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43 results for “fecal samples”
Colon Cancer Study of Fecal Samples in Shanghai, China
ClinicalTrials.gov study NCT01778595. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal
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Behavior and diet data collected from i) GPS video camera collars and ii) fecal samples collected from individuals from the Fortymile Caribou Herd
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Data from: Detection dog efficacy for collecting fecal samples from the critically endangered Cross River gorilla (Gorilla gorilla diehli) for genetic censusing
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Fecal pellet flux summary from samples collected during CCE LTER process cruises in the California Current system, 2007 – present.
The collection and enumeration of sinking fecal pellets on CCE LTER Process cruises has been led by Mike Stukel since 2007. Sinking particles are collected in VERTEX-style particle interceptor traps (PIT) with an 8:1 aspect ratio, 70-mm diameter, and a baffle on top comprised of 13 smaller beveled tubes with a similar 8:1 aspect ratio. Tubes are deployed with a formalin-brine for a duration of 2-5 days. After recovery, samples are gently split on a Folsom splitter and typically 3/8 to 1/2 of two separate tubes are utilized for fecal pellet enumeration. After the cruise, samples for fecal pellet enumeration are placed in a settling chamber to allow fecal pellets to settle out. Overlying water is then strained through a 60-um filter to collect any pellets that may have remained in the water. Pellets were then placed on a gridded Petri dish and analyzed using a Zeiss Discovery stereomicroscope. Pellets were separated from other particles and photographed with a dedicated camera. Image processing was then conducted using either Image J or Image Pro to extract area and maximum feret length for each fecal pellet. Pellets were classified by shape and shape-appropriate equations were used to determine the volume of each fecal pellet. Volume was converted to mass using the equations in Stukel et al. (2013). Fecal pellet mass flux is the sum of the mass of all fecal pellets for a sample multiplied by a conversion factor that takes into account the proportion of the gridded petri dish that was enumerated, the fraction of the PIT tube that was used for fecal pellet enumeration, the cross-sectional area of the PIT tube, and the deployment duration. Standard error of the mean is determined from the two samples enumerated for each sediment trap deployment. For more details please see Stukel et al. (2013) or Morrow et al. (submitted). Knauer, G. A., J. H. Martin and K. W. Bruland (1979). "Fluxes of particulate carbon, nitrogen, and phosphorus in the upper water column of the Northe
Noninvasive fecal sampling in Itatiaia National Park, Brazil: wild mammal identification and parasite detection
<p class="CAPA3"><b>Background</b>: Noninvasive collection of feces is a cost-effective strategy for monitoring free-living wild mammals. The aim of this study was to search for carnivore and artiodactyl species and investigate the gastrointestinal parasites in their feces, in Itatiaia National Park, Brazil.</p> <p class="CAPA3"><b>Methodology/Main Findings:</b> Between 2017 and 2018, feces from carnivores and artiodactyls were collected along trails in the park. Host species were identified from these feces through macroscopic and trichological examination and through molecular biology using mitochondrial gene fragments. To investigate parasites, the Faust, Lutz and modified Ritchie and Sheather techniques and enzyme immunoassays were used to detect <i>Cryptosporidium</i> sp. antigens. A total of 244 stools were collected in three regions of the park. The species identified were <i>C. brachyurus</i> (39.7%), <i>L. guttulus</i> (21.3%), <i>C. familiaris</i> (5.3%), <i>C. thous</i> (0.8%), <i>Puma</i> <i>yagouaroundi</i> (0.8%), <i>L. pardalis</i> (0.4%), <i>P</i>. <i>concolor</i> (0.4%) and <i>S. scrofa</i> (4.9%). The overall positivity for parasites was 81.1%. Helminths were more frequently detected in carnivore feces (70.9%), especially eggs of the family Ascarididae and <i>Toxocara</i> sp. Protozoa presented higher frequency in artiodactyl feces (87.1%), especially coproantigens of<i> Cryptosporidium</i> sp. This zoonotic protozoon was detected in eight mammal species, including one that may be invasive: animals from crossbreeding of domestic pig with wild boar. High values for parasite structural richness (R'), Shannon (H') and Simpson (D) parasite diversity indices were observed, especially in the feces of <i>C. brachyurus</i> (R' = 12, H' = 2.2761, D = 0.887). Significant differences in parasite diversity were observed between <i>C. brachyurus </i>and <i>C. familiaris</i>; and between <i>C. brachyurus</i> and <i>S. scrofa</i> (pooled t test = 0.01 and 0.03, respectively). The highest values for parasite similarity (Sorensen test ≥ 0.8) were found among species that are taxonomically close, such as <i>C. brachyurus</i> and <i>L. guttulus</i>.</p> <p class="CAPA3"><b>Conclusions/Significance</b>: This was the first parasitological survey on carnivore and artiodactyl feces collected noninvasively in Brazil. It enabled animal identification through correlations using three techniques and diagnosis of highly frequent parasite structures that can infect these animals.</p>
Balantioides coli in other zoonotic parasites detected in noninvasive fecal samples of artiodactyls with emphasis on the bioinvasive in a state park in Brazil
<p><strong>Background:</strong> Over the years the mammalian fauna, including artiodactyls, has been decreasing and changing due to the entry of bioinvaders into Conservation Units, highlighting, the free-living pig, <em>Sus scrofa</em>, also called feral pig or wild boar. As it is an exotic animal, it is relevant to analyze the gastrointestinal parasites, highlighting those with zoonotic potential that may be infecting these animals and native artiodactyls. To expand this information, this study aims to evaluate the gastrointestinal parasites of artiodactyls in fecal samples collected in the Pedra Selada State Park and in its buffer zones in Rio de Janeiro.</p> <p><strong>Methodology/Main Findings:</strong> Between 2020 and 2021, 101 fecal samples were collected with morphology compatible with artiodactyls in different areas of the Park. All collection points were georeferenced and plotted on maps. Part of the fecal material was submitted to identification of the host species by means of macroscopic and molecular analysis from PCR with primers that amplify the DNA fragment of the COI gene. The other part was submitted to parasite research by qualitative and quantitative coproparasitological techniques. The fecal samples that presented cysts of the Phylum Ciliophora were analyzed with primers that amplify a DNA fragment from the ITS1.5.8S.ITS2 region. Of the 101 samples collected, 72 (71.3%) were found in the covered areas of Pavão Valley, 24 (23.8%) in Grama Valley and 5 (4.9%) in Redondo Mountain. In general, it can be seen that the average length of stool varied very little. Regarding the average values of the weights, it can be seen that they varied a lot, highlighting a diversity of artiodactyls possibly associated with different age groups and sizes of the animals. Morphologically, the feces presented brownish coloration, were in the form of pellets, were rounded and slightly pointed, characteristics that are typically associated with the Order Artiodactyla. Regarding host identification through molecular analysis with the COI gene, 79 samples were identified as belonging to Sus scrofa and 2 as belonging to <em>Mazama gouazoubira</em>. In general, forms of protozoa are more evident than helminths. Protozoan cysts of the Phylum Ciliophora were the most detected forms of parasites, being present in 40 (39.6%) fecal samples. These structures were found only in the feces of Sus scrofa. In addition to these, other parasites were also identified in the feces of these animals, such as non-sporulated coccidian oocyst (2.9%), <em>Ascaris </em>spp. (1.8%), <em>Metrastrongylus </em>spp. (5.9%), strongylid eggs (3.9%), Trichuris spp. (3.9%), nematode larvae (7.9%) and taxonomically unidentified nematode egg (1%). Of the 40 samples in which cysts were detected, nucleotide sequences of protozoa of the Phylum Ciliophora originated from 26 can be interpreted, all of which are compatible with Balantioides coli. Of these, 13 were classified as genetic variant of type B0, one of type B1, 11 of type A0 and were only characterized as type A, not being fully framed in any of the pre-established subtypes.</p> <p><strong>Conclusions/Significance:</strong> It should be noted that parasites with zoonotic potential such as B. coli, highlighting the genetic variant of A0, were identified in the samples collected from Park and their buffer zones, this being the first study in Brazil that phylogenetically characterized this protozoan in free-living S. scrofa feces, placing this bioinvader as one of the reservoirs of this parasite.</p>
Noninvasive fecal sampling in Itatiaia National Park, Brazil: wild mammal identification and parasite detection
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Balantioides coli in other zoonotic parasites detected in noninvasive fecal samples of artiodactyls with emphasis on the bioinvasive in a state park in Brazil
Open the record for dataset details and reuse information.
Microbial RNAseq analysis of cecal and fecal samples collected from mice colonized with the microbiota of human twins discordant for obesity
GEO Series GSE48861. mouse gut metagenome. 59 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq of mouse small intestine samples from different Fecal Microbiota Transplantation treatment groups
GEO Series GSE137999. Mus musculus. 23 samples. Type: Expression profiling by high throughput sequencing.
Altered fecal small RNA profiles in colorectal cancer reflect gut microbiome composition in stool samples
GEO Series GSE132236. Homo sapiens. 80 samples. Type: Other.
Black capped and mountain chickadee nestling fecal samples
<p>Urban and suburban ecosystems are growing in size and number as the human population continues to increase. Not all cities are built the same, however, and it is still unclear how resident organisms are faring in increasingly urban habitats and whether cities are ecological sinks. To investigate how urbanization is affecting breeding success in insectivorous birds, we studied two species of chickadee, the <a>black-capped and mountain chickadee</a>[KG1] , along an urban-rural gradient in Boulder County, CO, USA. We used a citizen-science based experimental framework of nest boxes installed on private land throughout Boulder, CO, USA to local monitor breeding populations of chickadees relative to urbanization. Black-capped and mountain chickadees are two species of closely-related songbirds that co-occur broadly along an elevational gradient. Black-capped chickadees are considered to prefer nesting in low-elevation deciduous trees typically found in cities, while mountain chickadee prefer higher elevation, coniferous forests often considered more rural. However, both species do nest in relatively urbanized habitats, but little is known about how they are navigating these urban habitats. Using arthropod surveys & eDNA metabarcoding paired with field observations, we sought to determine if there are species differences between 1) how chickadee nestling condition varies with the level of urbanization of a nesting site and how urbanization of a nest site infleunces 2) insect availability, 3) nestling diet, and 4) adult provisioning effort. We found that there was no significant effect of urbanization on nestling condition in either species, and that urbanization did not significantly predict insect availability, nestling diet, or adult provisioning effort. We did detect however, differences in diet between the species, highlighting clear ecological niches between these species, despite overlapping breeding habitat. This is, to our knowledge, the first study documenting discrete ecological niches in prey preference for developing chicks and adds to a growing body of literature detailing ecological differentiation between these two species. How this divergence in diet contributes to these species ability to navigate increasingly urban habitats is less clear. It is likely that Boulder, Colorado is made of vegetation patches, effectively urban forest fragments, that allow chickadees living in the city to reproduce successful despite decreased prey quality and quantity associated with urban spaces.</p> <div> <div> <div class="msocomtxt"></div> </div> </div>
Gut Microbiome in Fecal Samples From Patients With Metastatic Cancer Undergoing Chemotherapy or Immunotherapy
ClinicalTrials.gov study NCT02960282. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Metabolome and Microbiomic in Fecal Samples
ClinicalTrials.gov study NCT00938028. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Novel Fecal Sample Collection Method for Metagenomic Analyses
ClinicalTrials.gov study NCT05172414. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Black capped and mountain chickadee nestling fecal samples
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The composition of the bacteria found in liver, spleen, oral cavity and fecal samples of mice subjected to an experimental periodontitis model
GEO Series GSE109664. mouse metagenome. 6 samples. Type: Other.
16S rRNA sequencing analysis of bacteiral community composition in antibiotic-treated mouse fecal sample
GEO Series GSE291841. feces metagenome. 36 samples. Type: Expression profiling by high throughput sequencing.
Obtaining and Storing Human Blood, Urine, and Fecal Samples for Spirochete-Related Epidemiological Research
ClinicalTrials.gov study NCT01089153. IPD Sharing: Not stated. Countries: 0. Publications: 0.
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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.