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2,021 results for “non-invasive”
Data from: Assessing individual patterns of Echinococcus multilocularis infection in urban coyotes: non-invasive genetic sampling as epidemiological tool
1. In epidemiological studies of wildlife parasites, faecal genotyping has been introduced to prevent bias in estimates of parasite prevalence from faecal samples collected in the field. Such an approach could be particularly relevant in the study of Echinococcus multilocularis transmission in urban settings, where estimates of prevalence and patterns of infection in wild canid hosts are key parameters used in zoonotic risk assessment and management. However, no previous study has evaluated the reliability of E. multilocularis faecal prevalence, and individual patterns of infection in definitive hosts remain poorly understood. 2. We evaluated faecal genotyping as an epidemiological tool, using E. multilocularis in urban coyotes Canis latrans as our study system. Combining parasitological analysis and multilocus individual genotyping of coyote faeces, we compared faecal parasite prevalence with the prevalence obtained from genotyped faecal samples. Furthermore, we assessed patterns of individual infection, such as re-infection rates and phenology of parasite egg excretion. 3. Of 425 feces collected in five urban sites, we genotyped 142 samples (33.4%) corresponding to 60 unique individual coyotes. Number of genotyped samples per coyote ranged between 1 and 10 (mean = 2.3). Genotypes were obtained at 4–6 microsatellite loci and had a mean reliability of 0.9975. 4. Faecal prevalence of E. multilocularis in genotyped coyotes was 25.0%, and similar to results previously obtained from non-genotyped faeces. Faecal genotyping allowed estimating a re-infection rate of individual coyotes of 57.1%, and to observe temporal patterns of parasite infection that were not detected using non-genotyped faeces. 5. Synthesis and applications. If compared to independent data obtained through coyote post-mortem examination, our results suggest that reliable estimates of overall parasite prevalence in definitive host populations can be efficiently obtained through well-designed field collection and traditional faecal parasitological analysis. However, faecal genotyping allows assessing the dynamics of individual infections, which could otherwise only be estimated by using invasive techniques. Combining faecal genotyping with parasitology has a great potential in assessing zoonotic risk transmission in urban areas, as well as advancing the field of wildlife ecology, disease ecology and conservation.
Data from: Real-time assessment of hybridization between wolves and dogs: combining non-invasive samples with ancestry informative markers
Wolves and dogs provide a paradigmatic example of the ecological and conservation implications of hybridization events between wild and domesticated forms. However, our understanding of such implications has been traditionally hampered by both high genetic similarity and the difficulties in obtaining tissue samples (TS), which limit our ability to assess ongoing hybridization events. To assess the occurrence and extension of hybridization in a pack of wolf-dog hybrids in Northwestern Iberia, we compared the power of 52 nuclear markers implemented on TS with a subset of 13 ancestry informative markers (AIMs) typed in non-invasive samples (NIS). We demonstrate that the 13 AIMs are as accurate as the 52 markers that were chosen without regard to the power to differentiate between wolves and dogs, also having the advantage of being rapidly screened on NIS. The efficiency of AIMs significantly outperformed ten random sets of similar size and an additional commercial set of 18 markers. Bayesian clustering analysis implemented on AIMs and NIS identified nine hybrids, two wolves and two dogs. Four hybrids were unambiguously assigned to F1xWolf backcrosses. Our approach (AIMs + NIS) overcomes previous difficulties related to sample availability and informative power of markers, allowing a quick identification of wolf-dog hybrids in the first phases of hybridization episodes. This provides managers with a reliable tool to evaluate hybridization, and estimate the success of their actions. This approach may be easily adapted for other pairs of wild/domesticated species, thus improving our understanding of the introgression of domestication genes into natural populations.
Data from: Non-invasive imaging of CSF-mediated brain clearance pathways via assessment of perivascular fluid movement with DTI MRI
The glymphatics system describes a CSF-mediated clearance pathway for the removal of potentially harmful molecules, such as amyloid beta, from the brain. As such, its components may represent new therapeutic targets to alleviate aberrant protein accumulation that defines the most prevalent neurodegenerative conditions. Currently, however, the absence of any non-invasive measurement technique prohibits detailed understanding of glymphatic function in the human brain and in turn, it's role in pathology. Here, we present the first non-invasive technique for the assessment of glymphatic inflow by using an ultra-long echo time, low b-value, multi-direction diffusion weighted MRI sequence to assess perivascular fluid movement (which represents a critical component of the glymphatic pathway) in the rat brain. This novel, quantitative and non-invasive approach may represent a valuable biomarker of CSF-mediated brain clearance, working towards the clinical need for reliable and early diagnostic indicators of neurodegenerative conditions such as Alzheimer's disease.
Data from: In situ measurements of animal morphological features; a non-invasive method
1) Measurements of morphological features are important for ecological studies, especially on free-ranging wild animal species. Conventionally, specimens either dead or in captivity are used for morphometric studies, which is difficult in the case of wild species for several reasons. Capturing would be even futile when research questions are relating to issues such as prey size selection or estimation of intake rate in under field conditions, where in situ morphometric measurements are inevitable. Remotely estimating morphometric features via, avian bill and head length are always laden with wide variances. Hence, we developed this technique for in situ measurements of animal morphology through digital photographs. 2) This non-invasive novel method for in situ estimation of individuals' morphometric measurements uses digital photographs' metadata. We extracted the metadata (field of view, focal length, subject-distance etc.,) in Exchangeable Image File Format (EXIF) from digital images using freely available software, and the unknown sizes were estimated from each image. Cardboard (fish) models were, at first, used to estimate the accuracy of measurements comparing actual and estimated values, and the same protocol was repeated on museum specimens (bird). Finally, we checked the repeatability of this method under field conditions using free ranging Chickens (Gallus gallus domesticus). The results under different conditions were subjected to rigorous statistical testing. 3) Upon comparing the actual with estimated values, obtained from three distinct types of objects (1. Cardboard model, 2. Museum specimens, and 3. Live birds under field conditions), variations were found non-significant affirming the assumption that actual value (Y) = estimated value (X) with inconsequential variance of the Y from X. Moreover, both the relative and absolute errors between the actual and estimated values were so low, indicating that this method yielded neither over-estimation nor under-estimation. 4) The advantage of this non-invasive method is that it could generate reasonably accurate morphometric measurements at a relatively low cost for routine morphometric works in field conditions. We envisage significant utility of this non-invasive technique in different fields of science such as biology, morphology, ecology, evolution, wildlife, conservation science, agriculture, forensics and engineering design.
Data from: Non-invasive genetic monitoring involving citizen science enables reconstruction of current pack dynamics in a re-establishing wolf population
Background: Carnivores are re-establishing in many human-populated areas, where their presence is often contentious. Reaching consensus over management decisions is often hampered by a dispute about the size of the local carnivore population. Understanding the reproductive dynamics and individual movements of the carnivores can provide support for management decisions, but individual-level information can be difficult to obtain from elusive, wide-ranging species. Non-invasive genetic sampling can yield such information, but makes subsequent reconstruction of population history challenging due to incomplete population coverage and error-prone data. Here, we combine a collaborative, volunteer-based sampling scheme with Bayesian pedigree reconstruction to describe the pack dynamics of an establishing grey wolf (Canis lupus) population in south-west Finland, where wolf breeding was recorded in 2006 for the first time in over a century. Results: Using DNA extracted mainly from faeces collected since 2008, we identified 81 individual wolves and assigned credible full parentages to 70 of these and partial parentages to a further 9, revealing 7 breeding pairs. Individuals used a range of strategies to obtain breeding opportunities, including dispersal to established or new packs, long-distance migration and inheriting breeding roles. Gene flow occurred between all packs but inbreeding events were rare. Conclusions: These findings demonstrate that characterizing ongoing pack dynamics can provide detailed, locally-relevant insight into the ecology of contentious species such as the wolf. Involving various stakeholders in data collection makes these results more likely to be accepted as unbiased and hence reliable grounds for management decisions.
Data from: Molecular ecology of the Neotropical otter (Lontra longicaudis): non-invasive sampling yields insights into local population dynamics
Non-invasive genetic analysis has been frequently employed to estimate ecological and population parameters for many secretive and/or threatened species. However, Neotropical carnivores have so far been scarcely targeted by such studies. The Neotropical otter (Lontra longicaudis) is a poorly-known species for which local levels of genetic diversity and demographic parameters are virtually absent. We employed non-invasive sampling and amplification of microsatellite loci to investigate population size and density, spatial organization, and relatedness of a wild Neotropical otter population in an Atlantic forest area in southern Brazil. We directly identified 28 individuals and estimate a rather high population density at the study site. Spatial organization analysis indicated that male cumulative displacement was higher than that of females, with the latter sex showing evidence of philopatric behaviour. Also, the reconstruction of genealogical relationships suggests that spatial organization in this otter appears to be influenced by relatedness. By allowing the testing of specific hypothesis targeting these issues, our results provided important glimpses into the Neotropical otter's population biology. Moreover, the findings of the present study reaffirm the power of non-invasive genetics to investigate the biology of this elusive species, and open up new avenues for ecological and demographic studies of other Neotropical carnivores.
Data from: Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers
Quantitative information regarding reproduction is essential for conserving endangered animals; however, some conventional quantitative methods can be damaging to the target population and their habitats. In the present study, the reproductive migration of a threatened endemic fish, three-lips (Opsariichthys uncirostris uncirostris), was non-invasively monitored by quantitative PCR of species-specific environmental DNA (eDNA), the usefulness of which has been under-studied. Water sampling and from-shore visual inspection were performed weekly along a tributary of Lake Biwa (Japan), where adult fish seasonally migrate upstream to reproduce as well as at lake sites near the river mouth. Species-specific eDNA was collected at all locations at times when the fish were visually observed and at certain sites where the fish were not observed. Log-transformed individual counts from visual inspection were positively correlated with log-transformed eDNA concentration in the river sites, indicating that eDNA analysis can be a reliable quantitative tool for fish abundance in rivers. Furthermore, distance from the lake did not influence eDNA concentration, suggesting that eDNA transport by river flow had a negligible effect on eDNA quantification. eDNA concentration and individual counts both gradually increased from May–July, then both decreased in August. Importantly, eDNA analysis showed that the fish occupied more habitats in the peak reproductive season and stayed for longer time at any given site. An additional underwater survey confirmed unexpected eDNA detections as true positives. eDNA analysis has great potential to quantitatively monitor reproductive fish migrations under certain conditions.
Data from: Examining disease prevalence for species of conservation concern using non-invasive spatial capture-recapture techniques
1. Non-invasive techniques have long been used to estimate wildlife population abundance and density. However, recent technological breakthroughs have facilitated non-invasive estimation of the proportion of animal populations with certain diseases. Giraffes Giraffa camelopardalisare increasingly becoming recognized as a species of conservation concern with decreasing population trajectories across their range in Africa. 2. Diseases may be an important component impacting giraffe population declines, and the emerging 'Giraffe Skin Disease' (GSD), characterized by the appearance of wrinkled skin and alopecic lesions on the limbs, neck, and chest of infected giraffe, may hinder movement causing increased susceptibility to predation. 3. We examined the prevalence of GSD in Tanzania's Ruaha National Park over a 4-month period in 2015, using photographic capture–recapture surveys via road-based transects. We divided the study area into five circuitous survey units, each approximately 100 km in length ($\bar x$ = 99.22 km, SD = 3.72), and surveyed for giraffes for four months. From these surveys, we developed a database of spatially-explicit giraffe photographs. 4. We processed these photos for individual identification and fitted spatial capture–recapture models to predict the spatial configuration of giraffe abundance and GSD prevalence within the study area. 5. Our results indicated that >86% of the giraffe population showed signs of GSD and that the disease was more prevalent in the northern and north-eastern portion of Ruaha National Park. 6. Synthesis and applications. Our research shows that data from non-invasive surveys can be used in spatial capture–recapture (SCR) models to estimate the proportion of a population affected by a visible disease. Researchers and conservationists can use SCR models to better examine the variation in parameters associated with these populations such as sex and age class, movement, and encounter rate, which may be linked to the prevalence of the disease, while incorporating broad spatial and temporal dimensions of the population in such areas. We discuss the implications of this research for conservation of threatened species with an emphasis on disease ecology and vulnerability to predations, and more broadly, for wildlife conservation.
Urinary suPAR: a non-invasive biomarker of infection and tissue inflammation for use in studies of large free-ranging mammals
<p>Studies of large free-ranging mammals incorporating physiological measurements typically require the collection of urine or faecal samples, due to ethical and practical concerns over trapping or darting animals. However, there is a dearth of validated biomarkers of immune activation and inflammation that can be measured non-invasively. We here evaluate the utility of urinary measurements of the soluble form of the urokinase plasminogen activator receptor (suPAR), for use as a health marker in studies of wild large mammals. We investigate how urinary suPAR concentrations change in response to viral infection and surgical trauma (inflammation), comparing it to the measurement of a marker of cellular immune activation, urinary neopterin, in captive rhesus macaques. We then test the field utility of urinary suPAR, assessing the effects of soil and faecal contamination, sunlight, storage at different temperatures, freeze-thaw cycles, and lyophilization. We find that suPAR concentrations rise markedly in response to both infection and surgery-associated inflammation, unlike urinary neopterin concentrations, which only rise in response to the former. Our field validation demonstrates that urinary suPAR is reasonably robust to many of the issues associated with field collection, sample processing, and storage, as long as samples can be stored in a freezer. Urinary suPAR is thus a promising biomarker applicable for monitoring various aspects of health in wild primates and potentially also other large mammals. </p>
Data associated with the study, "Non-Invasive Biomarkers for Detecting Progression Toward Hypovolemic Cardiovascular Instability In A Lower Body Negative Pressure Model".
<p>Raw data associated with the study entitled "Non-Invasive Biomarkers for Detecting Progression Toward Hypovolemic Cardiovascular Instability In A Lower Body Negative Pressure Model". There were 16 subjects with 1. electrocardiogram (ECG), 2. mean arterial pressure (MAP), 3) photoplethysmography (pleth), 4) Bioimpedance Cardiography measured via a Cheetah (Startling/Medtronic) system referred to as cheetah, 5) electrical impedance from a Sentec electrical impedance tomography system, referred to as ST, and electrical impedance from a sciospec impedance analyzer, referred to as SS. Each subject underwent a lower body negative pressure (LBNP) procedure, where the LBNP was increased modeling a small hemorrhage by drawing blood to their lower extremeties. The dataset contains 5 mat (MATLAB data files), with time reported in minutes on the day of the study, i.e.10 am = 600 minutes. The file details are as follows:</p><ul><li><strong>LBNP data</strong>: LBNP_level_times.mat. The data contains 1 structure (LBNPinf) of length 16 (corresponding to each subject) with the following fields<ul><li>ts: time vector in minutes</li><li>lbnp: LBNP value at each noted time</li></ul></li><li><strong>Vital Sign data</strong>: raw_labchart_data.mat. The data contains 1 structure array (Labchart) of length 16 (corresponding to each subject) with the following fields<ul><li>ts: time vector in minutes</li><li>ecgs: ECG data</li><li>MAP: MAP data</li><li>pleth: pleth data recorded from a single channel (V)</li></ul></li><li><strong>Sentec EIT data</strong>: raw_av_ST_impedance_data.mat. The data contains 1 structure array (STout) of length 16 (corresponding to each subject) with the following fields<ul><li>t_thx: time vector in minutes corresponding to thorax data</li><li>Z_thx: average impedance data at each time over the thorax</li><li>t_spl: time vector in minutes corresponding to abdomen data</li><li>Z_spl: average impedance data at each time over the abdomen</li></ul></li><li><strong>Sciospec EIS data</strong>: raw_sciospec_dat.mat. The data contains 1 cell array & 1 structure array (sciodat) of length 16 (corresponding to each subject).<ul><li>Cell array: Locations of the Sciospec measurements: 'Thoracic', 'Abdominal', 'Arm'</li><li>Sciodat fields:<ul><li>sciodat structure array of length 3 corresponding to the 'Thoracic', 'Abdominal', 'Arm' locations, respectively. Each component has the following fields<ul><li>tvec: time vector in minutes</li><li>fs: frequencies that the impedance is recorded over (Hz)</li><li>Zmat: matrix of impedance data size time versus frequency</li><li>erflg: not used</li></ul></li></ul></li></ul></li><li><strong>Bioimpedance cardiography data</strong>: raw_cheetah_bioimpedance.mat. The data contains a cell array of column labels (col_labs, 1x11) and a matrix (cheetah_db) of the BC data.</li></ul><p> </p><p> </p><p> </p>
How to better count elusive birds? Comparing non-invasive monitoring methods to estimate population size of the endangered Pin-tailed sandgrouse (Pterocles alchata)
<p>Data to run analyses for manuscript comparing non-invasive monitoring methods to estimate Pin-tailed sandgrouse abundance</p>
Dataset for: Differential responses to fertilization and competition among invasive, non-invasive alien and native Bidens species
<p class="manuscript">Comparative studies of invasive, non-invasive alien, and native congenic plant species can identify plant traits that drive invasiveness. In particular, functional traits associated with rapid growth rate and high fecundity likely facilitate invasive success. As such traits often exhibit high phenotypic plasticity, characterizing plastic responses to anthropogenic environmental changes such as eutrophication and disturbance is important for predicting the invasive success of alien plant species in the future. Here, we compared trait expression and phenotypic plasticity at the species level among invasive, non-invasive alien, and native <i>Bidens</i> species. Plants were grown under nutrient addition and competition treatments, and their functional, morphological, and seed traits were examined. Invasive <i>B. frondosa</i> exhibited higher phenotypic plasticity in most measured traits than did the alien non-invasive <i>B. pilosa</i> or native <i>B. bipinnata</i>. However, differential plastic responses to environmental treatments rarely altered the rank of trait values among the three <i>Bidens</i> species, except for the number of inflorescences. The achene size of <i>B. frondosa</i> was larger, but its pappus length was shorter than that of <i>B. pilosa</i>. Two species demonstrated opposite plastic responses of pappus length to fertilization. These results suggest that the plasticity of functional traits does not significantly contribute to the invasive success of <i>B. frondosa</i>. The dispersal efficiency of <i>B. frondosa</i> is expected to be lower than that of <i>B. pilosa</i>, suggesting that long-distance dispersal is likely not a critical factor in determining invasive success.</p>
Non-Invasive Rheo-MRI Study of Egg Yolk-Stabilized Emulsions: Yield Stress Decay and Protein Release
<p>Raw data for our publication "Non-Invasive Rheo-MRI Study of Egg Yolk-Stabilized Emulsions: Yield Stress Decay and Protein Release", including MRI (Paravision) and D-T2 maps (Topspin) datasets, rheological measurements (ASCII) and MATLAB scripts organised corresponding to each figure in the paper.</p>
Quantifying mothers' preferences for providing information about non-invasive prenatal testing in Sweden: evidence from a discrete choice experiment
<p>Training materials for a discrete choice experiment survey designed to quantify mothers' preferences for information about non-invasive prenatal testing in Sweden.</p>
MRI Dataset: Diffusion MRI as a potential non-invasive biomarker of neuroinflammation following intracerebral haemorrhage
<p>Raw MRI dataset of T2 and NODDI scans.</p> <p>Subjects: Adult male Sprague-Dawley rats, aged 10-12 weeks, 300-450g. Subjected to intracerebral haemorrhage induction by intracranial injection of 0.2 Type VII collagenase, recovered for 7 days prior to these MRI scans being performed. Further methodological information available upon request.</p>
A non-invasive BCG skin challenge model for assessing tuberculosis vaccine efficacy
<p>Flow cytometry FCS files for Figure 3 days 7 and 14.</p>
FIGURE 5 in A new blind snake of the genus Letheobia (Serpentes: Typhlopidae) from Rwanda with redescriptions of L. gracilis (Sternfeld, 1910) and L. graueri (Sternfeld, 1912) and the introduction of a non-invasive preparation procedure for scanning electron microscopy in zoology
FIGURE 5. Preserved holotypes of Letheobia gracilis (ZMB 22030, total length 465.4 mm; outside) and L. akagerae sp. nov. (ZFMK 100862, total length 457.5 mm; centre); showing the extreme elongation in the new species.
FIGURE 2 in A new blind snake of the genus Letheobia (Serpentes: Typhlopidae) from Rwanda with redescriptions of L. gracilis (Sternfeld, 1910) and L. graueri (Sternfeld, 1912) and the introduction of a non-invasive preparation procedure for scanning electron microscopy in zoology
FIGURE 2. SEM images of lateral view of the head of the holotype of Letheobia gracilis (ZMB 22030; top), the holotype of L. akagerae sp. nov. (ZFMK 100862, centre), and a specimen of L. graueri (ZFMK 63138, bottom).
FIGURE 1 in A new blind snake of the genus Letheobia (Serpentes: Typhlopidae) from Rwanda with redescriptions of L. gracilis (Sternfeld, 1910) and L. graueri (Sternfeld, 1912) and the introduction of a non-invasive preparation procedure for scanning electron microscopy in zoology
FIGURE 1. SEM images of head scalation of the holotype of Letheobia gracilis (ZMB 22030; left), the holotype of L. akagerae sp. nov. (ZFMK 100862, centre), and a specimen of L. graueri (ZFMK 63138, right), showing the dorsal side (top row) and the ventral side (bottom row).
FIGURE 3 in A new blind snake of the genus Letheobia (Serpentes: Typhlopidae) from Rwanda with redescriptions of L. gracilis (Sternfeld, 1910) and L. graueri (Sternfeld, 1912) and the introduction of a non-invasive preparation procedure for scanning electron microscopy in zoology
FIGURE 3. SEM images showing details of the scale pits in (A) the holotype of Letheobia graueri (ZMB 27161) and (B) the holotype of L. gracilis (ZMB 22030).
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.