80 research outputs found
Communicating outputs from risk assessment models: A picture paints a thousand words
No full textVisualisation and presentation of complex, feature rich data is often neglected within the area of quantitative risk assessment when, in reality, a clear representation of the data may greatly support the understanding of complex results and increase acceptance of results among risk managers. Feature rich data containing many explanatory variables can be very challenging to visualise effectively in a single graphic as the message can become cluttered when using two, or more, variables. As part of the international SPARE project (SPARE project team, 2018), a generic quantitative risk assessment (QRA) combining multiple routes and routes of entry was developed (Simons et al., 2019). The risk assessment provides an overall risk score for entry and exposure of three different pathogens into individual European Union (EU) countries: Classical swine fever (CSF), Bluetongue virus (BTV) and classical rabies.This paper describes the development of an application with graphical user interface (GUI) that allowed users, in particular risk managers, to explore the data and calculations behind the QRA. The aim was to produce an application that clearly illustrates the data and communicates the information without biasing their opinion in any way. To reach as wide an audience as possible the application should be easily accessed and understood without requiring the user to have detailed technical computing knowledge to use it.Development of the application followed a set of design principles focused on: context, software, data inputs and interactivity. This produced an application designed for a particular audience, written in a suitable language that allowed the user to explore the data within the context of a clearly defined risk question. Accessibility options for users with visual challenges was also considered and included within the design phase
From bibliometrics to altmetrics: A changing scholarly landscape
No full textPublished in C&RL News, November 2012
Fixation artifacts in rainbow-trout (Salmo-gairdner) gills - a morphometric evaluation
No full textPT: J; CR: ALBASSAM M, 1987, VET PATHOL, V24, P34 BENVILLE PE, 1968, TOXICOL APPL PHARM, V12, P156 CHRETIEN M, 1986, BIOL CELL, V56, P137 DAOUST PY, 1984, VET PATHOL, V21, P93 DEJOUR P, 1981, PRINCIPLES COMP RESP ELLER LL, 1975, PATHOLOGY FISHES, P305 GRIZZLE JM, 1981, T AM FISH SOC, V110, P29 HARGENS AR, 1974, COMP BIOCH PHYSL A, V48, P675 HERMAN RL, 1985, T AM FISH SOC, V114, P911 HUGHES GM, 1979, WATER RES, V13, P665 LAURENT P, 1984, FISH PHYSIOL, V10, P73 MALLATT J, 1985, CAN J FISH AQUAT SCI, V42, P630 NICHOLS DJ, 1987, COMP BIOCHEM PHYS A, V87, P703 PERRY SF, 1984, FISH PHYSL B, V10, P324 RANDALL DJ, 1981, EVOLUTION AIRBREATHI RHODIN JAG, 1964, ANAT REC, V148, P420 ROBERTS RJ, 1978, FISH PATHOL, P55 ROBIN ED, 1973, NEW ENGL J MED, V238, P292 SNEDECOR GW, 1980, STATISTICAL METHODS THOMPSON SW, 1966, SELECTED HISTOCHEMIC WALSH AH, 1975, PATHOLOGY FISHES, P515 WEST JB, 1982, PULMONARY PATHOPHYSI WOBESER G, 1975, J FISH RES BOARD CAN, V32, P2005 ZENKER WGE, 1987, COMP BIOCHEM PHYS A, V86, P423; NR: 24; TC: 21; J9: CAN J FISHERIES AQUAT SCI; PG: 6; GA: U5947Source type: Electronic(1
Stasimopus dylani Brandt & Sole & Lyle 2023, sp. nov.
No full textStasimopus dylani sp. nov. (Figures 3B, 5A; 8, 9, 10, 11A) Type material: Holotype Ô SOUTH AFRICA: Western Cape Province: Murraysburg (-31.8884, 23.7310), 21.v.2018, S. Brandt, C. Sole, E. Engelbrecht and E. Brand, (NCA 2019/663). Paratypes. Same data, 21.v.2018, 1Ô (NCA 2019/664); Eastern cape Province: Jansenville (-32.8772, 24.4952), 17.vii.2015, I. Engelbrecht and D. Kambas, 4ÔÔ (NCA 2019/697, NCA 2019/698, NCA 2019/699, NCA 2019/702), Willowmore (-33.0423, 23.1958), 15.v.2018, S. Brandt, C. Sole, E. Engelbrecht and E. Brand, 1♀ juv. (NCA 2019/676). Etymology: This species is a patronym in recognition of Dylan Cecil Brandt, for his unending support and encouragement of the first author during her postgraduate studies. Diagnosis: The males of S. dylani sp. nov. are distinguishable from other members of the genus occurring in the Karoo based on the following combination of characters. Differentiated from S. astutus, S. erythrognathus, S. malesociatus sp. nov., S. patersonae, S. steynsbergensis, S. karooensis sp. nov. and S. mandelai based on the pedipalp not extending beyond the tarsus of leg I. It is distinguished from S. palpiger by the pedipalp that is longer than leg I, which is not the case with S. dylani sp. nov. The species can be distinguished from S. schrieneri, S. ignis sp. nov., S. finni sp. nov. and S. maraisi based on the largest eye, which in these species is the ALE, whereas in S. dylani sp. nov. it is the AME. Description: Based on the holotype Ô (NCA 2019/663) and paratypes 5Ô (NCA 2019/664, NCA 2019/697, NCA 2019/698, NCA 2019/699, NCA 2019/702). Remarks: ♀: Known only from males. General: Ô: (Fig 5A) Medium bodied spiders, ranging between 10.68–13.03 (13.03) total length. Carapace: Ô: Carapace length 4.78–6.28 (6.28); width 4.42–5.74 (5.74). Black colouration, thoracic region with rugose texture. The fovea strongly procurved, between 1.00–1.38 (1.11) in length. Ocelli: Ô: (Fig 11A, Fig 3B) AME diameter 0.26–0.28 (0.28), PME diameter 0.16–0.20 (0.19), MOQ anterior width 1.30–1.67 (1.67), MOQ posterior width 1.72–2.09 (2.05); AME-AME 0.25, AME-ALE 0.15, ALE-ALE 1.08, PME-PME 1.02, PME-PLE 0.16, PLE-PLE 1.62. AER arrangement slightly recurved, PER recurved. Chelicerae: Ô: (Fig 8B) Two teeth rows present, 4 teeth in proventral row, 5 teeth in retroventral row; 12 cuspules in between. Sternum, labium and maxillae: Ô: (Fig 8A) Sternum length 2.27–3.48 (3.48); sternum width 2.47–3.05 (3.05). Sternum shape has distinct impressions of where the coxa are situated. Sigilla in the shape of a fused arrow, distal end fused, proximal end 1.06–1.45 (1.12) apart; cuspules absent on labium and maxilla. Abdomen: Ô: (Fig 5A) Abdomen length 5.56–6.75 (6.75); width 3.45–4.63 (4.63). Colour, do - dark grey, v - and laterally beige. Pedipalps: Ô: (Fig 10A, B) Total length 19.01; Segment lengths 1.77, 6.41, 4.82, -,6.02. Spination: spines absent. Bulb compact, embolus elongated, tapering into sharp point, extending downwards, almost parallel to tibia. Legs: Ô: Length order: I, IV, II, III. I Total length 22.94; Segment lengths 7.07, 3.23, 4.86, 5.62, 2.16; Spination: spines absent on femur and patella, with sparse setae. Tibia v - 19 large spines (extending pl & rl), covering only distal half. Metatarsus (Fig 10C) pl - 19 large spines extending v, 21 large spines rl (slightly v). Tarsus (Fig 10C) pl - 4 spines, rl - 4 spines, v - scopulate. II Total length 20.88; Segment lengths 6.42, 2.86, 4.32, 5.21, 2.07; Spination: spines absent on femur and patella, with sparse setae. Tibia v - 5–7 spines distally. Metatarsus pl - 12–13 large spines extending v, rl - 10–11 large spines extending v. Tarsus pl - 4 spines, rl- 3–4 spines, v - scopulate. III Total length 16.45; Segment lengths 4.64, 2.26, 2.55, 4.35, 2.66; Spination: spines absent on femur, with sparse setae. Patella, do (slightly pl)- 7 small spines. Tibia (Fig 10F), do - Distally dense patch of spines (approx. 25), extend to metatarsus. Metatarsus (Fig 10D), pl - 11 spines, do - small patch of spines proximally (approx. 15) connecting to tibia, rl - 3 spines, v - 5 spines. Tarsus (Fig 10D) pl - 8 spines, rl - 7 spines. IV Total length 22.85; Segment lengths 5.32, 2.65, 4.50, 7.42, 2.96; Spination: spines absent on femur, with sparse setae. Patella (Fig 10G), do - short red spines proximally, less dense distally, interspersed with black setae. Tibia short black setae. Metatarsus (Fig 10E) pl - 5 spines, rl - 6 spines. Tarsus (Fig 10E) pl - 10 spines, rl - 9 spines. Distribution and environment notes: The species is found in the localities indicated in Figure 9. The species appears to have a broader distribution in the Western and Eastern Cape provinces of South Africa. The areas typically had sandy soils. The juvenile female was collected from a flat pan. All the males were collected while they were crossing quite roads. The SUOJ locality had no rain on the day collected, but a slight drizzle did occur after collection, whereas the males from FRE were collected after very heavy rain.Published as part of Brandt, Shannon, Sole, Catherine & Lyle, Robin, 2023, An integrative taxonomy of the genus Stasimopus Simon 1892 (Araneae: Mygalomorphae) of the Karoo with the description of nine new species and a Stasimopus maraisi Hewitt 1914 male, pp. 1-60 in Zootaxa 5341 (1) on pages 19-24, DOI: 10.11646/zootaxa.5341.1.1, http://zenodo.org/record/832374
Stasimopus finni Brandt & Sole & Lyle 2023, sp. nov.
No full textStasimopus finni sp. nov. (Figures 5B, 11B, 13A, 14, 15) Type material: Holotype Ô SOUTH AFRICA: Eastern Cape Province, Somerset East (-32.9386, 25.6612), 14.v.2018, S. Brandt, C. Sole, E. Engelbrecht and E. Brand, (NCA 2019/605). Etymology: The specific epithet is patronym in honour of Finn Robert Pirk the son of the third author, who loves all creepy crawlies. Diagnosis: The males of S. finni sp. nov. are distinguishable from other members of the genus occurring in the Karoo based on the following combination of characters. It is differentiated from S. astutus, S. erythrognathus, S. malesociatus sp. nov., S. patersonae, S. steynsbergensis, S. karooensis sp. nov. and S. mandelai based on the pedipalp not reaching the tarsus of leg I. Distinguished from S. palpiger as the pedipalp is longer than leg I, which S. finni sp. nov. is not. The species has denser cheliceral denticles (>11) than S. schrieneri (<5), S. ignis sp. nov. (<5) and S. maraisi (<10). Stasimopus finni sp. nov. is in general more spinose on the legs than S. dylani sp. nov. (Tibia of leg I and IV). Description: Based on the holotype Ô (NCA 2019/605). Remarks: Ô: The left AME is reduced in size, making some eye measurements unreliable. ♀: Known only from the type male. General: Ô: (Fig 5B) Medium bodied spider, 10.84 total length. Carapace: Ô: Carapace length 4.76; width 4.05. Deep red-brown colouration, thoracic region with rugose texture. Fovea procurved, 0.81 in length. Ocelli: Ô: (Fig 11B) AME diameter 0.14, PME diameter 0.19, MOQ anterior width 1.22 (may not be accurate due to deformity), MOQ posterior width 1.71; AME-AME 0.31 (may not be accurate due to deformity)., AME-ALE 0.10, ALE-ALE 0.65, PME-PME 0.79, PME-PLE 0.16, PLE-PLE 1.14. AER procurved, PER recurved. Chelicerae: Ô: (Fig 13A) Two teeth rows present, 4 teeth proventral row, 4 in retroventral row; 11–13 cuspules between rows. Sternum, labium and maxillae: Ô: (Fig 14C) Sternum length 2.66; sternum width 2.19. Sternum shape has distinct impressions of where the coxa are situated. Sigilla in the shape of a fused arrow, distal end fused, proximal end 0.69 apart; cuspules on labium absent; maxilla absent. Abdomen: Ô: (Fig 5B) Abdomen length 6.08; width 4.30. Pale beige colouration with dark grey banding, smaller band near carapace, followed by broader and wider band, then a narrower band, lastly two shorter bands next to one another. Pedipalps: Ô: (Fig 14A, B) Total length 16.03; Segment lengths 1.57, 5.42, 4.15, -, 4.88. Spines absent. Bulb oval, embolus elongated, tapering retrolaterally into sharp point. Legs: Ô: Length order: I, IV, II, III. I Total length 17.40; Segment lengths 5.54, 2.36, 4.22, 3.93, 1.35; Spination: spines absent on femur, with sparse setae. Patella v - 2–3 spines distally. Tibia (Fig 14D) v - 16–18 large spines extend pl & rl, denser distally. Metatarsus (Fig 14D) v - 15–16 large spines extend pl & rl. Tarsus (Fig 14D) pl & rl - 1–2 small spines, v - scopulate. II Total length 15.53; Segment lengths 4.77, 2.23, 3.63, 3.57, 1.33; Spination: spines absent on femur, with sparse setae. Patella v - 2–3 spines distally. Tibia v - 16 large spines extend pl & rl, denser distally. Metatarsus v - 14–16 large spines, 1 distinctly large spine distally on pl and rl aspects. Tarsus pl & rl - 2–3 small spines, v - scopulate. III Total length 11.75; Segment lengths 3.01, 1.54, 1.38, 3.68, 2.14; Spination: spines absent on femur, with sparse setae. Patella do - 11 small spines. Tibia pl - 1 spine, almost v, do - 2 unorganised rows of red spinules (11 pl / do; 8–9 rl / do). Metatarsus do - 8 spines in two 2, v (Fig 14E)—18 spines, 3 are large and distal. Tarsus v (Fig 14E)—7 small spines, extend pl & rl, dense setae covering spines. IV Total length 17.38; Segment lengths 4.27, 2.31, 3.66, 4.85, 2.29; Spination: spines absent on femur, with sparse setae. Patella do - short dense red spines proximally, less dense distally; interspersed with fine black setae. Tibia pl / v - 2–3 small spines. Metatarsus pl - 8 spines, v (Fig 14F)—I5 spines (4 large spines distally), spines extend pl. Tarsus (Fig 14F) pl - 11–14 spines, extend v, v - 7 small spines. Distribution and environment notes: The species is found in the localities indicated in Figure 15. The species is only known from the type locality near Somerset East in the Eastern Cape province. The location was a flat between small hills. The vegetation was dominated by low shrubs and aloe plants. The soil was very hard, chalky and pale. The specimen was found in a short burrow (Approx. 10cm deep). FIGURE 15. Map of the locality where the Stasimopus finni sp. nov. specimen was collected. Numbers match the site numbers in Figure 1. Map created in QGIS version 3.4.8-Madeira (2019), available at: http://qgis.osgeo.org.Published as part of Brandt, Shannon, Sole, Catherine & Lyle, Robin, 2023, An integrative taxonomy of the genus Stasimopus Simon 1892 (Araneae: Mygalomorphae) of the Karoo with the description of nine new species and a Stasimopus maraisi Hewitt 1914 male, pp. 1-60 in Zootaxa 5341 (1) on pages 24-27, DOI: 10.11646/zootaxa.5341.1.1, http://zenodo.org/record/832374
Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke
Get PDFGenetic factors have been implicated in stroke risk, but few replicated associations have been reported. We conducted a genome-wide association study (GWAS) for ischemic stroke and its subtypes in 3,548 affected individuals and 5,972 controls, all of European ancestry. Replication of potential signals was performed in 5,859 affected individuals and 6,281 controls. We replicated previous associations for cardioembolic stroke near PITX2 and ZFHX3 and for large vessel stroke at a 9p21 locus. We identified a new association for large vessel stroke within HDAC9 (encoding histone deacetylase 9) on chromosome 7p21.1 (including further replication in an additional 735 affected individuals and 28,583 controls) (rs11984041; combined P = 1.87 × 10<sup>−11</sup>; odds ratio (OR) = 1.42, 95% confidence interval (CI) = 1.28–1.57). All four loci exhibited evidence for heterogeneity of effect across the stroke subtypes, with some and possibly all affecting risk for only one subtype. This suggests distinct genetic architectures for different stroke subtypes
Using bacterial biomarkers to identify early indicators of cystic fibrosis pulmonary exacerbation onset
No full textAcute periods of pulmonary exacerbation are the single most important cause of morbidity in cystic fibrosis patients, and may be associated with a loss of lung function. Intervening prior to the onset of a substantially increased inflammatory response may limit the associated damage to the airways. While a number of biomarker assays based on inflammatory markers have been developed, providing useful and important measures of disease during these periods, such factors are typically only elevated once the process of exacerbation has been initiated. Identifying biomarkers that can predict the onset of pulmonary exacerbation at an early stage would provide an opportunity to intervene before the establishment of a substantial immune response, with major implications for the advancement of cystic fibrosis care. The precise triggers of pulmonary exacerbation remain to be determined; however, the majority of models relate to the activity of microbes present in the patient's lower airways of cystic fibrosis. Advances in diagnostic microbiology now allow for the examination of these complex systems at a level likely to identify factors on which biomarker assays can be based. In this article, we discuss key considerations in the design and testing of assays that could predict pulmonary exacerbations
When can antibiotic treatments for trachoma be discontinued? Graduating communities in three African countries.
Get PDFBACKGROUND: Repeated mass azithromycin distributions are effective in controlling the ocular strains of chlamydia that cause trachoma. However, it is unclear when treatments can be discontinued. Investigators have proposed graduating communities when the prevalence of infection identified in children decreases below a threshold. While this can be tested empirically, results will not be available for years. Here we use a mathematical model to predict results with different graduation strategies in three African countries. METHODS: A stochastic model of trachoma transmission was constructed, using the parameters with the maximum likelihood of obtaining results observed from studies in Tanzania (with 16% infection in children pre-treatment), The Gambia (9%), and Ethiopia (64%). The expected prevalence of infection at 3 years was obtained, given different thresholds for graduation and varying the characteristics of the diagnostic test. RESULTS: The model projects that three annual treatments at 80% coverage would reduce the mean prevalence of infection to 0.03% in Tanzanian, 2.4% in Gambian, and 12.9% in the Ethiopian communities. If communities graduate when the prevalence of infection falls below 5%, then the mean prevalence at 3 years with the new strategy would be 0.3%, 3.9%, and 14.4%, respectively. Graduations reduced antibiotic usage by 63% in Tanzania, 56% in The Gambia, and 11% in Ethiopia. CONCLUSION: Models suggest that graduating communities from a program when the infection is reduced to 5% is a reasonable strategy and could reduce the amount of antibiotic distributed in some areas by more than 2-fold
T Cell responses to whole SARS Coronavirus in humans
Get PDFEffective vaccines should confer long-term protection against future outbreaks of severe acute respiratory syndrome (SARS) caused by a novel zoonotic coronavirus (SARS-CoV) with unknown animal reservoirs. We conducted a cohort study examining multiple parameters of immune responses to SARS-CoV infection, aiming to identify the immune correlates of protection. We used a matrix of overlapping peptides spanning whole SARS-CoV proteome to determine T cell responses from 128 SARS convalescent samples by ex vivo IFN-γ ELISPOT assays. Approximately 50% of convalescent SARS patients were positive for T cell responses, and 90% possessed strongly neutralizing Abs. Fifty-five novel T cell epitopes were identified, with spike protein dominating total T cell responses. CD8+ T cell responses were more frequent and of a greater magnitude than CD4+ T cell responses (p < 0.001).
Polychromatic cytometry analysis indicated that the virus-specific T cells from the severe group tended to be a central memory phenotype (CD27+/CD45RO+) with a significantly higher frequency of polyfunctional CD4+ T cells producing IFN-γ, TNF-α, and IL-2, and CD8+ T cells producing IFN-γ, TNF-α, and CD107a (degranulation), as compared with the mild-moderate group. Strong T cell responses correlated significantly (p < 0.05) with higher neutralizing Ab. The serum cytokine profile during acute infection indicated a significant elevation of innate immune responses. Increased Th2 cytokines were observed in patients with fatal infection. Our study provides a roadmap for the immunogenicity of SARS-CoV and types of immune responses that may be responsible for the virus clearance, and should serve as a benchmark for SARS-CoV vaccine design and evaluation
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