The importance of Ranunculus spp. for juvenile salmonids in lowland rivers

PhD ThesisMacrophytes could be integral to structuring lowland rivers and providing habitat for juvenile salmonids, but currently there is a lack of quantitative evidence evaluating this role. The aim of this thesis was to quantify the influence of a lowland macrophyte, Ranunculus, on juvenile salmonids and their environments in lowland rivers. A catchment-wide correlation study determined salmon and trout densities to be positively associated with Ranunculus cover, and velocity heterogeneity, respectively (Chapter 2). I subsequently implemented a spatially-and-temporally replicated Ranunculus manipulation experiment in a lowland river carrier. High Ranunculus cover supported higher abundances of salmon and trout throughout the summer feeding period. I also identified a strong influence of Ranunculus at the beginning of summer, when salmon abundances, site fidelity and increase in body length were highest (Chapter 3). Focusing on the beginning of summer, I then showed that higher total biomass of prey and a larger average size of prey were found in diets of salmon and trout captured in high Ranunculus cover, suggesting that Ranunculus was facilitating better foraging opportunities. Additionally, the dietary niche overlap between the two species was lowest in high cover, suggesting that abundance of Ranunculus reduced interspecific competition. There was a positive effect of Ranunculus on the growth rates of salmon, but an effect on trout growth was not detected (Chapter 4). Finally, I evaluated direct and indirect effects of Ranunculus on salmon abundance and growth rates (Chapter 5). I showed that salmon abundance was most influenced by the cover supplied by Ranunculus directly, but that this effect was mediated through negative influences of water depths and velocities. The positive influence of Ranunculus on salmon growth rates, however, was more intricately linked to changes in physical habitat and prey resources driven by Ranunculus, than to a direct source of cover. Together, these findings demonstrate a holistic role of Ranunculus in a lowland river, and its potential to improve the population viability of at-risk salmonid population

Conformation dependent monoclonal antibodies distinguish different replicating strains or conformers of prefibrillar Aβ oligomers

BACKGROUND: Age-related neurodegenerative diseases share a number of important pathological features, such as accumulation of misfolded proteins as amyloid oligomers and fibrils. Recent evidence suggests that soluble amyloid oligomers and not the insoluble amyloid fibrils may represent the primary pathological species of protein aggregates. RESULTS: We have produced several monoclonal antibodies that specifically recognize prefibrillar oligomers and do not recognize amyloid fibrils, monomer or natively folded proteins. Like the polyclonal antisera, the individual monoclonals recognize generic epitopes that do not depend on a specific linear amino acid sequence, but they display distinct preferences for different subsets of prefibrillar oligomers. Immunological analysis of a number of different prefibrillar Aβ oligomer preparations show that structural polymorphisms exist in Aβ prefibrillar oligomers that can be distinguished on the basis of their reactivity with monoclonal antibodies. Western blot analysis demonstrates that the conformers defined by the monoclonal antibodies have distinct size distributions, indicating that oligomer structure varies with size. The different conformational types of Aβ prefibrillar oligomers can serve as they serve as templates for monomer addition, indicating that they seed the conversion of Aβ monomer into more prefibrillar oligomers of the same type. CONCLUSIONS: These results indicate that distinct structural variants or conformers of prefibrillar Aβ oligomers exist that are capable of seeding their own replication. These conformers may be analogous to different strains of prions

Developing theoretically underpinned primary care resources for patients with asthma:an exemplar from the IMP2ART trial

Aim: This paper reports on the development of patient resources for the IMPlementing IMProved Asthma self-management as RouTine (IMP2ART) programme which aimed to: encourage patients to attend asthma reviews (invitation letters); encourage patients to enquire about asthma action plans (posters); equip patients with the knowledge to manage their asthma (information website).Background: To improve supported asthma self-management in UK primary care, the IMP2ART programme developed a whole-systems approach (patient resources, professional education, organisational strategies). Methods: Linked to behaviour change theory, we developed a range of patient resources for primary care general practices (an information website, invitation letters to invite patients for asthma reviews, posters to encourage asthma action plan ownership). We elicited qualitative feedback on the resources from people living with asthma in the UK (n=17). In addition, we conducted an online survey with volunteers in the UK-wide REgister for Asthma researCH (REACH) database to identify where they source asthma information, whether their information needs are met, and what information would be useful (n=95).Findings: Following feedback gathered from the interviews and the online survey, we refined our patient resources for the IMP2ART programme. Refinements included, highlighting the seriousness of asthma, enhancing trustworthiness, and including social support resources. We also made necessary colour and formatting changes to the resources. In addition, the patient resources were updated following the COVID-19 pandemic. The multi-stage development process enabled us to refine and optimise the patient resources. The IMP2ART strategy is now being tested in a UK-wide cluster RCT [ref: ISRCTN15448074].<br/

Citizen science reveals widespread negative effects of roads on amphibian distributions

Landscape structure is important for shaping the abundance and distribution of amphibians, but prior studies of landscape effects have been species or ecosystem-specific. Using a large-scale, citizen science-generated database, we examined the effects of habitat composition, road disturbance, and habitat split (i.e. the isolation of wetland from forest by intervening land use) on the distribution and richness of frogs and toads in the eastern and central United States. Undergraduates from nine biology and environmental science courses collated occupancy data and characterized landscape structure at 1617 sampling locations from the North American Amphibian Monitoring Program. Our analysis revealed that anuran species richness and individual species distributions were consistently constrained by both road density and traffic volume. In contrast, developed land around wetlands had small, or even positive effects on anuran species richness and distributions after controlling for road effects. Effects of upland habitat composition varied among species, and habitat split had only weak effects on species richness or individual species distributions. Mechanisms underlying road effects on amphibians involve direct mortality, behavioral barriers to movement, and reduction in the quality of roadside habitats. Our results suggest that the negative effects of roads on amphibians occur across broad geographic regions, affecting even common species, and they underscore the importance of developing effective strategies to mitigate the impacts of roads on amphibian populations

Expert range maps of global mammal distributions harmonised to three taxonomic authorities

Aim Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW). Location Global. Taxon All extant mammal species. Methods Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species). Results Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use. Main conclusion Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control.Output Status: Forthcoming/Available Online Output Type: Data Article Additional co-authors: Kira McCall, Ajay Ranipeta, Anna Schuerkmann, Michael A. Torselli, Thomas Lacher Jr, Russell A. Mittermeier, Anthony B. Rylands, Wes Sechrest, Don E. Wilson, Agustín M. Abba, Luis F. Aguirre, Joaquín Arroyo-Cabrales, Diego Astúa, Andrew M. Baker, Gill Braulik, Janet K. Braun, Jorge Brito, Peter E. Busher, Santiago F. Burneo, M. Alejandra Camacho, Paolo Cavallini, Elisandra de Almeida Chiquito, Joseph A. Cook, Tamás Cserkész, Gábor Csorba, Erika Cuéllar Soto, Valeria da Cunha Tavares, Tim R. B. Davenport, Thomas Deméré, Christiane Denys, Christopher R. Dickman, Mark D. B. Eldridge, Eduardo Fernandez-Duque, Charles M. Francis, Greta Frankham, William L. Franklin, Thales Freitas, J. Anthony Friend, Elizabeth L. Gadsby, Guilherme S. T. Garbino, Philippe Gaubert, Norberto Giannini, Thomas Giarla, Jason S. Gilchrist, Jaime Gongora, Steven M. Goodman, Sharon Gursky-Doyen, Klaus Hackländer, Mark S. Hafner, Melissa Hawkins, Kristofer M. Helgen, Steven Heritage, Arlo Hinckley, Stefan Hintsche, Mary Holden, Kay E. Holekamp, Rodney L. Honeycutt, Brent A. Huffman, Tatyana Humle, Rainer Hutterer, Carlos Ibáñez Ulargui, Stephen M. Jackson, Jan Janecka, Mary Janecka, Paula Jenkins, Rimvydas Juškaitis, Javier Juste, Roland Kays, C. William Kilpatrick, Tigga Kingston, John L. Koprowski, Boris Kryštufek, Tyrone Lavery, Thomas E. Lee Jr, Yuri L. R. Leite, Roberto Leonan M. Novaes, Burton K. Lim, Andrey Lissovsky, Raquel López-Antoñanzas, Adrià López-Baucells, Colin D. MacLeod, Michael A. Mares, Helene Marsh, Stefano Mattioli, Erik Meijaard, Ara Monadjem, F. Blake Morton, Grace Musser, Tilo Nadler, Ryan W. Norris, Agustina Ojeda, Nicté Ordóñez-Garza, Ulyses F. J. Pardiñas, Bruce D. Patterson, Ana Pavan, Michael Pennay, Calebe Pereira, Joyce Prado, Helder L. Queiroz, Matthew Richardson, Erin P. Riley, Stephen J. Rossiter, Daniel I. Rubenstein, Dennisse Ruelas, Jorge Salazar-Bravo, Stéphanie Schai-Braun, Cody J. Schank, Christoph Schwitzer, Lori K. Sheeran, Myron Shekelle, Georgy Shenbrot, Pipat Soisook, Sergio Solari, Richard Southgate, Mariella Superina, Andrew B. Taber, Maurício Talebi, Peter Taylor, Thong Vu Dinh, Nelson Ting, Diego G. Tirira, Susan Tsang, Samuel T. Turvey, Raul Valdez, Victor Van Cakenberghe, Geraldine Veron, Janette Wallis, Rod Wells, Danielle Whittaker, George Wittemyer, John Woinarski, Dietmar Zinner, Nathan S. Upham, Walter Jet

Southeastern Association of Law Libraries Annual Meeting

The 2009 SEAALL Annual Meeting was held in Athens Georgia, April 16-18, 2009

The role of networks to overcome large-scale challenges in tomography: The non-clinical tomography users research network

Our ability to visualize and quantify the internal structures of objects via computed tomography (CT) has fundamentally transformed science. As tomographic tools have become more broadly accessible, researchers across diverse disciplines have embraced the ability to investigate the 3D structure-function relationships of an enormous array of items. Whether studying organismal biology, animal models for human health, iterative manufacturing techniques, experimental medical devices, engineering structures, geological and planetary samples, prehistoric artifacts, or fossilized organisms, computed tomography has led to extensive methodological and basic sciences advances and is now a core element in science, technology, engineering, and mathematics (STEM) research and outreach toolkits. Tomorrow's scientific progress is built upon today's innovations. In our data-rich world, this requires access not only to publications but also to supporting data. Reliance on proprietary technologies, combined with the varied objectives of diverse research groups, has resulted in a fragmented tomography-imaging landscape, one that is functional at the individual lab level yet lacks the standardization needed to support efficient and equitable exchange and reuse of data. Developing standards and pipelines for the creation of new and future data, which can also be applied to existing datasets is a challenge that becomes increasingly difficult as the amount and diversity of legacy data grows. Global networks of CT users have proved an effective approach to addressing this kind of multifaceted challenge across a range of fields. Here we describe ongoing efforts to address barriers to recently proposed FAIR (Findability, Accessibility, Interoperability, Reuse) and open science principles by assembling interested parties from research and education communities, industry, publishers, and data repositories to approach these issues jointly in a focused, efficient, and practical way. By outlining the benefits of networks, generally, and drawing on examples from efforts by the Non-Clinical Tomography Users Research Network (NoCTURN), specifically, we illustrate how standardization of data and metadata for reuse can foster interdisciplinary collaborations and create new opportunities for future-looking, large-scale data initiatives

Expert range maps of global mammal distributions harmonised to three taxonomic authorities

AimComprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW).LocationGlobal.TaxonAll extant mammal species.MethodsRange maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species).ResultsRange maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use.Main conclusionExpert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control

Homologous recombination DNA repair defects in PALB2- associated breast cancers

Abstract: Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD

Health, education, and social care provision after diagnosis of childhood visual disability

Aim: To investigate the health, education, and social care provision for children newly diagnosed with visual disability.Method: This was a national prospective study, the British Childhood Visual Impairment and Blindness Study 2 (BCVIS2), ascertaining new diagnoses of visual impairment or severe visual impairment and blindness (SVIBL), or equivalent vi-sion. Data collection was performed by managing clinicians up to 1-year follow-up, and included health and developmental needs, and health, education, and social care provision.Results: BCVIS2 identified 784 children newly diagnosed with visual impairment/SVIBL (313 with visual impairment, 471 with SVIBL). Most children had associated systemic disorders (559 [71%], 167 [54%] with visual impairment, and 392 [84%] with SVIBL). Care from multidisciplinary teams was provided for 549 children (70%). Two-thirds (515) had not received an Education, Health, and Care Plan (EHCP). Fewer children with visual impairment had seen a specialist teacher (SVIBL 35%, visual impairment 28%, χ2p < 0.001), or had an EHCP (11% vs 7%, χ2p < 0 . 01).Interpretation: Families need additional support from managing clinicians to access recommended complex interventions such as the use of multidisciplinary teams and educational support. This need is pressing, as the population of children with visual impairment/SVIBL is expected to grow in size and complexity.This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited