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Purpose of Review: This review aims to provide a comprehensive overview of the diagnosis of brain death/death by neurologic criteria (BD/DNC) by emphasizing the clinical criteria established by the American Academy of Neurology (AAN) in light of their updated guidelines released in 2023. In this review, we will focus on the current implementation of ancillary tests including the catheter cerebral angiogram, nuclear scintigraphy, and transcranial Doppler, which provide support in diagnoses when clinical examination and apnea tests are inconclusive. Finally, we will also provide examples to discuss the implementation of certain imaging studies in the context of diagnosing BD/DNC. Recent Findings: Recent developments in the field of neurology have emphasized the importance of clinical criteria for diagnosing BD/DNC, with the AAN providing clear updated guidelines that include coma, apnea, and the absence of brainstem reflexes. Current ancillary tests, including the catheter cerebral angiogram, nuclear scintigraphy, and transcranial Doppler play a crucial role in confirming BD/DNC when the clinical assessment is limited. The role of commonly used imaging studies including computed tomography and magnetic resonance angiographies of the brain as well as CT/MR perfusion studies will also be discussed in the context of these new guidelines. Summary: BD/DNC represents the permanent cessation of brain functions, including the brainstem. This review article provides the historical context, clinical criteria, and pathophysiology that goes into making this diagnosis. Additionally, it explores the various ancillary tests and selected imaging studies that are currently used to diagnose BD/DNC under the newly updated AAN guidelines. Understanding the evolution of how to effectively use these diagnostic tools is crucial for healthcare professionals who encounter these BD/DNC cases in their practice.
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BACKGROUND: There lacks rapid standardized bedside testing to screen cognitive deficits following mild traumatic brain injury (mTBI). Immediate Post-Concussion Assessment & Cognitive Testing-Quick Test (ImPACT-QT) is an abbreviated-iPad form of computerized cognitive testing. The aim of this study is to test ImPACT-QT utility in inpatient settings. We hypothesize ImPACT-QT is feasible in the acute trauma setting. METHOD: Trauma patients ages 12-70 were administered ImPACT-QT (09/2022-09/2023). Encephalopathic/medically unstable patients were excluded. Mild traumatic brain injury was defined as documented-head trauma with loss-of-consciousness <30 minutes and arrival Glasgow Coma Scale 13-15. Patients answered Likert-scale surveys. Bivariate analyses compared demographics, attention, motor speed, and memory scores between mTBI and non-TBI controls. Multivariable logistic regression assessed memory score as a predictor of mTBI diagnosis. RESULTS: Of 233 patients evaluated (36 years [IQR 23-50], 71% [166/233] female), 179 (76%) were mTBI patients. For all patients, mean test-time was 9.3 ± 2 minutes with 93% (73/76) finding the test "easy to understand." Mild traumatic brain injury patients than non-TBI control had lower memory scores (25 [IQR 7-100] vs 43 [26-100], P = .001) while attention (5 [1-23] vs 11 [1-32]) and motor score (14 [3-28] vs 13 [4-32]) showed no significant differences. Multivariable-regression (adjustment: age, sex, race, education level, ISS, and time to test) demonstrated memory score predicted mTBI positive status (OR .96, CI .94-.98, P = .004). DISCUSSION: Immediate Post-Concussion Assessment & Cognitive Testing-Quick Test is feasible in trauma patients. Preliminary findings suggest acute mTBIs have lower memory but not attention/motor scores vs non-TBI trauma controls.
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Conmoción Encefálica , Pruebas Neuropsicológicas , Centros Traumatológicos , Humanos , Femenino , Masculino , Adulto , Conmoción Encefálica/diagnóstico , Conmoción Encefálica/complicaciones , Persona de Mediana Edad , Adolescente , Adulto Joven , Computadoras de Mano , Anciano , Disfunción Cognitiva/diagnóstico , Disfunción Cognitiva/etiología , Niño , Pruebas en el Punto de Atención , Escala de Coma de GlasgowRESUMEN
The Crested-tailed deer mouse, Habromyslophurus, is one of seven arboreal species within the genus Habromys. Species of this genus are monotypic, relatively rare, and occur in low densities. Their geographical distribution is highly fragmented due to being restricted to montane cloud forest in Mesoamerica and they are of conservation concern. All Habromys species are endemic to Mexico, except H.lophurus, which is also distributed in Guatemala and El Salvador. In this study, we obtained and characterized the first mitogenome and several thousand nuclear ultraconserved elements (UCEs) of H.lophurus to determine its phylogenetic position within neotomine-peromyscine mice. Its mitogenome sequence (16,509 bp) is only the second complete mitogenome obtained for this poorly known genus. We also obtained the first nuclear genomic data for H.lophurus, including 3,654 UCE loci, as well as a partial mitogenome of H.simulatus (6,349 bp), and 2,186 UCE for the outgroup Holochilussciureus. Phylogenetic analyses that included our newly generated genomic data coupled with previously published data from other neotomine-peromyscine mice confirm the placement of H.lophurus, H.simulatus, and H.ixtlani within a highly supported clade. The Habromys clade was nested within a clade that also contains members of the genus Peromyscus and provides further support for the hypothesis of the paraphyly of Peromyscus. These genomic resources will contribute to future phylogenomic studies that aim to further elucidate the evolutionary history of this rare and critically endangered genus of rodents.
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BACKGROUND: Little is known about the characteristics and determinants of post-stroke cognitive impairment in residents of low- and middle-income countries. The objective of this study was to determine the frequencies, patterns, and risk factors for cognitive impairment in a cross-sectional study of consecutive stroke patients cared for at Uganda's Mulago Hospital, located in sub-Saharan Africa. METHODS: 131 patients were enrolled a minimum of 3-months after hospital admission for stroke. A questionnaire, clinical examination findings, and laboratory test results were used to collect demographic information and data on vascular risk factors and clinical characteristics. Independent predictor variables associated with cognitive impairment were ascertained. Stroke impairments, disability, and handicap were assessed using the National Institute of Health Stroke Scale (NIHSS), Barthel Index (BI), and modified Rankin scale (mRS), respectively. The Montreal Cognitive Assessment (MoCA) was used to assess participants' cognitive function. Stepwise multiple logistic regression was used to identify variables independently associated with cognitive impairment. RESULTS: The overall mean MoCA score was 11.7-points (range 0.0-28.0-points) for 128 patients with available data of whom 66.4% were categorized as cognitively impaired (MoCA < 19-points). Increasing age (OR 1.04, 95% CI 1.00-1.07; p = 0.026), low level of education (OR 3.23, 95% CI 1.25-8.33; p = 0.016), functional handicap (mRS 3-5; OR 1.84, 95% CI 1.28-2.63; p < 0.001) and high LDL cholesterol (OR 2.74, 95% CI 1.14-6.56; p = 0.024) were independently associated with cognitive impairment. CONCLUSIONS: Our findings highlight the high burden and need for awareness of cognitive impairment in post stroke populations in the sub-Saharan region and serve to emphasize the importance of detailed cognitive assessment as part of routine clinical evaluation of patients who have had a stroke.
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Disfunción Cognitiva , Accidente Cerebrovascular , Humanos , Prevalencia , Uganda/epidemiología , Estudios Transversales , Disfunción Cognitiva/diagnóstico , Disfunción Cognitiva/epidemiología , Disfunción Cognitiva/etiología , Accidente Cerebrovascular/complicaciones , Accidente Cerebrovascular/epidemiología , Sobrevivientes , Pruebas NeuropsicológicasRESUMEN
Background Little is known about the characteristics and determinants of post-stroke cognitive impairments in low- and middle-income countries. The objective of this study was to determine the frequencies, patterns, and risk factors for cognitive impairment in a cross-sectional study of consecutive stroke patients cared for at Uganda's Mulago Hospital, located in sub-Saharan Africa. Methods From August 2019 to July 2020, patients were enrolled a minimum of 3-months post-stroke hospital admission. We collected data on their demographics, vascular risk factors and clinical factors using a questionnaire, clinical examination findings, and test results. Independent predictor variables associated with cognitive impairment were ascertained. Stroke impairments, disability, and handicap were assessed using the National Institute of Health Stroke Scale (NIHSS), Barthel Index (BI), and modified Rankin scale (mRS), respectively. The Montreal Cognitive Assessment (MoCA) was used to assess participants' cognitive function. Stepwise multiple logistic regression was used to identify variables independently associated with cognitive impairment. Results The overall mean MoCA score was 11.7-points (range 0.0-28.0-points) for 128 patients with available data of whom 66.4% were categorized as cognitively impaired (MoCA < 19-points). Increasing age (OR 1.04, 95% CI 1.00-1.07; p = 0.026), low level of education (OR 3.23, 95% CI 1.25-8.33; p = 0.016), functional handicap (mRS 3-5; OR 1.84, 95% CI 1.28-2.63; p < 0.001) and high LDL cholesterol (OR 2.74, 95% CI 1.14-6.56; p = 0.024) were independently associated with cognitive impairment. Discussion Further longitudinal, prospective studies are required to confirm these findings and identify strategies for reducing the risk of post-stroke cognitive impairment in this population.
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Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and RefSeq2 launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref. 3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.
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Biología Computacional , Bases de Datos Genéticas , Genómica , Genoma , Humanos , Difusión de la Información , Anotación de Secuencia Molecular , National Library of Medicine (U.S.) , Estados UnidosRESUMEN
Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in-solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat-derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field-collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low-quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples.
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Coyotes , Ecosistema , Animales , Coyotes/genética , ADN , Zorros/genética , Humanos , Polimorfismo de Nucleótido SimpleRESUMEN
We sought to evaluate the success rate of a benzodiazepine-sparing analgosedation protocol (ASP) in mechanically ventilated children and determine the effect of compliance with ASP on in-hospital outcome measures. In this single center study from a quaternary pediatric intensive care unit, our objective was to evaluate the ASP protocol, which included opiate and dexmedetomidine infusions and was used as first-line sedation for all intubated patients. In this study we included 424 patients. Sixty-nine percent (n = 293) were successfully sedated with the ASP. Thirty-one percent (n = 131) deviated from the ASP and received benzodiazepine infusions. Children sedated with the ASP had decrease in opiate withdrawal (OR 0.16, 0.08-0.32), decreased duration of mechanical ventilation (adjusted mean duration 1.81 vs. 3.39 days, p = 0.018), and decreased PICU length of stay (adjusted mean 3.15 vs. 4.7 days, p = 0.011), when compared to the cohort of children who received continuous benzodiazepine infusions. Using ASP, we report that 69% of mechanically ventilated children were successfully managed with no requirement for continuous benzodiazepine infusions. The 69% who were successfully managed with ASP included infants, severely ill patients, and children with chromosomal disorders and developmental disabilities. Use of ASP was associated with decreased need for methadone use, decreased duration of mechanical ventilation, and decreased ICU and hospital length of stay.
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The Caucasian Squirrel, Sciurus anomalus, is the only representative of the Sciuridae family in the Eastern Mediterranean region. In this study, the mitochondrial genome of the Sciurus anomalus species was generated, and we investigate its phylogenetic position within the Sciuridae family. The generated mitogenome sequence is 16,234 bp. It is composed of a control region and a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes.
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The marbled polecat, Vormela peregusna, is one of the least studied species in the Mustelidae family, especially with regard to phylogeography and genetic diversity. In this study, we determined the mitochondrial genome sequence of V. peregusna and investigated its position within the Mustelidae phylogeny. The generated mitogenome is 15,982 bp in length; it consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region.
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The Egyptian mongoose, Herpestes ichneumon, is the only extant mongoose in Europe, with populations still distributed in Africa and the Middle East. In this study, we present the first mitochondrial genome sequence of Herpestes ichneumon and we investigate its phylogenetic position within Feliformia suborder. The resultant mitogenome sequence is 16,775 bps, composed of a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Our results represent a valuable resource for further phylogeographical studies.
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The Mediterranean region is identified as one of the world's 36 biodiversity hotspots, with the Earth's most biologically rich yet threatened areas. Lebanon is a hub for Eastern Mediterranean Region (EMR) biodiversity with 9116 characterized plant and animal species (4486 fauna and 4630 flora). Using DNA barcoding as a tool has become crucial in the accurate identification of species in multiple contexts. It can also complement species morphological descriptions, which will add to our understanding of the biodiversity and richness of ecosystems and benefit conservation projects for endangered and endemic species. In this study, we create the first reference library of standard DNA markers for mammals and plants in the EMR, with a focus on endemic and endangered species. Plant leaves were collected from different nature reserves in Mount Lebanon, and mammal samples were obtained from taxidermized museum specimens or road kills. We generated the 12S rRNA sequences of 18 mammal species from 6 orders and 13 different families. We also obtained the trnL and rbcL barcode sequences of 52 plant species from 24 different families. Twenty-five plant species and two mammal species included in this study were sequenced for the first time using these markers.
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Biblioteca de Genes , Mamíferos/genética , Plantas/genética , Animales , Secuencia de Bases , Biodiversidad , Código de Barras del ADN Taxonómico , Ecosistema , Marcadores Genéticos , Región Mediterránea , Hojas de la Planta/genéticaRESUMEN
Janzen's influential "mountain passes are higher in the tropics" hypothesis predicts restricted gene flow and genetic isolation among populations spanning elevational gradients in the tropics. Few studies have tested this prediction, and studies that focus on population genetic structure in Southeast Asia are particularly underrepresented in the literature. Here, we test the hypothesis that mountain treeshrews (Tupaia montana) exhibit limited dispersal across their broad elevational range which spans ~2,300 m on two peaks in Kinabalu National Park (KNP) in Borneo: Mt Tambuyukon (MT) and Mt Kinabalu (MK). We sampled 83 individuals across elevations on both peaks and performed population genomics analyses on mitogenomes and single nucleotide polymorphisms from 4,106 ultraconserved element loci. We detected weak genetic structure and infer gene flow both across elevations and between peaks. We found higher genetic differentiation on MT than MK despite its lower elevation and associated environmental variation. This implies that, contrary to our hypothesis, genetic structure in this system is not primarily shaped by elevation. We propose that this pattern may instead be the result of historical processes and limited upslope gene flow on MT. Importantly, our results serve as a foundational estimate of genetic diversity and population structure from which to track potential future effects of climate change on mountain treeshrews in KNP, an important conservation stronghold for the mountain treeshrew and other montane species.
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Altitud , Flujo Génico , Animales , Borneo , Estructuras Genéticas , Humanos , MamíferosRESUMEN
Population monitoring is critical to effective conservation, but forest living taxa can be difficult to directly observe. This has been true of African forest elephants (Loxodonta cyclotis), for which we have limited information regarding population size and social behavior despite their threatened conservation status. In this study, we estimated demographic parameters using genetic capture-recapture of forest elephants in the southern Industrial Corridor of the Gamba Complex of Protected Areas in southwestern Gabon, which is considered a global stronghold for forest elephants. Additionally, we examined social networks, predicting that we would find matrilineal structure seen in both savanna and forest elephants. Given 95% confidence intervals, we estimate population size in the sampled area to be between 754 and 1,502 individuals and our best density estimate ranges from 0.47 to 0.80 elephants per km2. When extrapolated across the entire Industrial Corridor, this estimate suggests an elephant population size of 3,033 to 6,043 based on abundance or 1,684 to 2,832 based on density, approximately 40-80% smaller than previously suggested. Our social network analysis revealed approximately half of network components included females with different mitochondrial haplotypes suggesting a wider range of variation in forest elephant sociality than previously thought. This study emphasizes the threatened status of forest elephants and demonstrates the need to further refine baseline estimates of population size and knowledge on social behavior in this taxon, both of which will aid in determining how population dynamics in this keystone species may be changing through time in relation to increasing conservation threats.
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Conservación de los Recursos Naturales , Elefantes/fisiología , Especies en Peligro de Extinción , Bosques , Conducta Social , Animales , ADN Ambiental/aislamiento & purificación , ADN Mitocondrial/aislamiento & purificación , Seguimiento de Parámetros Ecológicos/métodos , Seguimiento de Parámetros Ecológicos/estadística & datos numéricos , Elefantes/psicología , Heces/química , Femenino , Gabón , Haplotipos , Masculino , Dinámica Poblacional/estadística & datos numéricos , Factores SexualesRESUMEN
Environmental DNA (eDNA) has been used to record the presence of many different organisms in several different aquatic and terrestrial environments. Although eDNA has been demonstrated as a useful tool for the detection of invasive and/or cryptic and declining species, this approach is subject to the same considerations that limit the interpretation of results from traditional survey techniques (e.g. imperfect detection). The wood turtle is a cryptic semi-aquatic species that is declining across its range and, like so many chelonian species, is in-need of a rapid and effective method for monitoring distribution and abundance. To meet this need, we used an eDNA approach to sample for wood turtle presence in northern Virginia streams. At the same time, we used repeat visual encounter surveys in an occupancy-modelling framework to validate our eDNA results and reveal the relationship of detection and occupancy for both methods. We sampled 37 stream reaches of varying size within and beyond the known distribution of the wood turtle across northern Virginia. Wood turtle occupancy probability was 0.54 (0.31, 0.76) and while detection probability for wood turtle occupancy was high (0.88; 0.58, 0.98), our detection of turtle abundance was markedly lower (0.28; 0.21, 0.37). We detected eDNA at 76% of sites confirmed occupied by VES and at an additional three sites where turtles were not detected but were known to occur. Environmental DNA occupancy probability was 0.55 (0.29, 0.78); directly comparable to the VES occupancy estimate. Higher probabilities of detecting wood turtle eDNA were associated with higher turtle densities, an increasing number of days since the last rainfall, lower water temperatures, and lower relative discharges. Our results suggest that eDNA technology holds promise for sampling aquatic chelonians in some systems, even when discharge is high and biomass is relatively low, when the approach is validated and sampling error is quantified.
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ADN Ambiental/análisis , ADN Ambiental/genética , Especies en Peligro de Extinción , Tortugas/genética , Animales , Organismos Acuáticos/genética , Biomasa , Costos y Análisis de Costo , Monitoreo del Ambiente/economía , Monitoreo del Ambiente/métodos , Dinámica Poblacional , Probabilidad , Ríos , VirginiaRESUMEN
Conventional drug discovery efforts at the ß2-adrenoceptor (ß2AR) have led to the development of ligands that bind almost exclusively to the receptor's hormone-binding orthosteric site. However, targeting the largely unexplored and evolutionarily unique allosteric sites has potential for developing more specific drugs with fewer side effects than orthosteric ligands. Using our recently developed approach for screening G protein-coupled receptors (GPCRs) with DNA-encoded small-molecule libraries, we have discovered and characterized the first ß2AR small-molecule positive allosteric modulators (PAMs)-compound (Cmpd)-6 [(R)-N-(4-amino-1-(4-(tert-butyl)phenyl)-4-oxobutan-2-yl)-5-(N-isopropyl-N-methylsulfamoyl)-2-((4-methoxyphenyl)thio)benzamide] and its analogs. We used purified human ß2ARs, occupied by a high-affinity agonist, for the affinity-based screening of over 500 million distinct library compounds, which yielded Cmpd-6. It exhibits a low micro-molar affinity for the agonist-occupied ß2AR and displays positive cooperativity with orthosteric agonists, thereby enhancing their binding to the receptor and ability to stabilize its active state. Cmpd-6 is cooperative with G protein and ß-arrestin1 (a.k.a. arrestin2) to stabilize high-affinity, agonist-bound active states of the ß2AR and potentiates downstream cAMP production and receptor recruitment of ß-arrestin2 (a.k.a. arrestin3). Cmpd-6 is specific for the ß2AR compared with the closely related ß1AR. Structure-activity studies of select Cmpd-6 analogs defined the chemical groups that are critical for its biologic activity. We thus introduce the first small-molecule PAMs for the ß2AR, which may serve as a lead molecule for the development of novel therapeutics. The approach described in this work establishes a broadly applicable proof-of-concept strategy for affinity-based discovery of small-molecule allosteric compounds targeting unique conformational states of GPCRs.
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Agonistas de Receptores Adrenérgicos beta 2/metabolismo , Receptores Adrenérgicos beta 2/química , Receptores Adrenérgicos beta 2/metabolismo , Bibliotecas de Moléculas Pequeñas/farmacología , Regulación Alostérica/efectos de los fármacos , Sitio Alostérico/efectos de los fármacos , Sinergismo Farmacológico , Proteínas de Unión al GTP/metabolismo , Biblioteca de Genes , Estructura Molecular , Bibliotecas de Moléculas Pequeñas/química , Relación Estructura-Actividad , Especificidad por Sustrato , beta-Arrestina 1/metabolismoRESUMEN
BACKGROUND: Children with cancer undergo serial invasive, painful procedures as a part of their diagnosis, treatment, and surveillance regimens that require procedural sedation (PS). Some may have a delay in their treatment plan due to same-day cancelation (SDC) of the procedure due to issues related to sedation or other factors. The objective of this report was to evaluate the factors resulting in the SDC of hematology and oncology patients in an outpatient pediatric sedation service. METHODS: Retrospective review of children with cancer or other hematologic disorders undergoing outpatient procedures using a dedicated pediatric sedation team from January 2012 to December 2017. The children with SDC were compared to controls (ie, patients not canceled) during the above study period. RESULTS: A total of 100 patients had SDC during the study. The median age was 10 years (25th percentile to 75th percentile: 7-10 years). The overall SDC rate was 3% and 78/100 (78%) had acute lymphoblastic leukemia. Most common procedure was lumbar puncture with intrathecal chemotherapy in 82/100 (82%) patients. Inadequate blood counts, acute illness, and not nil per os (NPO) accounted for 83% of the reasons for SDC. Type of health insurance, estimated household income, or distance traveled to the clinic did not impact SDC. CONCLUSIONS: The most common factors for SDC included inadequate blood counts, acute illness, and not meeting NPO guidelines. Understanding factors affecting SDC may help improve the efficiency of time-sensitive care delivered to children with cancer and other hematologic concerns by a pediatric sedation service.
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Sedación Profunda , Inyecciones Espinales , Leucemia-Linfoma Linfoblástico de Células Precursoras/terapia , Punción Espinal , Adolescente , Niño , Femenino , Humanos , Masculino , Estudios RetrospectivosRESUMEN
The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community.
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Secuencia de Consenso , Bases de Datos Genéticas , Sistemas de Lectura Abierta , Animales , Curaduría de Datos/métodos , Curaduría de Datos/normas , Bases de Datos Genéticas/normas , Guías como Asunto , Humanos , Ratones , Anotación de Secuencia Molecular , National Library of Medicine (U.S.) , Estados Unidos , Interfaz Usuario-ComputadorRESUMEN
The ß2-adrenergic receptor (ß2AR) has been a model system for understanding regulatory mechanisms of G-protein-coupled receptor (GPCR) actions and plays a significant role in cardiovascular and pulmonary diseases. Because all known ß-adrenergic receptor drugs target the orthosteric binding site of the receptor, we set out to isolate allosteric ligands for this receptor by panning DNA-encoded small-molecule libraries comprising 190 million distinct compounds against purified human ß2AR. Here, we report the discovery of a small-molecule negative allosteric modulator (antagonist), compound 15 [([4-((2S)-3-(((S)-3-(3-bromophenyl)-1-(methylamino)-1-oxopropan-2-yl)amino)-2-(2-cyclohexyl-2-phenylacetamido)-3-oxopropyl)benzamide], exhibiting a unique chemotype and low micromolar affinity for the ß2AR. Binding of 15 to the receptor cooperatively enhances orthosteric inverse agonist binding while negatively modulating binding of orthosteric agonists. Studies with a specific antibody that binds to an intracellular region of the ß2AR suggest that 15 binds in proximity to the G-protein binding site on the cytosolic surface of the ß2AR. In cell-signaling studies, 15 inhibits cAMP production through the ß2AR, but not that mediated by other Gs-coupled receptors. Compound 15 also similarly inhibits ß-arrestin recruitment to the activated ß2AR. This study presents an allosteric small-molecule ligand for the ß2AR and introduces a broadly applicable method for screening DNA-encoded small-molecule libraries against purified GPCR targets. Importantly, such an approach could facilitate the discovery of GPCR drugs with tailored allosteric effects.