Genenames.org: the HGNC resources in 2023.

The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and names to human genes. The HGNC database (www.genenames.org) currently contains over 43 000 approved gene symbols, over 19 200 of which are assigned to protein-coding genes, 14 000 to pseudogenes and nearly 9000 to non-coding RNA genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC nomenclature advisors and links to related genomic, clinical, and proteomic information. Here, we describe updates to our resource, including improvements to our search facility and new download features.

The risks of using unapproved gene symbols.

The use of approved nomenclature in publications is vital to enable effective scientific communication and is particularly crucial when discussing genes of clinical relevance. Here, we discuss several examples of cases where the failure of researchers to use a HUGO Gene Nomenclature Committee (HGNC)-approved symbol in publications has led to confusion between unrelated human genes in the literature. We also inform authors of the steps they can take to ensure that they use approved nomenclature in their manuscripts and discuss how referencing HGNC IDs can remove ambiguity when referring to genes that have previously been published with confusing alias symbols.

The Quest for Orthologs orthology benchmark service in 2022.

The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.

The impact of whole of patient nursing assessment frameworks on hospital inpatients: A scoping literature review.

INTRODUCTION: A comprehensive patient assessment is essential for safe patient care. Patient assessment frameworks for nurses are generally restricted to patients who already have altered vital signs and are at risk of deterioration, or to specific risks or body systems such as falls, pressure injury and the Glasgow Coma Score. Comprehensive and structured evidence-based nursing assessment frameworks that consider the whole patient and extend beyond vital signs, specific risks and single systems are not routinely used in inpatient settings but are important to establish early risks for patient deterioration. AIM: The aim of this review was to identify nursing assessment tools or frameworks used to holistically assess hospitalized patients and to identify the impact of these tools on patient and health service outcomes. METHODS: A scoping literature review was conducted. Medical Literature Analysis and Retrieval System Online (MEDLINE), Cumulative Index of Nursing and Allied Health Literature (CINAHL), ProQuest Dissertations and Thesis, Embase and Scopus were databases used in the search. The initial search was conducted in August 2021 and repeated in November 2022. No date parameters were set. The Participants, Concept, Context (PCC) framework was used to guide the development of the research question and consolidate inclusion and exclusion criteria. The PRISMA-ScR Checklist Item was followed to ensure a methodologically sound checklist was used. RESULTS: Ten primary research studies evaluating six nursing assessment frameworks were included. Of the five nursing assessment frameworks, none were explicitly designed for general ward nursing, but rather the emergency department or specific patient cohorts, such as oncology. Four studies reported on reliability and/or validity; two reported on patient outcomes and four on staff satisfaction. CONCLUSION: Evidence-based nursing patient assessment frameworks for use in general inpatient wards are lacking. Existing assessment tools are largely designed for specific patient cohorts, specific body systems or the already deteriorating patient. IMPLICATIONS FOR THE PROFESSION AND PATIENT CARE: A framework to enable a structured approach to patient assessment in this environment is needed for patient safety, consistency in assessment, nursing staff enablement and confidence to escalate care. Routine systematic nursing assessment could also aid timely patient escalation. IMPACT: What problem did the study address? This study addresses the lack of evidence-based nursing assessment frameworks for use in hospitalized patients. The impact of this is that it highlights the need for an evidence-based, whole of patient assessment framework for use by nurses for patients admitted to a ward environment. What were the main findings? This review identified limited comprehensive, patient assessment frameworks for use in general ward inpatient areas. Those identified were not validated for this patient cohort and are aimed at patients already deteriorating. Where and on whom will the research have an impact? This review has the potential to impact future research and patient care. It highlights that most research is focussed on processes to detect and escalate care for the already deteriorating patient. There is a need for an evidence-based routine nursing assessment framework for patients admitted to a ward environment to promote positive patient outcomes and prevent deterioration. PATIENT AND PUBLIC CONTRIBUTION: This review contributes to existing knowledge of nursing patient assessment frameworks, yet it also highlights several gaps. Currently, there are no known, validated, holistic, structured nursing patient assessment frameworks for use in general ward inpatient settings. However, areas that do use such assessment frameworks (e.g. the emergency department) have shown positive patient outcomes and staff usability. Hospitalized ward patients would benefit from routine, structured nursing assessments targeting positive patient outcomes prior to the onset of deterioration.

Updates to HCOP: the HGNC comparison of orthology predictions tool.

Multiple resources currently exist that predict orthologous relationships between genes. These resources differ both in the methodologies used and in the species they make predictions for. The HGNC Comparison of Orthology Predictions (HCOP) search tool integrates and displays data from multiple ortholog prediction resources for a specified human gene or set of genes. An indication of the reliability of a prediction is provided by the number of resources that support it. HCOP was originally designed to show orthology predictions between human and mouse but has been expanded to include data from a current total of 20 selected vertebrate and model organism species. The HCOP pipeline used to fetch and integrate the information from the disparate ortholog and nomenclature data resources has recently been rewritten, both to enable the inclusion of new data and to take advantage of modern web technologies. Data from HCOP are used extensively in our work naming genes as the Vertebrate Gene Nomenclature Committee (https://vertebrate.genenames.org).

The importance of being the HGNC.

The HUGO Gene Nomenclature Committee (HGNC) has been providing standardized symbols and names for human genes since the late 1970s. As funding agencies change their priorities, finding financial support for critical biomedical resources such as the HGNC becomes ever more challenging. In this article, we outline the key roles the HGNC currently plays in aiding communication and the need for these activities to be maintained.

Genenames.org: the HGNC and VGNC resources in 2021.

The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problematic symbols, we are working towards stabilizing symbols where possible; over 2000 symbols for disease associated genes are now marked as stable in our symbol reports. All of our data is available at the HGNC website https://www.genenames.org. The Vertebrate Gene Nomenclature Committee (VGNC) was established to assign standardized nomenclature in line with human for vertebrate species lacking their own nomenclature committee. In addition to the previous VGNC core species of chimpanzee, cow, horse and dog, we now name genes in cat, macaque and pig. Gene groups have been added to VGNC and currently include two complex families: olfactory receptors (ORs) and cytochrome P450s (CYPs). In collaboration with specialists we have also named CYPs in species beyond our core set. All VGNC data is available at https://vertebrate.genenames.org/. This article provides an overview of our online data and resources, focusing on updates over the last two years.

Technology enhanced assessment: Ottawa consensus statement and recommendations.

INTRODUCTION: In 2011, a consensus report was produced on technology-enhanced assessment (TEA), its good practices, and future perspectives. Since then, technological advances have enabled innovative practices and tools that have revolutionised how learners are assessed. In this updated consensus, we bring together the potential of technology and the ultimate goals of assessment on learner attainment, faculty development, and improved healthcare practices. METHODS: As a material for the report, we used the scholarly publications on TEA in both HPE and general higher education, feedback from 2020 Ottawa Conference workshops, and scholarly publications on assessment technology practices during the Covid-19 pandemic. RESULTS AND CONCLUSION: The group identified areas of consensus that remained to be resolved and issues that arose in the evolution of TEA. We adopted a three-stage approach (readiness to adopt technology, application of assessment technology, and evaluation/dissemination). The application stage adopted an assessment 'lifecycle' approach and targeted five key foci: (1) Advancing authenticity of assessment, (2) Engaging learners with assessment, (3) Enhancing design and scheduling, (4) Optimising assessment delivery and recording learner achievement, and (5) Tracking learner progress and faculty activity and thereby supporting longitudinal learning and continuous assessment.

Genenames.org: the HGNC and VGNC resources in 2019.

The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 40 000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 to assign standardized nomenclature in line with human for vertebrate species that lack their own nomenclature committees. The VGNC initially assigned nomenclature for over 15000 protein-coding genes in chimpanzee. We have extended this process to other vertebrate species, naming over 14000 protein-coding genes in cow and dog and over 13 000 in horse to date. Our HGNC website https://www.genenames.org has undergone a major design update, simplifying the homepage to provide easy access to our search tools and making the site more mobile friendly. Our gene families pages are now known as 'gene groups' and have increased in number to over 1200, with nearly half of all named genes currently assigned to at least one gene group. This article provides an overview of our online data and resources, focusing on our work over the last two years.

A unified nomenclature for vertebrate olfactory receptors.

BACKGROUND: Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~ 1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights. RESULTS: Here, we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5. Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~ 50% in dog and cow and to ~ 30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature. CONCLUSIONS: We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.

Expression and function of spineless orthologs correlate with distal deutocerebral appendage morphology across Arthropoda.

The deutocerebral (second) head segment is putatively homologous across Arthropoda, in spite of remarkable disparity of form and function of deutocerebral appendages. In Mandibulata this segment bears a pair of sensory antennae, whereas in Chelicerata the same segment bears a pair of feeding appendages called chelicerae. Part of the evidence for the homology of deutocerebral appendages is the conserved function of homothorax (hth), which has been shown to specify antennal or cheliceral fate in the absence of Hox signaling, in both mandibulate and chelicerate exemplars. However, the genetic basis for the morphological disparity of antenna and chelicera is not understood. To test whether downstream targets of hth have diverged in a lineage-specific manner, we examined the evolution of the function and expression of spineless (ss), which in two holometabolous insects is known to act as a hth target and distal antennal determinant. Toward expanding phylogenetic representation of gene expression data, here we show that strong expression of ss is observed in developing antennae of a hemimetabolous insect, a centipede, and an amphipod crustacean. By contrast, ss orthologs are not expressed throughout the cheliceral limb buds of spiders or harvestmen during developmental stages when appendage fate is specified. RNA interference-mediated knockdown of ss in Oncopeltus fasciatus, which bears a simple plesiomorphic antenna, resulted in homeotic distal antenna-to-leg transformation, comparable to data from holometabolous insect counterparts. Knockdown of hth in Oncopeltus fasciatus abrogated ss expression, suggesting conservation of upstream regulation. These data suggest that ss may be a flagellar (distal antennal) determinant more broadly, and that this function was acquired at the base of Mandibulata.

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.

Exploring informal workplace learning in primary healthcare for continuous professional development.

BACKGROUND AND OBJECTIVES: All health and social care professionals learn on the job through both formal and informal learning processes, which contributes to continuous professional development (CPD). This study explored workplace learning in General Practices, specifically looking at the role of informal learning and the workplace practices that appear to support or restrict that learning, as well as how technology was integrated into these learning processes. METHODS: Three focus groups with general practitioners, practice nurses, managerial and administrative staff were conducted followed by twelve individual semi-structured interviews with participants drawn from the focus groups. Three observations of multi-disciplinary team meetings were used to establish potential team-based learning activities. RESULTS: Triggers for informal workplace learning included patients presenting challenging or unusual conditions; exposure to others' professional practice; and policy driven changes through revised guidance and protocols. By exploring how these triggers were acted upon, we identified mechanisms through which the primary care workplace supports or restricts informal learning through working practices, existing technologies and inter-professional structures. CONCLUSION: Informal workplace learning was identified as arising from both opportunistic encounters and more planned activities, which are both supported and restricted through a variety of mechanisms. Maximising informal learning opportunities and removing barriers to doing so should be a priority for primary care practitioners, managers and educators.

Using transprofessional care in the emergency department to reduce patient admissions: A retrospective audit of medical histories.

The demand for emergency department (ED) services has increased significantly, due to our increasingly ageing population and limited access to primary care. This article reports outcomes from a transprofessional model of care in an ED in Victoria, Australia. Nurses, physiotherapists, social workers, and occupational therapists undertook additional education to increase the range of services they could provide and thereby expedite patient flow through the ED. One hundred patients who received this service were matched against 50 patients who did not. The most common reasons for patient admission were limb injury/limb pain (n = 47, 23.5%) and falls (n = 46, 23.0%). Transprofessional interventions included applying supportive bandages, slings, zimmer splints and controlled ankle motion (CAM) boots, and referral to new services such as case management and mental health teams. The rate of hospital admissions was significantly lower in the transprofessional group (n = 27, 18.0%) than in the reference group (n = 19, 38%, p = 0.005). This group also had a slightly lower re-presentation rate (n = 4, 2.7%) than patients in the reference group (n = 2, 4.0%). There are many benefits that support this model of care that in turn reduces ED overcrowding and work stress. A transprofessional model may offer a creative solution to meeting the varied needs of patients presenting for emergency care.

Initiatives to reduce overcrowding and access block in Australian emergency departments: a literature review.

Australian emergency departments are experiencing an increasing demand for their services. Patient throughput continues to expand resulting in overcrowding and access block where patients cannot gain entry to appropriate hospital beds. This is despite both state and federal governments implementing numerous schemes to address the complex causes of stress on emergency departments. This paper explores the current literature and highlights the key strategies adopted by different emergency departments to reduce delays and streamline patient flow, including: waiting room nurses; streaming; rapid assessment teams; short stay units and care coordination programmes. Many of these initiatives have proven successful at reducing the number of people re-presenting to the emergency department, addressing time delays and improving the management of existing resources and patient flow. More recent changes include increasing the scope of practice and workload for triage nurses. With the recent introduction of the National Emergency Access Target, which requires that most patients presenting to Australian emergency departments are reviewed and transferred or discharged from the department within 4h, traditional roles of nurses in the emergency department are changing and expanding to meet the needs of modern healthcare systems.

Attenuation of bone morphogenetic protein signaling during amphibian limb development results in the generation of stage-specific defects.

The vertebrate limb is one of the most intensively studied organs in the field of developmental biology. Limb development in tetrapod vertebrates is highly conserved and dependent on the interaction of several important molecular pathways. The bone morphogenetic protein (BMP) signaling cascade is one of these pathways and has been shown to be crucial for several aspects of limb development. Here, we have used a Xenopus laevis transgenic line, in which expression of the inhibitor Noggin is under the control of the heat-shock promoter hsp70 to examine the effects of attenuation of BMP signaling at different stages of limb development. Remarkably different phenotypes were produced at different stages, illustrating the varied roles of BMP in development of the limb. Very early limb buds appeared to be refractory to the effects of BMP attenuation, developing normally in most cases. Ectopic limbs were produced by overexpression of Noggin corresponding to a brief window of limb development at about stage 49/50, as recently described by Christen et al. (2012). Attenuation of BMP signaling in stage 51 or 52 tadpoles lead to a reduction in the number of digits formed, resulting in hypodactyly or ectrodactyly, as well as occasional defects in the more proximal tibia-fibula. Finally, inhibition at stage 54 (paddle stage) led to the formation of dramatically shortened digits resulting from loss of distal phalanges. Transcriptome analysis has revealed the possibility that more Noggin-sensitive members of the BMP family could be involved in limb development than previously suspected. Our analysis demonstrates the usefulness of heat-shock-driven gene expression as an effective method for inhibiting a developmental pathway at different times during limb development.

Work and social adjustment in patients with anorexia nervosa.

OBJECTIVE AND METHODS: The Work and Social Adjustment Scale (WSAS) assesses patients' perceptions of impairment in everyday functioning and has been reported as a simple and reliable self-report measure in different psychiatric disorders. This study compared WSAS data from an anorexia nervosa (AN) patient group with that from healthy controls (HCs) and published data from other patient groups. A total of 160 female participants (AN, 77; HC, 83) completed the WSAS as well as measures of eating disorder symptom severity and brief assessments of anxiety and depression. RESULTS: Work and Social Adjustment Scale scores for the AN group were found to be in the severely impaired range, whereas the scores for those within the HC group indicated very little, or no impairment. Total WSAS scores in the AN group were significantly correlated with severity of clinical symptoms, and eating disorder-specific symptoms were the best predictor of social and occupational functional impairment. The greatest impairment in the AN group was reported in the realm of social leisure. CONCLUSIONS: Consistent with reports in other clinical populations, it is suggested that the WSAS could be an extremely useful and meaningful measure to assess social and occupational functioning in people with eating disorders, in addition to eating disorder-specific assessments.

The VGNC: expanding standardized vertebrate gene nomenclature.

The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 as a sister project to the HUGO Gene Nomenclature Committee, to approve gene nomenclature in vertebrate species without an existing dedicated nomenclature committee. The VGNC aims to harmonize gene nomenclature across selected vertebrate species in line with human gene nomenclature, with orthologs assigned the same nomenclature where possible. This article presents an overview of the VGNC project and discussion of key findings resulting from this work to date. VGNC-approved nomenclature is accessible at https://vertebrate.genenames.org and is additionally displayed by the NCBI, Ensembl, and UniProt databases.

Ecstasy and related drug consumption and the effect on emergency department resource use.

BACKGROUND: Ecstasy and other recreational related drug use and substance related presentations to the emergency department (ED) are increasing. The aim of this study was to identify, quantify, and describe the ED resources used to care for patients diagnosed with ecstasy and related drug (ERD) use. METHOD: A retrospective case study design. RESULTS: Eighty-nine patients (89%) needed one to one (n=25) and/or one to two nursing care (n=83). Security presence was required for 37 patients (37%) and the Emergency Psychiatric Service team reviewed 29 patients (29%). Most patients (n=80, 80%) received an Emergency Short Stay Unit admission, but continued to receive care in the ED, and were not transferred to the short stay unit (n=74, 92.5%). Most patients (n=86, 86%) were discharged home, after 5hr 49mins (median) in ED. CONCLUSION: Extensive human resources were required to care for patients diagnosed with ERD use. Nursing staffing levels required to care for this patient cohort during times of peak presentations should be reviewed. It is important the government acknowledges the National Emergency Access Target is not suitable for all presenting patients. A dedicated model of care is recommended to support care requirements and reduce pressure on busy EDs.