A new experimental evidence-weighted signaling pathway resource in FlyBase.

Research in model organisms is central to the characterization of signaling pathways in multicellular organisms. Here, we present the comprehensive and systematic curation of 17 Drosophila signaling pathways using the Gene Ontology framework to establish a dynamic resource that has been incorporated into FlyBase, providing visualization and data integration tools to aid research projects. By restricting to experimental evidence reported in the research literature and quantifying the amount of such evidence for each gene in a pathway, we captured the landscape of empirical knowledge of signaling pathways in Drosophila.

PANGEA: a new gene set enrichment tool for Drosophila and common research organisms.

Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an 'omics' study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.

The Gene Ontology knowledgebase in 2023.

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms.

PANGEA: A New Gene Set Enrichment Tool for and Common Research Organisms.

Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an 'omics' study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.

Using FlyBase: A Database of Drosophila Genes and Genetics.

Since 1992, FlyBase has provided a freely available online database of information about the model organism Drosophila melanogaster. Data in FlyBase is curated manually from research papers as well as computationally from a variety of relevant sources, to serve as an information hub that enables and accelerates research discovery. This chapter aims to give users new to the database an overview of the layout and types of data available, as well as introducing some tools with which to access the data.

FlyBase: updates to the Drosophila melanogaster knowledge base.

FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays ('ribbons') of expression and disease data.

Emergency Care Considerations for the Transgender Patient: Complications of Gender-Affirming Treatments.

The transgender population presents a unique challenge for the emergency nurse. There are types of surgeries, medications, complications, and differences in laboratory testing that are unique to transgender people. In addition, emergency nurses are increasingly encountering more transgender patients in the emergency department for care, referrals, and education.

Phase I Trial of Dabrafenib and Pazopanib in Mutated Advanced Malignancies.

Purpose: Several tumor types carry mutations and vascular endothelial growth factor pathway upregulation. Resistance mechanisms to BRAF inhibitors can include platelet-derived growth factor-β upregulation. Dabrafenib, a BRAF inhibitor, and pazopanib, a multikinase inhibitor that targets vascular endothelial growth factor and platelet-derived growth factor, have not been combined previously.

FlyBase 2.0: the next generation.

FlyBase (flybase.org) is a knowledge base that supports the community of researchers that use the fruit fly, Drosophila melanogaster, as a model organism. The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila.

Interdisciplinary rehabilitation for a patient with incomplete cervical spinal cord injury and multimorbidity: A case report.

Rationale: This report describes interdisciplinary rehabilitation for a 51-year-old male recovering from incomplete cervical spinal cord injury (SCI) and multiple comorbidities following an automobile accident.

Patient Concerns: The patient was admitted to a rehabilitation specialty hospital approximately 2 months post SCI and 2 separate surgical fusion procedures (C3-C6).

Diagnoses: Clinical presentation at the rehabilitation hospital included moderate to severe motor strength loss in both upper and lower extremities, a percutaneous endoscopic gastronomy tube (PEG), dysphagia, bowel/bladder incontinence, dependence on a mechanical lift and tilting wheelchair due to severe orthostatic hypotension, and pre-existing shoulder pain from bilateral joint degeneration.

Exploring FlyBase Data Using QuickSearch.

FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data.

FlyBase at 25: looking to the future.

Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions, and reagents such as stocks and cDNAs.

Veliparib Alone or in Combination with Mitomycin C in Patients with Solid Tumors With Functional Deficiency in Homologous Recombination Repair.

Background: BRCA germline mutations are being targeted for development of PARP inhibitors. BRCA genes collaborate with several others in the Fanconi Anemia (FA) pathway. We screened cancer patients' tumors for FA functional defects then aimed to establish the safety/feasibility of administering PARP inhibitors as monotherapy and combined with a DNA-breaking agent.

An analysis of Brain Trauma Foundation traumatic brain injury guideline compliance and patient outcome.

Introduction: Evidence-based guidelines for the care of severe traumatic brain injury have been available from the Brain Trauma Foundation (BTF) since 1995. A total of 15 recommendations compose the current guidelines. Although each individual guideline has been validated in isolation, to date, little research has examined the guidelines in composite.

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.

Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome assembly for over 7 years. With the enormous amount of information now attached to the D. melanogaster genome in public repositories and individual laboratories, the replacement of the previous assembly by the new one is a major event requiring careful migration of annotations and genome-anchored data to the new, improved assembly.

FlyBase: improvements to the bibliography.

An accurate, comprehensive, non-redundant and up-to-date bibliography is a crucial component of any Model Organism Database (MOD). Principally, the bibliography provides a set of references that are specific to the field served by the MOD. Moreover, it serves as a backbone to which all curated biological data can be attributed.

Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage.

We report the rational design and in vivo testing of mosaic proteins for a polyvalent pan-filoviral vaccine using a computational strategy designed for the Human Immunodeficiency Virus type 1 (HIV-1) but also appropriate for Hepatitis C virus (HCV) and potentially other diverse viruses. Mosaics are sets of artificial recombinant proteins that are based on natural proteins. The recombinants are computationally selected using a genetic algorithm to optimize the coverage of potential cytotoxic T lymphocyte (CTL) epitopes.

FlyBase 101--the basics of navigating FlyBase.

FlyBase (http://flybase.org) is the leading database and web portal for genetic and genomic information on the fruit fly Drosophila melanogaster and related fly species. Whether you use the fruit fly as an experimental system or want to apply Drosophila biological knowledge to another field of study, FlyBase can help you successfully navigate the wealth of available Drosophila data.

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses.

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today.

Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity.

Immunological control of hepatitis C virus (HCV) is possible and is probably mediated by host T-cell responses, but the genetic diversity of the virus poses a major challenge to vaccine development. We considered monovalent and polyvalent candidates for an HCV vaccine, including natural, consensus and synthetic 'mosaic' sequence cocktails. Mosaic vaccine reagents were designed using a computational approach first applied to and demonstrated experimentally for human immunodeficiency virus type 1 (HIV-Delta).

Effects of 2,4-diaminoquinazoline derivatives on SMN expression and phenotype in a mouse model for spinal muscular atrophy.

Proximal spinal muscular atrophy (SMA), one of the most common genetic causes of infant death, results from the selective loss of motor neurons in the spinal cord. SMA is a consequence of low levels of survival motor neuron (SMN) protein. In humans, the SMN gene is duplicated; SMA results from the loss of SMN1 but SMN2 remains intact.

Phase I active immunotherapy with combination of two chimeric, human epidermal growth factor receptor 2, B-cell epitopes fused to a promiscuous T-cell epitope in patients with metastatic and/or recurrent solid tumors.

PURPOSE To evaluate the maximum-tolerated dose (MTD), safety profile, and immunogenicity of two chimeric, B-cell epitopes derived from the human epidermal growth factor receptor (HER2) extracellular domain in a combination vaccine with a promiscuous T-cell epitope (ie, MVF) and nor-muramyl-dipeptide as adjuvant emulsified in SEPPIC ISA 720. PATIENTS AND METHODS Eligible patients with metastatic and/or recurrent solid tumors received three inoculations on days 1, 22, and 43 at doses of total peptide that ranged from 0.5 to 3.

The seismic analyzer: interpreting and illustrating 2D seismic data.

We present a toolbox for quickly interpreting and illustrating 2D slices of seismic volumetric reflection data. Searching for oil and gas involves creating a structural overview of seismic reflection data to identify hydrocarbon reservoirs. We improve the search of seismic structures by precalculating the horizon structures of the seismic data prior to interpretation.

DcpS as a therapeutic target for spinal muscular atrophy.

Spinal muscular atrophy (SMA) is caused by deletion or mutation of both copies of the SMN1 gene, which produces an essential protein known as SMN. The severity of SMA is modified by variable copy number of a second gene,SMN2, which produces an mRNA that is incorrectly spliced with deletion of the last exon. We described previously the discovery of potent C5-substituted quinazolines that increase SMN2 gene expression by 2-fold.