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  • 1
    In: ICES Journal of Marine Science, Oxford University Press (OUP), Vol. 76, No. 4 ( 2019-07-01), p. 960-973
    Abstract: Large scombrids, commercial tuna species, are regularly assessed and managed. However, most of the small scombrids, many mackerels and bonitos, lack accurate catch data to implement traditional stock assessments despite their economic importance in many small-scale fisheries. In this study, we analysed different approaches using length composition data from multiple fleets with different gear selectivity to assess small scombrids in the Atlantic Ocean. Using simulated populations, we compared two length-based methods (length-based spawning potential ratio and length-based integrated mixed effects ), under different length data grouping scenarios. We found that using length data from the fleet targeting the broadest range of sizes resulted in the lowest bias in spawning potential ratio of all options tested. Based on these results, we used biological and length data to estimate a quantitative proxy of current stock status for ten small scombrid stocks in the Atlantic Ocean. We found that some stocks are likely to be overfished, such as little tunny (Euthynnus alletteratus) in the Southeast Atlantic and wahoo (Acanthocybium solandri) in the Northwest Atlantic. This is a starting point in the estimation of stock status for these species, but should not be thought of as a replacement for other more data-intensive assessments.
    Type of Medium: Online Resource
    ISSN: 1054-3139 , 1095-9289
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
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    detail.hit.zdb_id: 1468003-8
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    SSG: 21,3
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  • 2
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  ICES Journal of Marine Science Vol. 78, No. 7 ( 2021-10-09), p. 2420-2431
    In: ICES Journal of Marine Science, Oxford University Press (OUP), Vol. 78, No. 7 ( 2021-10-09), p. 2420-2431
    Abstract: The predominant policy for remedying the world fishing crisis aims at maximum sustainable yield (MSY) by adjusting gear selectivity and fishing effort to maintain sustainable stock levels. The yellowfin tuna (Thunnus albacares) fishery in the Sea of Oman has experienced intense increases in removals since 1980, with particularly high levels since the 1990s. Here, we apply a statistical catch-at-age model to time-series of catches and fishery-dependent length composition data to obtain a preliminary and general understanding of the population dynamics of this stock since the start of the fishery in 1950–2019. Despite limited data, population models consistently indicate a sharp decline in population status since the beginning of the time-series across a variety of assumptions on stock productivity and life history. The gillnet fishery takes almost exclusively immature individuals, with high fishing intensity and removal rates. Both reference models indicate the population is essentially at the same relative stock status in 2019 (10% of unfished), but with very different future projections and higher absolute stock size when recruitment is estimated. The yellowfin tuna population in 2019 is below estimated MSY reference points (based either on unfished size or spawning output at MSY) for current relative stock size, and over the fishing intensity at MSY, indicating current overfishing. Adjusting the interactions of that fishery with the population, while continuing to collected biological composition data representative of each fleet in the fishery, will help mitigate current stock decline and provide the ability to refine future population status determination and forecasts through more informed stock assessments.
    Type of Medium: Online Resource
    ISSN: 1054-3139 , 1095-9289
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2463178-4
    detail.hit.zdb_id: 1468003-8
    detail.hit.zdb_id: 29056-7
    SSG: 12
    SSG: 21,3
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  • 3
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  ICES Journal of Marine Science Vol. 77, No. 1 ( 2020-01-01), p. 97-108
    In: ICES Journal of Marine Science, Oxford University Press (OUP), Vol. 77, No. 1 ( 2020-01-01), p. 97-108
    Abstract: Performance evaluation of data-limited, length-based methods is instrumental in determining and quantifying their accuracy under various scenarios and in providing guidance about model applicability and limitations. We conducted a simulation–estimation analysis to compare the performance of four length-based stock assessment methods: length-based Thompson and Bell (TB), length-based spawning potential ratio (LBSPR), length-based integrated mixed effects (LIME), and length-based risk analysis (LBRA), under varying life history, exploitation status, and recruitment error scenarios. Across all scenarios, TB and LBSPR were the most consistent and accurate assessment methods. LBRA is highly biased, but precautionary, and LIME is more suitable for assessments with time-series longer than a year. All methods have difficulties when assessing short-lived species. The methods are less accurate in estimating the degree of recruitment overfishing when the stocks are severely overexploited, and inconsistent in determining growth overfishing when the stocks are underexploited. Increased recruitment error reduces precision but can decrease bias in estimations. This study highlights the importance of quantifying the accuracy of stock assessment methods and testing methods under different scenarios to determine their strengths and weaknesses and provides guidance on which methods to employ in various situations.
    Type of Medium: Online Resource
    ISSN: 1054-3139 , 1095-9289
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2463178-4
    detail.hit.zdb_id: 1468003-8
    detail.hit.zdb_id: 29056-7
    SSG: 12
    SSG: 21,3
    Location Call Number Limitation Availability
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  • 4
    In: Brain, Oxford University Press (OUP), Vol. 143, No. 8 ( 2020-08-01), p. 2437-2453
    Abstract: In pleiotropic diseases, multiple organ systems are affected causing a variety of clinical manifestations. Here, we report a pleiotropic disorder with a unique constellation of neurological, endocrine, exocrine, and haematological findings that is caused by biallelic MADD variants. MADD, the mitogen-activated protein kinase (MAPK) activating death domain protein, regulates various cellular functions, such as vesicle trafficking, activity of the Rab3 and Rab27 small GTPases, tumour necrosis factor-α (TNF-α)-induced signalling and prevention of cell death. Through national collaboration and GeneMatcher, we collected 23 patients with 21 different pathogenic MADD variants identified by next-generation sequencing. We clinically evaluated the series of patients and categorized the phenotypes in two groups. Group 1 consists of 14 patients with severe developmental delay, endo- and exocrine dysfunction, impairment of the sensory and autonomic nervous system, and haematological anomalies. The clinical course during the first years of life can be potentially fatal. The nine patients in Group 2 have a predominant neurological phenotype comprising mild-to-severe developmental delay, hypotonia, speech impairment, and seizures. Analysis of mRNA revealed multiple aberrant MADD transcripts in two patient-derived fibroblast cell lines. Relative quantification of MADD mRNA and protein in fibroblasts of five affected individuals showed a drastic reduction or loss of MADD. We conducted functional tests to determine the impact of the variants on different pathways. Treatment of patient-derived fibroblasts with TNF-α resulted in reduced phosphorylation of the extracellular signal-regulated kinases 1 and 2, enhanced activation of the pro-apoptotic enzymes caspase-3 and -7 and increased apoptosis compared to control cells. We analysed internalization of epidermal growth factor in patient cells and identified a defect in endocytosis of epidermal growth factor. We conclude that MADD deficiency underlies multiple cellular defects that can be attributed to alterations of TNF-α-dependent signalling pathways and defects in vesicular trafficking. Our data highlight the multifaceted role of MADD as a signalling molecule in different organs and reveal its physiological role in regulating the function of the sensory and autonomic nervous system and endo- and exocrine glands.
    Type of Medium: Online Resource
    ISSN: 0006-8950 , 1460-2156
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
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    SSG: 12
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  • 5
    In: Brain, Oxford University Press (OUP), Vol. 146, No. 4 ( 2023-04-19), p. 1420-1435
    Abstract: Sphingolipids are a diverse family of lipids with critical structural and signalling functions in the mammalian nervous system, where they are abundant in myelin membranes. Serine palmitoyltransferase, the enzyme that catalyses the rate-limiting reaction of sphingolipid synthesis, is composed of multiple subunits including an activating subunit, SPTSSA. Sphingolipids are both essential and cytotoxic and their synthesis must therefore be tightly regulated. Key to the homeostatic regulation are the ORMDL proteins that are bound to serine palmitoyltransferase and mediate feedback inhibition of enzymatic activity when sphingolipid levels become excessive. Exome sequencing identified potential disease-causing variants in SPTSSA in three children presenting with a complex form of hereditary spastic paraplegia. The effect of these variants on the catalytic activity and homeostatic regulation of serine palmitoyltransferase was investigated in human embryonic kidney cells, patient fibroblasts and Drosophila. Our results showed that two different pathogenic variants in SPTSSA caused a hereditary spastic paraplegia resulting in progressive motor disturbance with variable sensorineural hearing loss and language/cognitive dysfunction in three individuals. The variants in SPTSSA impaired the negative regulation of serine palmitoyltransferase by ORMDLs leading to excessive sphingolipid synthesis based on biochemical studies and in vivo studies in Drosophila. These findings support the pathogenicity of the SPTSSA variants and point to excessive sphingolipid synthesis due to impaired homeostatic regulation of serine palmitoyltransferase as responsible for defects in early brain development and function.
    Type of Medium: Online Resource
    ISSN: 0006-8950 , 1460-2156
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1474117-9
    SSG: 12
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  • 6
    In: Brain, Oxford University Press (OUP), Vol. 145, No. 10 ( 2022-10-21), p. 3383-3390
    Abstract: The endocannabinoid system is a highly conserved and ubiquitous signalling pathway with broad-ranging effects. Despite critical pathway functions, gene variants have not previously been conclusively linked to human disease. We identified nine children from eight families with heterozygous, de novo truncating variants in the last exon of DAGLA with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. All children displayed paroxysms of nystagmus or eye deviation accompanied by compensatory head posture and worsened incoordination most frequently after waking. RNA sequencing showed clear expression of the truncated transcript and no differences were found between mutant and wild-type DAGLA activity. Immunofluorescence staining of patient-derived fibroblasts and HEK cells expressing the mutant protein showed distinct perinuclear aggregation not detected in control samples. This report establishes truncating variants in the last DAGLA exon as the cause of a unique paediatric syndrome. Because enzymatic activity was preserved, the observed mislocalization of the truncated protein may account for the observed phenotype. Potential mechanisms include DAGLA haploinsufficiency at the plasma membrane or dominant negative effect. To our knowledge, this is the first report directly linking an endocannabinoid system component with human genetic disease and sets the stage for potential future therapeutic avenues.
    Type of Medium: Online Resource
    ISSN: 0006-8950 , 1460-2156
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1474117-9
    SSG: 12
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  • 7
    In: Postgraduate Medical Journal, Oxford University Press (OUP), Vol. 95, No. 1128 ( 2019-10-01), p. 569-572
    Abstract: It is well recognised that medical training globally and at all levels lacks sufficient incorporation of genetics and genomics education to keep up with the rapid advances and growing application of genomics to clinical care. However, the best strategy to implement these desired changes into postgraduate medical training and engage learners is still unclear. We developed a novel elective rotation in ‘Genomic Medicine and Undiagnosed Diseases’ for categorical Internal Medicine Residents to address this educational gap and serve as an adaptable model for training that can be applied broadly across different specialties and at other institutions. Key curriculum goals achieved include increased understanding about genetic testing modalities and tools available for diagnosis and risk analysis, the role of genetics-trained allied health professionals, and indications and limitations of genetic and genomic testing in both rare and common conditions.
    Type of Medium: Online Resource
    ISSN: 0032-5473 , 1469-0756
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2009568-5
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  • 8
    In: Clinical Infectious Diseases, Oxford University Press (OUP), Vol. 76, No. 10 ( 2023-05-24), p. 1847-1849
    Abstract: A nationwide tuberculosis outbreak linked to a viable bone allograft product contaminated with Mycobacterium tuberculosis was identified in June 2021. Our subsequent investigation identified 73 healthcare personnel with new latent tuberculosis infection following exposure to the contaminated product, product recipients, surgical instruments, or medical waste.
    Type of Medium: Online Resource
    ISSN: 1058-4838 , 1537-6591
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2002229-3
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  • 9
    In: Human Molecular Genetics, Oxford University Press (OUP), Vol. 31, No. 17 ( 2022-08-25), p. 2934-2950
    Abstract: DROSHA encodes a ribonuclease that is a subunit of the Microprocessor complex and is involved in the first step of microRNA (miRNA) biogenesis. To date, DROSHA has not yet been associated with a Mendelian disease. Here, we describe two individuals with profound intellectual disability, epilepsy, white matter atrophy, microcephaly and dysmorphic features, who carry damaging de novo heterozygous variants in DROSHA. DROSHA is constrained for missense variants and moderately intolerant to loss-of-function (o/e = 0.24). The loss of the fruit fly ortholog drosha causes developmental arrest and death in third instar larvae, a severe reduction in brain size and loss of imaginal discs in the larva. Loss of drosha in eye clones causes small and rough eyes in adult flies. One of the identified DROSHA variants (p.Asp1219Gly) behaves as a strong loss-of-function allele in flies, while another variant (p.Arg1342Trp) is less damaging in our assays. In worms, a knock-in that mimics the p.Asp1219Gly variant at a worm equivalent residue causes loss of miRNA expression and heterochronicity, a phenotype characteristic of the loss of miRNA. Together, our data show that the DROSHA variants found in the individuals presented here are damaging based on functional studies in model organisms and likely underlie the severe phenotype involving the nervous system.
    Type of Medium: Online Resource
    ISSN: 0964-6906 , 1460-2083
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1474816-2
    SSG: 12
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  • 10
    In: Human Molecular Genetics, Oxford University Press (OUP), ( 2023-08-08)
    Abstract: Rab GTPases are important regulators of intracellular vesicular trafficking. RAB5C is a member of the Rab GTPase family that plays an important role in the endocytic pathway, membrane protein recycling and signaling. Here we report on 12 individuals with nine different heterozygous de novo variants in RAB5C. All but one patient with missense variants (n = 9) exhibited macrocephaly, combined with mild-to-moderate developmental delay. Patients with loss of function variants (n = 2) had an apparently more severe clinical phenotype with refractory epilepsy and intellectual disability but a normal head circumference. Four missense variants were investigated experimentally. In vitro biochemical studies revealed that all four variants were damaging, resulting in increased nucleotide exchange rate, attenuated responsivity to guanine exchange factors and heterogeneous effects on interactions with effector proteins. Studies in C. elegans confirmed that all four variants were damaging in vivo and showed defects in endocytic pathway function. The variant heterozygotes displayed phenotypes that were not observed in null heterozygotes, with two shown to be through a dominant negative mechanism. Expression of the human RAB5C variants in zebrafish embryos resulted in defective development, further underscoring the damaging effects of the RAB5C variants. Our combined bioinformatic, in vitro and in vivo experimental studies and clinical data support the association of RAB5C missense variants with a neurodevelopmental disorder characterized by macrocephaly and mild-to-moderate developmental delay through disruption of the endocytic pathway.
    Type of Medium: Online Resource
    ISSN: 0964-6906 , 1460-2083
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1474816-2
    SSG: 12
    Location Call Number Limitation Availability
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