: There has been a paradigm shift in the treatment of Hepatitis C (HCV) from the interferon-era to direct-acting antiviral (DAA) drugs. Cure of HCV for the key risk group, those with a history of injecting drug use, may provide a range of benefits to an individual's quality of life that can be additional to that of a clinical cure. The interferon-era provided evidence that cure of HCV can be a turning point for those who use drugs, supporting a recovery journey.

Local Control Outcomes Using Stereotactic Body Radiation Therapy or Surgical Resection for Metastatic Sarcoma.

Purpose: Traditional management of metastatic sarcoma primarily relies on systemic therapy, with surgery often used for tumor control. We analyzed the rates of recurrence, overall survival, and treatment complications in patients undergoing either surgical resection or stereotactic body radiation therapy (SBRT) for metastatic sarcoma of the bone and/or soft tissue.

Methods And Materials: The records of patients with metastatic sarcoma between 2009 and 2020 were reviewed.

Clinical group and modified TNM stage for rhabdomyosarcoma: A review from the Children's Oncology Group.

The Children's Oncology Group (COG) uses Clinical Group (CG) and modified Tumor Node Metastasis (TNM) stage to classify rhabdomyosarcoma (RMS). CG is based on surgicopathologic findings and is determined after the completion of initial surgical procedure(s) but prior to chemotherapy and/or radiation therapy. The modified TNM stage is based on clinical and radiographic findings and is assigned prior to any treatment.

Transformation of identity in substance use as a pathway to recovery and the potential of treatment for hepatitis C: a systematic review protocol.

Introduction: Hepatitis C virus (HCV) is a strongly stigmatised disease as it is framed within the context of injecting substance use. HCV provides the identity of 'dirty' or 'junky', with perceptions by others being beyond the control of the individual. People who experience problematic substance use are often viewed as being outside acceptable social behaviours, thus viewed as having tainted identities or second-class citizens.

An update on rhabdomyosarcoma risk stratification and the rationale for current and future Children's Oncology Group clinical trials.

Children and adolescents with rhabdomyosarcoma (RMS) comprise a heterogeneous population with variable overall survival rates ranging between approximately 6% and 100% depending on defined risk factors. Although the risk stratification of patients has been refined across five decades of collaborative group studies, molecular prognostic biomarkers beyond FOXO1 fusion status have yet to be incorporated prospectively in upfront risk-based therapy assignments. This review describes the evolution of risk-based therapy and the current risk stratification, defines a new risk stratification incorporating novel biomarkers, and provides the rationale for the current and upcoming Children's Oncology Group RMS studies.

Ensembl 2022.

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation.