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1. Pride or prejudice? : in what ways does the ethnicity and culture of medical students, alongside the process of medical acculturation, impact on medical students' mental health, wellbeing and professional attainment

Author

Bass, D. and Sarra, N.

Subjects
610.92
Abstract

It has been shown in a number of studies that medical students are more vulnerable to mental illness and psychological distress than other students. Research by the General Medical Council (2017) found that differential attainment with regard to ethnicity exists in both postgraduate and undergraduate contexts, in recruitment, and across exam pass rates; this indicates that medical education and training may not be fair. The focus of this research project, arising from over 25 years of experience in this area, is to explore some of the factors related to students’ ethnicity and cultural environments that may have an impact on their mental health and well- being. It also considers the medical acculturation process that may make it more likely that some medical students will experience psychological and academic difficulties during their training. A qualitative thematic analysis (Braun & Clarke, 2005) of the assessment sessions of 24 medical students from different ethnicities and family backgrounds highlights the ways in which students’ lived experiences, both personal and in their medical training, affect their personal well-being and academic performance. The themes identified in this research are examined using a sociological and psychoanalytic lens, as well as that of critical race theory as in combination these offer the broad perspective and critique necessary to consider the sociocultural as well as the psychological aspects of this research enquiry. Sociology and anthropology consider the surrounding historical, social and cultural context of any action and interaction, whereas the focus of the psychoanalytic method is on what lies beneath the surface, in the unseen and the unspoken. As part of the methodology of this thesis, this research also considers the narrative arc and socio-cultural context of the research literature on this topic as a way of investigating patterns of thinking over time within Medicine and its social environment. The focus of this investigation is on the ways in which invisible, silent and unspoken currents within families, communities, institutions and wider society shape these students’ relationships with themselves and others. This research considers the possible reasons for the systemic silencing 3 of particular narratives, the effect this has, and how this can happen in subtle and complex ways. The themes illuminate factors within medical culture that create psychological pressure on all students. They also reveal dynamics of exclusion from pathways of influence, knowledge and support that can reinforce the effects of trauma, including intergenerational trauma. Individual and intergenerational trauma can be a result of experiences that include family difficulties, experiences of immigration and systems of inequality. This research adds to the debate about factors that impact on the mental health of all medical students and doctors as well as the ways that systemic discrimination and pathways of privilege may operate. It suggests different ways of thinking and acting that could be effective at an individual, clinical and whole- institution level, and reflects on what ‘culturally competent’ practice really means.

Published
2020

3. Haplosporidium acetes n. sp. infecting the hepatopancreas of jelly prawns Acetes sibogae australis from Moreton Bay, Australia

Author

Diggles, B. K., Bass, D., Bateman, K. S., Chong, Roger, Daumich, C., Hawkins, Karen A, Hazelgrove, R., Kerr, R., Moody, N. J. G., Ross, S., Stentiford, G. D., Diggles, B. K., Bass, D., Bateman, K. S., Chong, Roger, Daumich, C., Hawkins, Karen A, Hazelgrove, R., Kerr, R., Moody, N. J. G., Ross, S., and Stentiford, G. D.

Abstract

Wild Acetes sibogae australis from northern Moreton Bay, Australia displaying opacity of the hepatopancreas were sampled and examined histologically, revealing infection by multinucleate plasmodia of a haplosporidian-like parasite in the epithelial cells of the hepatopancreas. A morphological and phylogenetic investigation identified the parasite as a novel species of the order Haplosporida, and the parasite is described as Haplosporidium acetes n. sp. This is the first report of disease caused by a haplosporidian in wild Australian decapod crustaceans, and the first record of haplosporidiosis in sergestid shrimp. Infections of H. acetes were observed in all cell types (R, B, F and E) within the hepatopancreas. Infected epithelial cells became hypertrophied as they filled with haplosporidian parasites and, in heavy infections, caused almost complete displacement of normal hepatopancreas tissue. Although sporulation was not observed, infected jelly prawns appeared terminally diseased. Infections became grossly evident in around 5% of wild prawns during early autumn at a time of year when jelly prawn populations decline rapidly with decreasing water temperatures, however histopathology indicated at least 13% of apparently normal jelly prawns were also infected. Further studies are required in order to determine if this parasite influences jelly prawn population dynamics. In addition, we report co-infection of a novel microsporidian parasite in the Enterocytozoon Group Microsporidia (EGM) infecting nuclei of hepatopancreatic epithelial cells. The microsporidian was phylogenetically distinct from Enterocytozoon hepatopenaei (EHP) known to infect penaeid shrimp in Asia.

Published
2022

4. Co-infections and multiple stressors in fish

Author

Gorgoglione, B., Bailey, C., Fast, M. D., Bass, D., Saraiva, M., Mikolaj Adamek, Noguera, P., Ciulli, S., Palíková, M., Aguirre-Gil, I., Bigarré, L., Haenen, O., Gorgoglione B., Bailey C., Fast M.D., Bass D., Saraiva M., Adamek M., Noguera P., Ciulli S., Palikova M., Aguirre-Gil I., Bigarre L., and Haenen O.

Subjects
Co-infections, stressors, fish, sturgeon
Abstract

Fish are typically exposed to multiple physical, chemical and biological stressors. The cumulative impact of co-infections between parasites, bacteria, viruses and (a)biotic environmental pressures may trigger complex interactions, eliciting different pathological and immunological outcomes than those classically assessed. New cross-disciplinary studies attempt to measure the impact of environmental stressors in modulating the host response to pathogens. Scientific advances are needed to reduce pressure on natural populations, improve fish stock management, and to design more efficient diagnostic tools or vaccination strategies. An EAFP-promoted workshop, held on 10th September 2019 in Porto, Portugal, was dedicated to sharing research experiences on the interaction between heterogenous pathogens and multiple stressors in fish. The workshop involved around 200 attendants, opened by a keynote talk (Fast), and followed by a further twelve oral presentations, including three in the format of lash poster presentations. Contributions illustrated cross-disciplinary approaches to study complex host-pathogen and stressors interactions.

Published
2020

5. Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale

Author

Hilton, S, Picot, E, Schreiter, S, Bass, D, Norman, K, Oliver, AE, Moore, JD, Mauchline, TH, Mills, PR, Teakle, GR, Clark, IM, Hirsch, PR, van der Gast, CJ, Bending, GD, Hilton, S, Picot, E, Schreiter, S, Bass, D, Norman, K, Oliver, AE, Moore, JD, Mauchline, TH, Mills, PR, Teakle, GR, Clark, IM, Hirsch, PR, van der Gast, CJ, and Bending, GD

Abstract

Background: The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and crucially relationships between microbiota composition and plant health. Here we investigated landscape scale rhizosphere microbial assembly processes in oilseed rape (OSR), the UK’s third most cultivated crop by area and the world's third largest source of vegetable oil, which suffers from yield decline associated with the frequency it is grown in rotations. By including 37 conventional farmers’ fields with varying OSR rotation frequencies, we present an innovative approach to identify microbial signatures characteristic of microbiomes which are beneficial and harmful to the host. Results: We show that OSR yield decline is linked to rotation frequency in real-world agricultural systems. We demonstrate fundamental differences in the environmental and agronomic drivers of protist, bacterial and fungal communities between root, rhizosphere soil and bulk soil compartments. We further discovered that the assembly of fungi, but neither bacteria nor protists, was influenced by OSR rotation frequency. However, there were individual abundant bacterial OTUs that correlated with either yield or rotation frequency. A variety of fungal and protist pathogens were detected in roots and rhizosphere soil of OSR, and several increased relative abundance in root or rhizosphere compartments as OSR rotation frequency increased. Importantly, the relative abundance of the fungal pathogen Olpidium brassicae both increased with short rotations and was significantly associated with low yield. In contrast, the root endophyte Tetracladium spp. showed the reverse associations with both rotation frequency and yield to O. brassicae, suggesting that they are signatures of a microbiome which benefits the host. We also identified a variety of novel protist and fungal clades which are highl

Published
2021

7. Safety and efficacy of intravenous belimumab in children with systemic lupus erythematosus: results from a randomised, placebo-controlled trial

Author

Brunner, HI, Abud-Mendoza, C, Viola, DO, Penades, IC, Levy, D, Anton, J, Calderon, JE, Chasnyk, VG, Ferrandiz, MA, Keltsev, V, Gastanaga, MEP, Shishov, M, Boteanu, AL, Henrickson, M, Bass, D, Clark, K, Hammer, A, Ji, BN, Nino, A, Roth, DA, Struemper, H, Wang, ML, Martini, A, Lovell, D, Ruperto, N, Paediat Rheumatology, and Pediat Rheumatology Collab

Subjects
systemic lupus erythematosus, treatment, DMARDs (biologic)
Abstract

Objectives This ongoing Phase-2, randomised, placebo-controlled, double-blind study evaluated the efficacy, safety and pharmacokinetics of intravenous belimumab in childhood-onset systemic lupus erythematosus (cSLE). Methods Patients (5 to 17 years) were randomised to belimumab 10 mg/kg intravenous or placebo every 4 weeks, plus standard SLE therapy. Primary endpoint: SLE Responder Index (SRI4) response rate (Week 52). Key major secondary endpoints: proportion of patients achieving the Paediatric Rheumatology International Trials Organisation/American College of Rheumatology (PRINTO/ACR) response using 50 and '30 alternative' definitions (Week 52), and sustained response (Weeks 44 to 52) by SRI4 and Parent Global Assessment of well-being (Parent-global). Safety and pharmacokinetics were assessed. Study not powered for statistical testing. Results Ninety-three patients were randomised (belimumab, n=53; placebo, n=40). At Week 52, there were numerically more SRI4 responders with belimumab versus placebo (52.8% vs 43.6%; OR 1.49 (95% CI 0.64 to 3.46)). PRINTO/ACR 30 alternative (52.8% vs 27.5%; OR 2.92 (95% CI 1.19 to 7.17)) and PRINTO/ACR 50 (60.4% vs 35.0%; OR 2.74 (95% CI 1.15 to 6.54)) responses were more frequent with belimumab than placebo, as were sustained responses for SRI4 (belimumab, 43.4%; placebo, 41.0%; OR 1.08 (95% CI 0.46 to 2.52)) and Parent-global (belimumab, 59.1%; placebo, 33.3%; OR 3.49 (95% CI 1.23 to 9.91)). Serious adverse events were reported in 17.0% of belimumab patients and 35.0% of placebo patients; one death occurred (placebo). Week-52, geometric mean (95% CI) belimumab trough concentration was 56.2 (45.2 to 69.8) mu g/mL. Conclusion The belimumab intravenous pharmacokinetics and benefit-risk profile in cSLE are consistent with adult belimumab studies and the 10 mg/kg every 4 weeks dose is appropriate.

Published
2020

9. Halioticida noduliformans infection in eggs of lobster (Homarus gammarus) reveals its generalist parasitic strategy in marine invertebrates

Author

Holt, C, Foster, R, Daniels, CL, van der Giezen, M, Feist, SW, Stentiford, GD, and Bass, D

Subjects
Gills, Likelihood Functions, Halioticida noduliformans, 18S rRNA gene, Bayes Theorem, Article, Nephropidae, Oomycete, Oomycetes, Animals, Homarus gammarus, Haliphthoros, Phylogeny, ComputingMethodologies_COMPUTERGRAPHICS, Ovum
Abstract

Graphical abstract, Highlights • First record of Halioticida noduliformans in European lobster eggs and gills. • Coinfection with Lagenidium callinectes detected in European lobster eggs. • Phylogenetic analyses confirm ‘Haliphthoros sp. NJM 0034’ is H. noduliformans. • Novel Oomycete-specific 18S rRNA gene PCR primers developed and tested. • Oomycete-specific primers detect wide diversity in environmental samples., A parasite exhibiting Oomycete-like morphology and pathogenesis was isolated from discoloured eggs of the European lobster (Homarus gammarus) and later found in gill tissues of adults. Group-specific Oomycete primers were designed to amplify the 18S ribosomal small subunit (SSU), which initially identified the organism as the same as the ‘Haliphthoros’ sp. NJM 0034 strain (AB178865.1) previously isolated from abalone (imported from South Australia to Japan). However, in accordance with other published SSU-based phylogenies, the NJM 0034 isolate did not group with other known Haliphthoros species in our Maximum Likelihood and Bayesian phylogenies. Instead, the strain formed an orphan lineage, diverging before the separation of the Saprolegniales and Pythiales. Based upon 28S large subunit (LSU) phylogeny, our own isolate and the previously unidentified 0034 strain are both identical to the abalone pathogen Halioticida noduliformans. The genus shares morphological similarities with Haliphthoros and Halocrusticida and forms a clade with these in LSU phylogenies. Here, we confirm the first recorded occurrence of H. noduliformans in European lobsters and associate its presence with pathology of the egg mass, likely leading to reduced fecundity.

Published
2018

10. Pancam multispectral imaging results from the Opportunity rover at Meridiani Planum

Author

Bell, III, J.F., Squyres, S.W., Arvidson, R.E., Arneson, H.M., Bass, D., Calvin, W., Farrand, W.H., Goetz, W., Golombek, M., Greeley, R., Grotzinger, J., Guinness, E., Hayes, A.G., Hubbard, M.Y.H., Herkenhoff, K.E., Johnson, M.J., Johnson, J.R., Joseph, J., Kinch, K.M., Lemmon, M.T., Li, R., Madsen, M.B., Maki, J.N., Malin, M., McCartney, E., McLennan, S., McSween, Jr., H.Y., Ming, D.W., Morris, R.V., Dobrea, E.Z. Noe, Parker, T.J., Proton, J., Rice, Jr., J.W., Seelos, F., Soderblom, J.M., Soderblom, L.A., Sohl-Dickstein, J.N., Sullivan, R.J., Weitz, C.M., and Wolff, M.J.

Subjects
Opportunity (Space probe) -- Research, Mars probes -- Research -- Discovery and exploration, Mars (Planet) -- Discovery and exploration -- Research, Science and technology, Discovery and exploration, Research
Abstract

Panoramic Camera (Pancam) images from Meridiani Planum reveal a low-albedo, generally flat, and relatively rock-free surface. Within and around impact craters and fractures, laminated outcrop rocks with higher albedo are observed. Fine-grained materials include dark sand, bright ferric iron-rich dust, angular rock clasts, and millimeter-size spheroidal granules that are eroding out of the laminated rocks. Spectra of sand, clasts, and one dark plains rock are consistent with mafic silicates such as pyroxene and olivine. Spectra of both the spherules and the laminated outcrop materials indicate the presence of crystalline ferric oxides or oxyhydroxides. Atmospheric observations show a steady decline in dust opacity during the mission. Astronomical observations captured solar transits by Phobos and Deimos and time-lapse observations of sunsets., On 24 January 2004 UTC, the Mars Exploration Rover Opportunity landed on Mars within the classical low-albedo Noachian terrain of Meridiani Planum. The landing region was previously identified in orbital [...]

Published
2004

11. Pancam multispectral imaging results from the Spirit rover at Gusev crater

Author

Bell, III, J.F., Squyres, S.W., Arvidson, R.E., Arneson, H.M., Bass, D., Blaney, D., Cabrol, N., Calvin, W., Farmer, J., Farrand, W.H., Goetz, W., Golombek, M., Grant, J.A., Greeley, R., Guinness, E., Hayes, A.G., Hubbard, M.Y.H., Herkenhoff, K.E., Johnson, M.J., Johnson, J.R., Joseph, J., Kinch, K.M., Lemmon, M.T., Li, R., Madsen, M.B., Maki, J.N., Malin, M., McCartney, E., McLennan, S., McSween H.Y., Jr., Ming, D.W., Moersch, J.E., Morris, R.V., Noe Dobrea, E.Z., Parker, T.J., Proton, J., Rice, Jr., J.W., Seelos, F., Soderblom, J., Soderblom, L.A., Sohl-Dickstein, J.N., Sullivan, R.J., Wolff, M.J., and Wang, A.

Subjects
Spirit (Space probe) -- Observations, Mars (Planet) -- Research -- Properties, Geology -- Research -- Observations, Science and technology, Observations, Research, Properties
Abstract

Panoramic Camera images at Gusev crater reveal a rock-strewn surface interspersed with high- to moderate-albedo fine-grained deposits occurring in part as drifts or in small circular swales or hollows. Optically thick coatings of fine-grained ferric iron-rich dust dominate most bright soil and rock surfaces. Spectra of some darker rock surfaces and rock regions exposed by brushing or grinding show near-infrared spectral signatures consistent with the presence of mafic silicates such as pyroxene or olivine. Atmospheric observations show a steady decline in dust opacity during the mission, and astronomical observations captured solar transits by the martian moons, Phobos and Deimos, as well as a view of Earth from the martian surface., On 4 January 2004 universal time coordinated, the Mars Exploration Rover, Spirit, landed on Mars at 14.5692°S, 175.4729°E, within the crater Gusev, a 160-km-diameter Noachian-age impact crater. Previous orbital remote [...]

Published
2004

13. The topological classification of endomorphisms of vector bundles

Author

Bass, D. W.

Subjects
510, QA Mathematics
Abstract

I have made an attempt in this thesis at a systematic topological classification of the endomorphisms of a vector bundle . Chapter one provides the motivation for such a classification and for the notions of 'local' and 'global' topological equivalence of bundle endomorphisms that are given in Chapter 2. Both the local and global classification problems turned out to be a great deal more difficult than anticipated. A complete local and global classification of the generic endomorphisms of real and complex line bundles over a smooth manifold is given in Chapter 2. For real plane bundles, the local classification problem is partly solved, but no attempt is made at the global problem. Chapter 3 gives the complete local classification for generic endomorphisms that have bifurcations of codimension one. Finally in Chapter 4 an attempt is made at the codimensions two and four local classification problems. Only partial results and conjectures are offered. Other notions of local equivalence are suggested.

Published
1975

14. H2O at the Phoenix Landing Site

Author

Smith, P. H., Tamppari, L. K., Arvidson, R. E., Bass, D., Blaney, D., Boynton, W. V., Carswell, A., Catling, D. C., Clark, B. C., Duck, T., DeJong, E., Fisher, D., Goetz, W., Gunnlaugsson, H. P., Hecht, M. H., Hipkin, V., Hoffman, J., Hviid, S. F., Keller, H. U., Kounaves, S. P., Lange, C. F., Lemmon, M. T., Madsen, M. B., Markiewicz, W. J., Marshall, J., McKay, C. P., Mellon, M. T., Ming, D. W., Morris, R. V., Pike, W. T., Renno, N., Staufer, U., Stoker, C., Taylor, P., Whiteway, J. A., and Zent, A. P.

Published
2009

16. Evidence from Opportunity's Microscopic Imager for Water on Meridiani Planum

Author

Herkenhoff, K. E., Squyres, S. W., Arvidson, R., Bass, D. S., Bell, J. F., III, Bertelsen, P., Ehlmann, B. L., Farrand, W., Gaddis, L., Greeley, R., Grotzinger, J., Hayes, A. G., Hviid, S. F., Johnson, J. R., Jolliff, B., Kinch, K. M., Knoll, A. H., Madsen, M. B., Maki, J. N., McLennan, S. M., McSween, H. Y., Ming, D. W., Rice, J. W., Jr., Richter, L., Sims, M., Smith, P. H., Soderblom, L. A., Spanovich, N., Sullivan, R., Thompson, S., Wdowiak, T., Weitz, C., and Whelley, P.

Published
2004

17. Textures of the Soils and Rocks at Gusev Crater from Spirit's Microscopic Imager

Author

Herkenhoff, K. E., Squyres, S. W., Arvidson, R., Bass, D. S., Bell, J. F., III, Bertelsen, P., Cabrol, N. A., Gaddis, L., Hayes, A. G., Hviid, S. F., Johnson, J. R., Kinch, K. M., Madsen, M. B., Maki, J. N., McLennan, S. M., McSween, H. Y., Rice, J. W., Jr., Sims, M., Smith, P. H., Soderblom, L. A., Spanovich, N., Sullivan, R., and Wang, A.

Published
2004

22. Marteilia refringens and Marteilia pararefringens sp. nov. are distinct parasites of bivalves and have different European distributions

Author

Kerr, R., Ward, G. M., Stentiford, G. D., Alfjorden, A., Mortensen, S., Bignell, J. P., Feist, S. W., Villalba, A., Carballal, M. J., Cao, A., Arzul, Isabelle, Ryder, D., Bass, D., Kerr, R., Ward, G. M., Stentiford, G. D., Alfjorden, A., Mortensen, S., Bignell, J. P., Feist, S. W., Villalba, A., Carballal, M. J., Cao, A., Arzul, Isabelle, Ryder, D., and Bass, D.

Abstract

Marteilia refringens causes marteiliosis in oysters, mussels and other bivalve molluscs. This parasite previously comprised two species, M. refringens and Marteilia maurini, which were synonymized in 2007 and subsequently referred to as M. refringens ‘O-type’ and ‘M-type’. O-type has caused mass mortalities of the flat oyster Ostrea edulis. We used high throughput sequencing and histology to intensively screen flat oysters and mussels (Mytilus edulis) from the UK, Sweden and Norway for infection by both types and to generate multi-gene datasets to clarify their genetic distinctiveness. Mussels from the UK, Norway and Sweden were more frequently polymerase chain reaction (PCR)-positive for M-type (75/849) than oysters (11/542). We did not detect O-type in any northern European samples, and no histology-confirmed Marteilia-infected oysters were found in the UK, Norway and Sweden, even where co-habiting mussels were infected by the M-type. The two genetic lineages within ‘M. refringens’ are robustly distinguishable at species level. We therefore formally define them as separate species: M. refringens (previously O-type) and Marteilia pararefringens sp. nov. (M-type). We designed and tested new Marteilia-specific PCR primers amplifying from the 3’ end of the 18S rRNA gene through to the 5.8S gene, which specifically amplified the target region from both tissue and environmental samples.

Published
2018
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23. Plant rhizosphere selection of plasmodiophorid lineages from bulk soil: The importance of 'Hidden' diversity

Author

Bass, D, van der Gast, Christopher, Thomson, S, Neuhauser, S, Hilton, S, Bending, GD, Bass, D, van der Gast, Christopher, Thomson, S, Neuhauser, S, Hilton, S, and Bending, GD

Abstract

© 2018 Bass, van der Gast, Thomson, Neuhauser, Hilton and Bending. Microbial communities closely associated with the rhizosphere can have strong positive and negative impacts on plant health and growth. We used a group-specific amplicon approach to investigate local scale drivers in the diversity and distribution of plasmodiophorids in rhizosphere/root and bulk soil samples from oilseed rape (OSR) and wheat agri-systems. Plasmodiophorids are plant- and stramenopile-associated protists including well known plant pathogens as well as symptomless endobiotic species. We detected 28 plasmodiophorid lineages (OTUs), many of them novel, and showed that plasmodiophorid communities were highly dissimilar and significantly divergent between wheat and OSR rhizospheres and between rhizosphere and bulk soil samples. Bulk soil communities were not significantly different between OSR and wheat systems. Wheat and OSR rhizospheres selected for different plasmodiophorid lineages. An OTU corresponding to Spongospora nasturtii was positively selected in the OSR rhizosphere, as were two genetically distinct OTUs. Two novel lineages related to Sorosphaerula veronicae were significantly associated with wheat rhizosphere samples, indicating unknown plant-protist relationships. We show that group-targeted eDNA approaches to microbial symbiont-host ecology reveal significant novel diversity and enable inference of differential activity and potential interactions between sequence types, as well as their presence.

Published
2018

25. Debugging diversity – a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool

Author

Schnell, I., Bohmann, K., Schultze, S., Richter, S., Murray, D., Sinding, M., Bass, D., Cadle, J., Campbell, M., Dolch, R., Edwards, D., Gray, T., Hansen, T., Hoa, A., Noer, C., Heise-Pavlov, S., Sander Pedersen, A., Ramamonjisoa, J., Siddall, M., Tilker, A., Traeholt, C., Wilkinson, N., Woodcock, P., Yu, D., Bertelsen, M., Bunce, Michael, Gilbert, M., Schnell, I., Bohmann, K., Schultze, S., Richter, S., Murray, D., Sinding, M., Bass, D., Cadle, J., Campbell, M., Dolch, R., Edwards, D., Gray, T., Hansen, T., Hoa, A., Noer, C., Heise-Pavlov, S., Sander Pedersen, A., Ramamonjisoa, J., Siddall, M., Tilker, A., Traeholt, C., Wilkinson, N., Woodcock, P., Yu, D., Bertelsen, M., Bunce, Michael, and Gilbert, M.

Abstract

The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and amphibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate biodiversity.

Published
2018

26. Scientific objectives of the DYNAMO mission

Author

Chassefière, E., Forget, F., Hourdin, F., Vial, F., Rème, H., Mazelle, C., Vignes, D., Sauvaud, J.-A., Blelly, P.-L., Toublanc, D., Berthelier, J.-J., Cerisier, J.-C., Chanteur, G., Duvet, L., Menvielle, M., Lilensten, J., Witasse, O., Touboul, P., Quèmerais, E., Bertaux, J.-L., Hulot, G., Cohen, Y., Lognonné, P., Barriot, J.P., Balmino, G., Blanc, M., Pinet, P., Parrot, M., Trotignon, J.-G., Moncuquet, M., Bougeret, J.-L., Issautier, K., Lellouch, E., Meyer, N., Sotin, C., Grasset, O., Barlier, F., Berger, C., Tarits, P., Dyment, J., Breuer, D., Spohn, T., Pätzold, M., Sperveslage, K., Gough, P., Buckley, A., Szego, K., Sasaki, S., Smrekar, S., Lyons, D., Acuna, M., Connerney, J., Purucker, M., Lin, R., Luhmann, J., Mitchell, D., Leblanc, F., Johnson, R., Clarke, J., Nagy, A., Young, D., Bougher, S., Keating, G., Haberle, R., Jakosky, B., Hodges, R., Parmentier, M., Waite, H., and Bass, D.

Published
2001
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28. Paediatric trauma care

Author

Cywes, S, Kibel, S. M., Bass, D. H., Rode, H., Millar, A. J. W., and De Wet, J.

Abstract

Paediatric trauma care varies in different countries. In South Africa injury is the leading cause of death in the 5 - 14-yearold age group - 1,5 - 3,8 times higher than in the USA. In 1978 the Child Safety Centre was established and prospectively collected data on paediatric injuries. The various types of injuries are discussed. Trauma is responsible for the highest percentage of years of life lost but the least amount of money is being spent on research and prevention of injuries. The Child Accident Prevention Foundation of Southern Africa has been constituted to research, prevent and reduce the risk factors of the injuries and to improve facilities for the injured child.

Published
2017

29. Five years' experience of injured children

Author

Kibel, S. M., Bass, D. H., and Cywes, S.

Abstract

This study was undertaken to analyse admission data on all patients seen in the Red Cross War Memorial Children's Hospital Trauma Unit during the period 24 April 1984 - 31 March 1989. Data were retrieved from computerised records completed on admission and were reviewed descriptively. Variations in age, sex and population group paUem for different causes of injury were evaluated together with data on the nature and place of injury and time seen. Data for analysis of nature of injury by cause were also retrieved, but over a 2-year period only (1986-1987). Accuracy of recorded data was assessed from a random sample of hospital records. During the 5-year period 57468 patients were seen in the Trauma Unit, of whom 17,1% were admitted. In addition 6377 cases of poisoning and 119 of near-drowning were seen by the medical departments. Forty-three per cent of injuries were due to falls, which were the most important cause of injury in both admitted and non-admitted patients of all age, sex and population groups. Other main cause groups were bumps and blows (15%), transport (11%) and burns (11%). Transport and burn injuries had the highest admission rates. This is the first study of children's injuries in southern Africa and provides information essential to future design of paediatric trauma care systems and accident prevention programmes.

Published
2017

30. Parahepatospora carcini n. gen., n. sp., a parasite 1 of invasive Carcinus maenas with intermediate features of sporogony between the Enterocytozoon clade and other Microsporidia

Author

Bojko, J, Clark, F, Bass, D, Dunn, AM, Stewart-Clark, S, Stebbing, PD, and Stentiford, GD

Subjects
parasitic diseases, fungi
Abstract

Parahepatospora carcini n. gen. n. sp., is a novel microsporidian parasite discovered infecting the cytoplasm of epithelial cells of the hepatopancreas of a single Carcinus maenas specimen. The crab was sampled from within its invasive range in Atlantic Canada (Nova Scotia). Histopathology and transmission electron microscopy were used to show the development of the parasite within a simple interfacial membrane, culminating in the formation of unikaryotic spores with 5-6 turns of an isofilar polar filament. Formation of a multinucleate meront (>12 nuclei observed) preceded thickening and invagination of the plasmodial membrane, and in many cases, formation of spore extrusion precursors (polar filaments, anchoring disk) prior to complete separation of pre-sporoblasts from the sporogonial plasmodium. This developmental feature is intermediate between the Enterocytozoonidae (formation of spore extrusion precursors within the sporont plasmodium) and all other Microsporidia (formation of spore extrusion precursors after separation of sporont from the sporont plasmodium). SSU rRNA-based gene phylogenies place P. carcini within microsporidian Clade IV, between the Enterocytozoonidae and the so-called Enterocytospora-clade, which includes Enterocytospora artemiae and Globulispora mitoportans. Both of these groups contain gut-infecting microsporidians of aquatic invertebrates, fish and humans. According to morphological and phylogenetic characters, we propose that P. carcini occupies a basal position to the Enterocytozoonidae. We discuss the discovery of this parasite from a taxonomic perspective and consider its origins and presence within a high profile invasive host on the Atlantic Canadian coastline.

Published
2017

32. Supplementary Material for: Acne Fulminans: Treatment Experience from 26 Patients

Author

Massa, A.F., Burmeister, L., Bass, D., and Zouboulis, C.C.

Abstract

Background /Aim: Acne fulminans is a rare form of acne vulgaris with acute clinical deterioration including systemic signs. Etiopathogenesis and management remain largely unknown. Our aim is to assess the efficacy of a combined therapeutic regimen of systemic isotretinoin and prednisolone following the recent concepts of acne pathogenesis and drug kinetics. Methods: A prospective case series was recruited over 15 years. Isotretinoin 0.5 mg/kg bw/d (0.25-0-0.25) and prednisolone 30 mg/d (10-10-10) were administered concomitantly with prednisolone being tapered after that time. The overall efficacy was evaluated at month 1 and every month thereafter. Daily drug doses were split to reduce the risk for adverse effects. Results: 26 patients (20 male, 77%) at a mean age of 19 years and a history of acne vulgaris of 3.2 years presented acutely necrotic and ulcerating skin papules (100%), fever (45%), arthralgia (38.5%), leukocytosis (88.5%) and elevated erythrocyte sedimentation rate (100%). After one month of treatment resolution of systemic signs was achieved in all patients and a >50% skin lesion improvement in 17 patients (65%). Conclusion: The concomitant administration of isotretinoin (0.5 mg/kg bw/d, 0.25-0-0.25) and prednisolone 30 mg/d (10-10-10) is able to resolve systemic signs and markedly improve skin lesions in 65% of the patients at one month.

Published
2017
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33. Efficacy and Safety of Subcutaneous Belimumab in Anti-Double-Stranded DNA-Positive, Hypocomplementemic Patients With Systemic Lupus Erythematosus

Author

Doria, A., primary, Stohl, W., additional, Schwarting, A., additional, Okada, M., additional, Scheinberg, M., additional, van Vollenhoven, R., additional, Hammer, A. E., additional, Groark, J., additional, Bass, D., additional, Fox, N. L., additional, Roth, D., additional, and Gordon, D., additional

Published
2018
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36. Fine endophytes (Glomus tenue) are related to Mucoromycotina, not Glomeromycota

Author

Orchard, S., Hilton, S., Bending, G.D., Dickie, I.A., Standish, R.J., Gleeson, D.B., Jeffery, R.P., Powell, J.R., Walker, C., Bass, D., Monk, J., Simonin, A., Ryan, M.H., Orchard, S., Hilton, S., Bending, G.D., Dickie, I.A., Standish, R.J., Gleeson, D.B., Jeffery, R.P., Powell, J.R., Walker, C., Bass, D., Monk, J., Simonin, A., and Ryan, M.H.

Published
2017

37. Soil protistology rebooted: 30 fundamental questions to start with

Author

Geisen, S., Mitchell, E.A.D., Wilkinson, D.M., Adl, S., Bonkowski, M., Brown, M.W., Fiore-Donno, A.M., Heger, T.J., Jassey, V.E.J., Krashevska, V., Lahr, D.J.G., Marcisz, K., Mulot, M., Payne, R., Singer, D., Anderson, O.R., Charman, D.J., Ekelund, F., Griffiths, B.S., Rønn, R., Smirnov, A., Bass, ´D., Belbahri, L., Berney, C., Blandenier, Q., Chatzinotas, Antonis, Clarholm, M., Dunthorn, M., Feest, A., Fernández, L.D., Foissner, W., Fournier, B., Gentekaki, E., Hájek, M., Helder, J., Jousset, A., Koller, R., Kumar, S., La Terza, A., Lamentowicz, M., Mazei, Y., Santos, S.S., Seppey, C.V.W., Spiegel, F.W., Walochnik, J., Winding, A., Lara, E., Geisen, S., Mitchell, E.A.D., Wilkinson, D.M., Adl, S., Bonkowski, M., Brown, M.W., Fiore-Donno, A.M., Heger, T.J., Jassey, V.E.J., Krashevska, V., Lahr, D.J.G., Marcisz, K., Mulot, M., Payne, R., Singer, D., Anderson, O.R., Charman, D.J., Ekelund, F., Griffiths, B.S., Rønn, R., Smirnov, A., Bass, ´D., Belbahri, L., Berney, C., Blandenier, Q., Chatzinotas, Antonis, Clarholm, M., Dunthorn, M., Feest, A., Fernández, L.D., Foissner, W., Fournier, B., Gentekaki, E., Hájek, M., Helder, J., Jousset, A., Koller, R., Kumar, S., La Terza, A., Lamentowicz, M., Mazei, Y., Santos, S.S., Seppey, C.V.W., Spiegel, F.W., Walochnik, J., Winding, A., and Lara, E.

Abstract

Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this, protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in soil studies. Recent methodological advances, particularly in molecular biology techniques, have made the study of soil protists more accessible, and have created a resurgence of interest in soil protistology. This ongoing revolution now enables comprehensive investigations of the structure and functioning of soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive review, we provide a synthesis of research gaps that should be prioritized in future studies of soil protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics that will establish soil protistology as a hub discipline connecting different fundamental and applied fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers in biology.

Published
2017

38. UniEuk : Time to Speak a Common Language in Protistology!

Author

Berney, C, Ciuprina, A, Bender, S, Brodie, J, Edgcomb, V, Kim, E, Rajan, J, Parfrey, LW, Adl, S, Audic, S, Bass, D, Caron, DA, Cochrane, G, Czech, L, Dunthorn, M, Geisen, S, Glöckner, FO, Mahé, F, Quast, C, Kaye, JZ, Simpson, AGB, Stamatakis, A, del Campo, J, Yilmaz, P, de Vargas, C, Berney, C, Ciuprina, A, Bender, S, Brodie, J, Edgcomb, V, Kim, E, Rajan, J, Parfrey, LW, Adl, S, Audic, S, Bass, D, Caron, DA, Cochrane, G, Czech, L, Dunthorn, M, Geisen, S, Glöckner, FO, Mahé, F, Quast, C, Kaye, JZ, Simpson, AGB, Stamatakis, A, del Campo, J, Yilmaz, P, and de Vargas, C

Abstract

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.

Published
2017

39. Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs

Author

Dupont, A.Ö.C., Griffiths, R.I., Bell, T., and Bass, D.

Subjects
Agriculture and Soil Science
Abstract

A recent large-scale assessment of bacterial communities across a range of UK soil types showed that bacterial community structure was strongly determined by soil pH. We analysed a data set of eukaryotic 454 sequencing 18S rDNA from the surveyed samples and showed significant differences in eukaryotic assemblages according to pH class, mostly between low pH and higher pH soils. Soil eukaryote communities (per sample) differed most at the taxonomic rank approximating to order level. Taxonomies assigned with the Protist Ribosomal Reference and the Silva 119 databases were taxonomically inconsistent, mostly due to differing 18S annotations, although general structure and composition according to pH were coherent. A relatively small number of lineages, mostly putative parasitic protists and fungi, drive most differences between pH classes, with weaker contributions from bacterivores and autotrophs. Overall, soil parasites included a large diversity of alveolates, in particular apicomplexans. Phylogenetic analysis of alveolate lineages demonstrates a large diversity of unknown gregarines, novel perkinsids, coccidians, colpodellids and uncharacterized alveolates. Other novel and/or divergent lineages were revealed across the eukaryote tree of life. Our study provides an in-depth taxonomic evaluation of micro-eukaryotic diversity, and reveals novel lineages and insights into their relationships with environmental variables across soil gradients.

Published
2016
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40. Planning Ahead for Mars Sample Science in the Human Exploration Era

Author

Beaty, D. W., Niles, P. B., Bass, D. S., Bell, M. S., Bleacher, J. E., Cabrol, N. A., Conrad, P. G., Eppler, D. B., Hamilton, V. E., Hays, L. E., Head, J. W., Kahre, M. A., Levy, J. S., Lyons, T. W., Macalady, J. L., Rafkin, S. C. R., Rice, J. W., and Rice, M. S.

Abstract

NASA recently requested that MEPAG evaluate the scientific objectives that could/should be carried out by a potential human mission to Mars that, for planning purposes, is assumed to launch in 2035. One of the key working conclusions is that sample-based science stands out as one of the more important aspects of a potential overall science package (recognizing that there would additionally be other scientific aspects of such a mission that would not be sample-based).

Published
2015

42. Fine endophytes (Glomus tenue ) are related to Mucoromycotina, not Glomeromycota

Author

Orchard, S., Hilton, S., Bending, G.D., Dickie, I.A., Standish, R.J., Gleeson, D.B., Jeffery, R.P., Powell, J.R., Walker, C., Bass, D., Monk, J., Simonin, A., Ryan, M.H., Orchard, S., Hilton, S., Bending, G.D., Dickie, I.A., Standish, R.J., Gleeson, D.B., Jeffery, R.P., Powell, J.R., Walker, C., Bass, D., Monk, J., Simonin, A., and Ryan, M.H.

Published
2016

44. Novel virus discovery and genome reconstruction from field RNA samples reveals highly divergent viruses in dipteran hosts

Author

Cook, S., Chung, B. Y. W., Bass, D., Moureau, Grégory, Tang, S. Y., McAlister, E., Culverwell, C. L., Glucksman, E., Wang, H., Brown, T. D. K., Gould, E. A., Harbach, R. E., de Lamballerie, Xavier, and Firth, A. E.

Subjects
fungi
Abstract

We investigated whether small RNA (sRNA) sequenced from field-collected mosquitoes and chironomids (Diptera) can be used as a proxy signature of viral prevalence within a range of species and viral groups, using sRNAs sequenced from wild-caught specimens, to inform total RNA deep sequencing of samples of particular interest. Using this strategy, we sequenced from adult Anopheles maculipennis s.l. mosquitoes the apparently nearly complete genome of one previously undescribed virus related to chronic bee paralysis virus, and, from a pool of Ochlerotatus caspius and Oc. detritus mosquitoes, a nearly complete entomobirnavirus genome. We also reconstructed long sequences (1503-6557 nt) related to at least nine other viruses. Crucially, several of the sequences detected were reconstructed from host organisms highly divergent from those in which related viruses have been previously isolated or discovered. It is clear that viral transmission and maintenance cycles in nature are likely to be significantly more complex and taxonomically diverse than previously expected.

Published
2013

46. Report of the 2018 Joint Mars Rover Mission Joint Science Working Group (JSWG)

Author

Beaty, D., Kminek, G., Allwood, A., Arvidson, R., Borg, L., Farmer, J., Goesmann, F., Grant, J., Hauber, E., Murchie, S., Ori, G., Ruff, S., Rull, F., Sephton, M., Sherwood Lollar, B., Smith, C., Westall, F., Pacros, A., Wilson, M., Meyer, M., Vago, J., Bass, D., Joudrier, L., Laubach, S., Feldman, S., Trautner, R., and Milkovich, S.

Subjects
MOMA [ExoMars], Planets and Comets
Published
2012

49. Description of Seakeeping Experiments Carried Out on CCGA Roberts Sisters II Model IOT761

Author

Akinturk, A., Cumming, D., Oates, C., Bass, D., and Millan, J.

Subjects
Motion Induced Interruptions, Seakeeping, IOT761, Fishing Vessel
Abstract

This report describes a set of seakeeping experiments carried out during the summer and into the fall of 2009 as part of the Fishing Vessel Safety Project on a 1:10.67 scale model of the 65 ft (19.81 m) long fishing vessel CCGA Roberts Sisters II, designated IOT761, in the Institute for Ocean Technology (IOT) Offshore Engineering Basin (OEB). The data from these tests was used to correlate with the full-scale data acquired during sea trials carried out off St. John's, NL November 15, 2004. The objective of the experiments was to acquire quality model scale seakeeping data to correlate with full-scale data, as well as to validate numerical prediction software under development at Memorial University of Newfoundland (MUN). This document describes the model fabrication, instrumentation, data analysis procedure, provides the results of the sea trial / physical model / numerical model correlation exercise and recommendations to improve the overall correlation in future.

Published
2009
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50. A numerical freeing port study on small fishing vessels

Author

Chin, S. and Bass, D.

Subjects
deck, water, vessel, ingress, freeing port, flaps, egress
Abstract

Freeing ports on fishing vessels are a significant safety feature. They are designed to reduce the build up of green water on deck that may lead to loss of stability. At a more mundane level they reduce wetness on decks that are the working platforms for the fishers. Wet decks that are moving working platforms are clearly a hazard. The present study deals more with the build up of water on deck rather than just general deck wetness. It attempts to quantify the amount of water on deck for different freeing port configurations, using parameters such as number of freeing ports, freeing port areas, deck area etc. The study uses numerical simulations to evaluate these parameters. One particular vessel has been used throughout the study, namely a typical fibreglass 65 foot fishing vessel of recent design. The main conclusions of the study are that generally there is not a great deal of difference between the amounts of water on deck for the different freeing port configurations. Although larger freeing ports allow more water on deck if the ingress and egress of water flowing through the freeing ports is unhindered in both directions, for freeing ports fitted with some device (such as ‘flaps’) that hinders the in-flow but not the out-flow then having larger freeing ports is shown to be beneficial. The benefits here are more to do with stability than general deck wetness. It is in fact clear from some of the results that larger freeing ports lead to wetter decks. The motions of the vessel in the study with water on deck have been evaluated and it is shown that different freeing port configurations can lead to different motions of the vessel, particularly in the early stages of flooding.

Published
2009

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