Find research datasets worth reusing

Fig. 6 in Ordovician opabiniid-like animals and the role of the proboscis in euarthropod head evolution

Fig. 6 | Castle Bank euarthropod A (NMW.2021.3 G.8) from the Castle Bank biota. a Overview of whole specimen. Boxes indicate areas detailed in Fig. 7. b Explanatory drawing of (a). an annulations of proboscis, cf-l leftblades of caudal fan, cf-r right blades of caudalfan, df dorsal furrow in trunk, fl dorsolateral flap, ic internal canal of proboscis, ls lateral sclerite, pr proboscis, re subrectangular elements posterior to lateral sclerites, sp spine on proboscis.

Fig. 8 in Ordovician opabiniid-like animals and the role of the proboscis in euarthropod head evolution

Fig. 8 | Details of Castle Bank euarthropod A (NMW.2021.3 G.8), photographed using fluorescence. a Overview of whole specimen. b Details of tail fan with spinose margin. c Details of proboscis with dorsal spines. sp spine.

Fig. 2 in Ordovician opabiniid-like animals and the role of the proboscis in euarthropod head evolution

Fig. 2 | Details of anterior of Mieridduryn bonniae nov. gen. et sp. (NMW.2021.3 G.7). a Anteriorof the head region including proboscis, mouth, gut, view of anterior details including spinous proboscis, mouth and gut. b Mouth and anterior flapswith strengtheningrays.c Explanatory drawingof (b). anannulations on proboscis, gu gut, lfleftdorsolateral flap, mo mouth, rf rightdorsolateral flap, sb setal blades, sp spines on proboscis, sr strengthening rays.

Fig. 1 in Ordovician opabiniid-like animals and the role of the proboscis in euarthropod head evolution

Fig. 1 | Mieridduryn bonniae nov. gen. et sp. from the Castle Bank Biota (NMW.2021.3 G.7). a Overview of whole specimen. Boxes indicate areas depicted in Fig. 2. b Explanatory drawing of (a). Dashed white line indicates ventralmost point of left dorsolateral flaps, and demonstrates the twisted nature of the specimen. Bluelinesindicate filamentous setalstructures.dsdorsalsclerite,gu gut, lfleftdorsolateral flap, llleftlobopod, momouth,pr proboscis,rf rightdorsolateral flap, rl right lobopod, sr strengthening ray, sp dorsal spines on proboscis.

Fig. 5 in Ordovician opabiniid-like animals and the role of the proboscis in euarthropod head evolution

Fig. 5 | Details of trunk of Mieridduryn bonniae nov. gen. et sp. (NMW.2021.3 G.7). a Overview of trunk. b Details of left dorsolateral flap and associated setal blades. c, d details of lobopodous limbs with annulations and spines. an annulations on lobopodous limbs, lf left dorsolateral flap, ll left lobopodous limb, sb setal blade, sp spines on posterior margin of lobopodous limb.

opencc-by-4.0Aug 2022View details →

EI STFC Power of Light animation - introducing Big Questions and Diamond Light Source

The ‘Power of Light’ project brings together research scientists, higher institution educators and research fellows, teachers, and STEM ambassadors to co-create engaging and accessible resources. The Power of Light project creates opportunities for classrooms and community settings to investigate examples of scientists’ current innovative research that is taking place in UK’s national synchrotron science facility at Diamond Light Source.  This co-created animation identifies examples of Big Questions, introduces the synchrotron, and the value of exploring very small elements in our world to inform our thikning about Big Questions. During pilot sessions in both classroom and community settings, the animation has been successfully engaging curious minds and introducing areas of scientific research that can be explored further through the Power of Light 'zines'. This resource encourages a dialogue about the value of working in multidisciplinary ways to build and use knowledge in epistemically insightful ways. The particle accelerator at Diamond enables scientists to investigate the complexity of relationships in the structures of ‘things’ by investigating how atoms behave. The scientists we have been working with explain that they enter an area of research with a defined question that scientific methods and the facilities at Diamond can help them investigate. During their scientific research into a precise question further, and often unexpected, lines of enquiry can be disclosed. The Power of Light project confirms that learning about science (and how building scientific knowledge ‘works’) takes us on a journey of discovery about being human and the nature of the world around us.

opencc-zeroDec 2022View details →

Data from: aniMotum, an R package for animal movement data: rapid quality control, behavioural estimation and simulation

1. Animal tracking data are indispensable for understanding the ecology, behaviour and physiology of mobile or cryptic species. Meaningful signals in these data can be obscured by noise due to imperfect measurement technologies, requiring rigorous quality control as part of any comprehensive analysis. 2. State-space models are powerful tools that separate signal from noise. These tools are ideal for quality control of error-prone location data and for inferring where animals are and what they are doing when they record or transmit other information. However, these statistical models can be challenging and time-consuming to fit to diverse animal tracking data sets. 3. The R package aniMotum eases the tasks of conducting quality control on and inference of changes in movement from animal tracking data. This is achieved via: 1) a simple but extensible workflow that accommodates both novice and experienced users; 2) automated processes that alleviate complexity from data processing and model specification/fitting steps; 3) simple movement models coupled with a powerful numerical optimization approach for rapid and reliable model fitting. 4. We highlight aniMotum's capabilities through three applications to real animal tracking data. Full R code for these and additional applications are included as Supporting Information so users can gain a deeper understanding of how to use aniMotum for their own analyses.

opencc-zeroDec 2022View details →

Code and data from: A hierarchical approach for estimating state-specific mortality and state transition in dispersing animals with incomplete death records

Unbiased mortality estimates are fundamental for testing ecological and evolutionary theory as well as for developing effective conservation actions. However, mortality estimates are often confounded by dispersal, especially in studies where dead-recovery is not possible. In such instances, missing individuals (i.e. individuals with unobserved time of death) may have died or permanently emigrated from a study area, making inferences about their fate difficult. Mortality before and during dispersal, as well as the decision to disperse, usually depend on a suite of individual, social, and environmental covariates, which in turn can be used to draw conclusions about the fate of missing individuals. Here, we propose a Bayesian hierarchical model that takes into account time-varying covariates to estimate transitions between life-history states and mortality in each state using mark-resighting data with missing individuals. Specifically, our framework estimates mortality rates in two states (resident and dispersing state) by treating the fate of missing individuals as a latent (i.e. unobserved) variable that is statistically inferred based on information from individuals with a known fate and given the individual, social, and environmental conditions at the time of disappearance. Our model also estimates rates of state transition (i.e. emigration) to assess whether a missing individual was more likely to have died or survived due to unobserved emigration from the study area. We used simulations to check the validity of our model and assessed its performance with data of varying degrees of uncertainty. Our modeling framework provided accurate mortality and emigration estimates for simulated data of different sample sizes, proportions of missing individuals, and resighting intervals. Variation in sample size appeared to affect the precision of estimated parameters the most. Our approach offers a solution to estimating unbiased mortality of both resident and dispersing individuals as well as the probability of emigration using mark-resighting data with incomplete death records. Conditional on the availability of data on known-fate individuals and relevant time-varying covariates, our model can reconstruct the fate (death or emigration) of missing individuals. The modularity of our framework allows mortality analyses to be tailored to a variety of species-specific life histories.

Supplementary Material - Marine animal forests in turbid environments are overlooked seascapes in urban areas

Figures S1, S2, and S3 of the manuscript "Marine animal forests in turbid environments are overlooked seascapes in urban areas" accepted in the open-access journal Ocean and Coastal Research (Soares et al. 2023)

Literature review of occurrence and transmission dynamics of SARS-CoV2 in mammal animals

A literature review has been conducted, focusing on susceptibility of wild and domestic animal species reported under field and laboratory conditions, considering different diagnostic tests (e.g., virus isolation, RNA and antibody detection), infection dynamic, pathogenesis, immunity and further transmission of the virus. Review protocol and data extraction tables are available. The following review questions were considered: <ul> <li>Which mammal species have been reported positive to SARS CoV 2 in the field (either at RNA, isolated virus, antibodies), and their geographical distribution?</li> </ul> <ul> <li>Which wild and domestic mammal species are susceptible to SARS CoV 2 in laboratory conditions</li> <li>Dynamic of infection and pathogenesis: <ul> <li>What are confirmed infection routes for these species?</li> <li>What is the length of the incubation period in these species</li> <li>What are the clinical signs, if any, their severity, duration, etc.</li> <li>Which species are able to shed the virus (even in absence of clinical signs)</li> <li>Do these species develop protective immunity</li> </ul> </li> <li>Which of these species can further transmit the disease to same/other species ?</li> <li>What are the genetic virus variants in each species where it is isolated?</li> <li>In which animals vaccines against SARS CoV 2 have been tested, and what are the results in terms of immunogenicity, protection to challenge, or safety?</li> </ul> <ul> <li>Which diagnostic tests are used in animals to detect SARS CoV <ul> <li>Type of test</li> <li>Test performance (Se, Sp)</li> <li>Sample matrix used</li> </ul> </li> </ul>

Ressources - Video games as a tool for ecological learning : the case of Animal Crossing - COROLLER & FLINOIS - 2023

The present repository includes :  <ol> <li>Survey answers - 200 people, anonymized. Quizz about animals and vegetals that are and are not present in the game ANIMAL CROSSING NEW HORIZONS. Personal questions (age,, gender, location). Self  assesment of "Naturalistic Fiber". At the end, question about the video game Animal CROSSING, and then free space</li> <li>Translated R code, based on the present dataset. Runs figures and tests used in our paper "Video games as a tool for ecological learning : the case of "Animal Crossing : New Horizons" during Covid-19 quarantine"</li> <li>The survey itself is available (in french unfortunately) at the following link : <a href="https://forms.gle/GgwULMcg8KnBqDt26">https://forms.gle/GgwULMcg8KnBqDt26</a>, if the link is broken, please don't hesitate to contact me</li> <li>Nintendo Game Content guide at the following link : <a href="https://www.nintendo.co.jp/networkservice_guideline/en/index.html">https://www.nintendo.co.jp/networkservice_guideline/en/index.html</a></li> <li>Appendix (S1 : table of raw datas ; S2 : Normal and QQ plots)</li> <li>Approval of Ethical Research Committee of Université de Sherbrooke (Canada, QC)  </li> </ol> <blockquote> " [...] furthermore, after reviewing the application for review, no ethical issues were identified by the committee.The committee notes that:The data were collected from a population of individuals who do not a priori present the characteristics of a vulnerable population; The risks associated with participation in the research are minimal; The data collected are anonymous; Individuals have been informed that the data may be used for scientific purposes; However, we remind you that in the future, any research project, as defined in the policy, must be approved by the research ethics committee before proceeding with the collection of data. Therefore, please accept this letter in lieu of an ethics certificate from the Research Ethics Board - Education and Social Sciences of the Université de Sherbrooke. This letter may be used when submitting for publication or presentation of the results of this study or for any results of this study or for any other request related to the ethical approval of this project. " Mme Ariane Tessier Coordonnatrice à l'éthique de la recherche - Université de Sherbrooke, CA QC </blockquote> If you have any problem with the present ressources, or if you want to work and publish works containing these datas, please contact me at :  simoncoroller.biologie@gmail.com  CC : Simon.Coroller@usherbrooke.ca I would gladly discuss with you !  Best wishes. COROLLER & FLINOIS

Animations of Uncertainty in Scalar Volume Data

A collection of videos presenting the animations created for the master's thesis with the title "Visualization of Uncertainty in 3D Scalar Data Using Extended 2D Transfer Functions and Animations" of Tobias Neeb, master's student at Hochschule Worms (DE).  The videos present animations of the application examples given in the thesis. Goal of the thesis here is to investigate possible new insights regarding uncertainty visualization by extending the functionality of classification widgets of the 2D transfer function-editor in OpenWalnut, by introducting color maps, widget animations and a variety of new widget shapes.   The animations present a volume rendering of different scalar datasets from which the mean and standard deviation has been derived. The histogram of the 2DTF-editor here presents the 2D-distribution of mean and standard deviation(stdDev) as value pairs, the x-axis presenting the mean-field, while the y-axis presents the stdDev-field.

opencc-zeroFeb 2023View details →

Secondary ion mass spectrometry, a powerful tool for revealing ink formulations and animal skins in medieval manuscripts

Book production by medieval scriptoria has gained growing interest in recent studies. In this context, identifying ink compositions and parchment animal species from illuminated manuscripts is of great importance. Here, we introduce time-of-flight secondary ion mass spectrometry (ToF-SIMS) as a non-invasive tool to identify both inks and animal skins in manuscripts, at the same time. For this purpose, both positive and negative ion spectra in inked and non-inked areas were recorded. Chemical compositions of pigments (decoration) or black inks (text) were determined by searching for characteristic ion mass peaks. Animal skins were identified by data processing of raw ToF-SIMS spectra using principal component analysis (PCA). In illuminated manuscripts from the fifteenth to sixteenth century, malachite (green), azurite (blue), cinnabar (red) inorganic pigments, as well as iron-gall black ink, were identified. Carbon black and indigo (blue) organic pigments were also identified. Animal skins were identified in modern parchments of known animal species by a two-step PCA procedure. We believe the proposed method will find extensive application in material studies of medieval manuscripts, as it is non-invasive, highly sensitive and able to identify both inks and animal skins at the same time, even from traces of pigments and tiny scanned areas.

Fig. 3 in Invertebrate animals as a component of the traditional medicine trade in KwaZulu-Natal, South Africa

Fig. 3. Traditional healer's regalia. A, wrist-band from Pondoland made from shells of the gastropod Nerita albicilla (the black and white coloration symbolising the black and white components of many traditional remedies); B, diviner's necklace with glass beads and marine shells, Mtubatuba area, Zululand (Natal Museum 7147).

Fig. 2 in Invertebrate animals as a component of the traditional medicine trade in KwaZulu-Natal, South Africa

Fig. 2. Samples of invertebrate animals for sale in market. A, dried, live-collected chitons of the genera Chiton, Dinoplax and Onithochiton; B, ring cowries (Cypraea annulus), many with dried bodies inside; C, organ-pipe coral (Tubipora musica) from localities as much as 2000 km distant in northern Mozambique; D, starfish (Protoreaster lincki) collected alive in sheltered localities in Mozambique.

Fig. 1 in Invertebrate animals as a component of the traditional medicine trade in KwaZulu-Natal, South Africa

Fig. 1. Stalls in the Warwick Triangle market, Durban. A, typical stall selling a wide range of products, nearly all of animal origin; B, neatly organised stall of a Mozambican trader, displaying a range of animal products, many of tropical origin. Note Cypraea annulus head-bands in foreground.

Fig. 5. Traditional nomenclature - isongololo. A in Invertebrate animals as a component of the traditional medicine trade in KwaZulu-Natal, South Africa

Fig. 5. Traditional nomenclature - isongololo. A, isongololo, the well-known juliform millipedes and B, isongololo lasolwandle, the shell of the cephalopod mollusc Spirula spirula.

Fig. 4. Traditional nomenclature - imfinyezi. A, a in Invertebrate animals as a component of the traditional medicine trade in KwaZulu-Natal, South Africa

Fig. 4. Traditional nomenclature - imfinyezi. A, a chiton imfinyezi yasolwandle (Dinoplax sp.) and B, a pill millipede imfinyezi yentaba or imfinyezi yangaphandle (Sphaerotherium sp.), showing the superficially similar shape and body segmentation.

opencc-by-4.0Mar 2023View details →

European Union Summary Report on Antimicrobial Resistance in Zoonotic and Indicator Bacteria from Humans, Animals and Food in 2020/2021

All tables produced for the European Union Summary Report on Antimicrobial Resistance in Zoonotic and Indicator Bacteria from Humans, Animals and Food in 2021: - Campylobacter - E. coli - MRSA - Salmonella - ESBL Annexes A to F are also included.