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856 results for “time course”
Spontaneous motor tempo over the course of a week: The role of the time of the day, chronotype, and arousal
<p>The spontaneous motor tempo (SMT) or internal tempo describes the natural pace of predictive and emergent movements such as walking or hand clapping. One of the main research interests in the study of the spontaneous motor tempo relates to factors affecting its pace. Previous studies suggest an influence of the circadian rhythm (i.e., 24-h cycle of the biological clock), physiological arousal changes, and potentially also musical experience. This study aimed at investigating these effects in participants‘ everyday life by measuring their SMT four times a day over seven consecutive days, using an experience sampling method. The pace of the SMT was assessed with a finger-tapping paradigm in a selfdeveloped web application. Measured as the inter-tap interval, the overall mean SMT was 650 ms (SD = 253 ms). Using multi-level modelling (MLM), results show that the pace of the SMT sped up over the course of the day, and that this effect depended on the participants’ chronotype, since participants tending towards morning type were faster in the morning compared to participants tending towards evening type. During the day, the pace of the SMT of morning types stayed relatively constant, whereas it became faster for evening-type participants. Furthermore, higher arousal in participants led to a faster pace of the SMT. Musical sophistication did not influence the SMT. These results indicate that the circadian rhythm influences the internal tempo, since the pace of SMT is not only dependent on the time of the day, but also on the individual entrainment to the 24-h cycle (chronotype).</p>
Systematic analysis of alternative splicing in time course data using Spycone
<p>Spycone is available as a python package that provides systematic analysis of time course transcriptomics data. Figure 1 shows the workflow of Spycone. It uses gene or isoform expression and a biological network as an input. It employs the sum of changes of all isoforms relative abundance (total isoform usage) across time points to detect IS events. It further provides downstream analysis such as clustering by total isoform usage, gene set enrichment analysis, network enrichment, and splicing factors analysis.</p> <p>The SARS-Cov-2 infection and cancer dataset are used as an application demonstration for our Spycone tool and a simulation dataset is used for benchmark analysis. </p> <p>The rhinovirus dataset and SARS-Cov-2 infection (3 time points) for the tutorial in the documentation are included here. </p> <p>The simulated dataset from the 2 models described in the manuscript are uploaded as zen_simdata_{model}_{noise}.csv.</p> <p>A gtf file used in the splicing factor analysis, both in the manuscript and tutorial. Derived from ensembl GRCh38.99.</p>
"The sound comes from a meadow in the Sierra Nevada Mountains in California. The meadow is at an elevation of 2400 meters near a mountain named Olancha Peak, which is 3700 meters in altitude. Ihave a group of friends with which Ibackpack (trek) into the mountains. Our goal was to spend some time in the mountains and hike to the top of Olancha Peak (…) By the time we reached the meadow, we were in a forest and there was still snow on the ground in some places. We took the trip in June of 2006. The Sierra Nevada Mountains are a large mountain range. Much of the range is protected by national parks or preserved areas we call 'wilderness areas' (…) Ihave been backpacking for nearly 40 years and Iwill hopefully continue with this challenging activity for 40 years more! Many of my friends are much younger than Iam and it gives me much satisfaction to be able to have as much or more stamina for this activity than they have! When we are on these trips, we hike up peaks, catch fish, drink some whiskey around campfires and enjoy our time in the beautiful solitude. My memories of this trip were of the steep, hot hike from the desert to the cool meadow; the overall beauty of the nature, the absolute solitude of our campsite near the meadow; the strenuous hike to the top of Olancha Peak; the camaraderie of my friends; and, of course the sound of the frogs in the meadow. The frog sounds were astounding to me and Iwould listen in awe of the creature's instinctual desire to reproduce and continue the existence of their kind. Surely there were different species in the meadow for some of the frog sounds were different than others. The sounds only occurred after the Sun went down for the evening. Istood next to the creek in the meadow and recorded the sounds using my digital camera." [Peter/plentz1960]16 in Collecting Sounds. Online Sharing of Field Recordings as Cultural Practice
"The sound comes from a meadow in the Sierra Nevada Mountains in California. The meadow is at an elevation of 2400 meters near a mountain named Olancha Peak, which is 3700 meters in altitude. Ihave a group of friends with which Ibackpack (trek) into the mountains. Our goal was to spend some time in the mountains and hike to the top of Olancha Peak (…) By the time we reached the meadow, we were in a forest and there was still snow on the ground in some places. We took the trip in June of 2006. The Sierra Nevada Mountains are a large mountain range. Much of the range is protected by national parks or preserved areas we call 'wilderness areas' (…) Ihave been backpacking for nearly 40 years and Iwill hopefully continue with this challenging activity for 40 years more! Many of my friends are much younger than Iam and it gives me much satisfaction to be able to have as much or more stamina for this activity than they have! When we are on these trips, we hike up peaks, catch fish, drink some whiskey around campfires and enjoy our time in the beautiful solitude. My memories of this trip were of the steep, hot hike from the desert to the cool meadow; the overall beauty of the nature, the absolute solitude of our campsite near the meadow; the strenuous hike to the top of Olancha Peak; the camaraderie of my friends; and, of course the sound of the frogs in the meadow. The frog sounds were astounding to me and Iwould listen in awe of the creature's instinctual desire to reproduce and continue the existence of their kind. Surely there were different species in the meadow for some of the frog sounds were different than others. The sounds only occurred after the Sun went down for the evening. Istood next to the creek in the meadow and recorded the sounds using my digital camera." [Peter/plentz1960]16
Fluorescence images of ybx1 mutant neuromasts [time course, wt]
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Fluorescence images of ybx1 mutant neuromasts [time course, het]
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Time course of metabolic variations in human neutrophils with PMA treatment alone or in combination with DPI: Part 1
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3D time-course iSIM dataset HeLa cells MitoTracker Red CMXRos
<p>2020-03-17</p> <p>Microscopy dataset:</p> <p>- Type: Fluorescence, 3D, time-course, iSIM Visitech, 100x Silicon NA 1.35 (65 nm x 65 nm x 300 nm xyz pixel sizes), 20s time interval</p> <p>- Cell type: HeLa, labelled with MitoTracker Red CMXRos</p> <p> </p> <p>Romain F. Laine, r.laine@ucl.ac.uk, MRC-LMCB, UCL, London, UK</p>
Dataset: Partial-volume modeling reveals reduced gray matter in specific thalamic nuclei early in the time course of psychosis and chronic schizophrenia
<p>This repository contains the files needed to reproduce the results presented in the paper "Partial-volume modeling reveals reduced gray matter in specific thalamic nuclei early in the time course of psychosis and chronic schizophrenia" (DOI: 10.1002/hbm.25108) </p> <p>In order to ensure the reproducibility of our study, the individual gray matter concentration/probability images as well as the thalamic nuclei parcellations, in native and MNI spaces, are freely available in this repository. The demographic information table including age, gender and intracranial volume for each subject is also available.</p>
Data from: Eco-evolutionary feedbacks predict the time course of rapid life history evolution
Organisms can change their environment and, in so doing, change the selection they experience and how they evolve. Population density is one potential mediator of such interactions because high population densities can impact the ecosystem and reduce resource availability. At present, such interactions are best known from theory and laboratory experiments. Here we quantify the importance of such interactions in nature by transplanting guppies from a stream where they co-occur with predators into tributaries that previously lacked both guppies and predators. If guppies evolve solely because of the immediate reduction in mortality rate, the strength of selection and rate of evolution should be greatest at the outset then decline as the population adapts to its new environment. If indirect effects caused by the increase in guppy population density in the absence of predation prevail, then there should be a lag in guppy evolution because time is required for them to modify their environment. The duration of this lag is predicted to be associated with the environmental modification caused by guppies. We observed a lag in life history evolution associated with increases in population density and altered ecology. How guppies evolved matched predictions derived from evolutionary theory that incorporates such density effects.
Zebrafish embryos time-course, 5'UTR nup43
<p>This Zenodo file contains data for the 5′ UTR-nup43-sfGFP mRNA reporter. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 2 of Reimão-Pinto et al., Dev Cell, 2024.</p> <p>Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.</p> <p>Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.</p>
Zebrafish embryos time-course, 5'UTRs hnrnpl and egfl6
<p>This Zenodo file contains data for the 5′ UTR-hnrnpl-sfGFP and 5′ UTR-egfl6-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 2 of Reimão-Pinto et al., Dev Cell, 2024.</p> <p>Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.</p> <p>Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.</p>
Zebrafish embryos time-course, M&Z 5'UTRs scarb2c
<p>This Zenodo file contains data for the maternal and zygotic 5′ UTR-scarb2c-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 7 of Reimão-Pinto et al., Dev Cell, 2024.</p> <p>Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.</p> <p>Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.</p>
Zebrafish embryos time-course, M&Z 5'UTRs cfl1l
<p>This Zenodo file contains data for the maternal and zygotic 5′ UTR-cfl1l-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 7 of Reimão-Pinto et al., Dev Cell, 2024.</p> <p>Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.</p> <p>Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.</p>
Spectrum, time course, stages, and a proposal for the diagnosis of histamine intolerance in general practice: A Nonrandomized, Quasi-Experimental Study - Supplementary material 1 and supplementary material 2 for "Spectrum, time course, stages, and a proposal for the diagnosis of histamine intolerance in general practice: A Nonrandomized, Quasi-Experimental Study"
<p><span>File name: Supplementary material 1. All data.xls</span></p> <p><span>Title of data: Questionnaire, all patients’ answers. Number of patient-doctor meetings with upper respiratory symptoms in primary care</span></p> <p><span>Description of data: The administered questionnaires (first/initial and second/post-diet). All patients’ answers. Number of patient-doctor meetings 01.09.2021-27.09.2024. with upper respiratory symptoms in primary care.</span></p> <p><span> </span></p> <p><span>File name: Supplementary material 2. Educational material and proposed questionnaire.doc</span></p> <p><span>Title of data: Proposed questionnaire for histamine intolerance in primary care. Educational material for patients with histamine intolerance</span></p> <p><span>Description of data: Proposed questionnaire for HIT in primary care. Educational material for patients to help establish </span><span>cause-and-effect relationships between their meals and their experienced symptoms. Food-symptom diary.<span><br></span></span></p>
Supplementary material S24: Time course of the loudest Varroa jolting pulse compared to that of a honeybee colony and single bee individual.
<p>Time course of the loudest <em>Varroa </em>jolt on brood-comb with the signal from the full colony and a single bee. The signal seen here in each panel is the integral of the magnitude of acceleration with respect to time. The background vibration that is inherent to the room was calculated and subtracted from this data. The loudest jolt (red) is here compared to the signal of a single bee (black) and the vibrations of the full colony at low and high signal (black). High signal is captured when the frame containing the accelerometer is empty of brood. Low signal is captured when the frame is fully loaded with brood and/or honey. The whooping signal (panel a) was captured during a period of high signal.</p>
Taking up and terminating leisure-time physical activity over the life course: The role of life events in the familial and occupational life domains
<p>Dataset used for the analyses in the following publication:</p> <p>Lenze, L., Klostermann, C., Lamprecht, M. & Nagel, S. (2021). Taking up and terminating leisure-time physical activity over the life course: The role of life events in the familial and occupational life domains. <em>International Journal of Environmental Research and Public Health</em>, <em>18</em>, 9809. https://doi.org/10.3390/ijerph18189809</p>
The time course of acclimation to the stress of triose phosphate use limitation
<p>Triose-phosphate utilization (TPU) limits the maximum rate at which plants can photosynthesize. However, TPU is almost never found to be limiting photosynthesis under ambient conditions for plants. This, along with previous results showing adaptability of TPU at low temperature, suggest that TPU capacity is regulated to be just above the photosynthetic rate achievable under the prevailing conditions. A set of experiments were performed to study the adaptability of TPU capacity when plants are acclimated to elevated CO<sub>2</sub> concentrations. Plants held at 1500 ppm CO<sub>2</sub> were initially TPU-limited. After 30 hours, they no longer exhibited TPU limitations, but they did not elevate their TPU capacity. Instead, the maximum rates of carboxylation and electron transport declined. A time course of regulatory responses was established. A step increase of CO<sub>2</sub> first caused PSI to be oxidized, but after 40 s, both PSI and PSII had excess electrons as a result of acceptor-side limitations. Electron flow to PSI slowed, and the proton motive force increased. Eventually, non-photochemical quenching reduced electron flow sufficiently to balance the TPU limitation. Over several minutes rubisco deactivated contributing to regulation of metabolism to overcome the TPU limitation.</p>
The process of HDAC11 Assay Development: time-course study follow-up-effect of additives
<p>Since the activity of HDAC11 has been observed to be quite low as per the previous data, a preliminary test was performed to check any drastic increase in the activity in the presence of an additive. </p> <p>version2 (v2) has updated reaction recipe.</p>
The process of HDAC11 Assay Development: time-course study follow-up
<p>The time of incubation and conc. of the developer to be used are important parameters during HDAC11 assay optimization and thus, have been considered here.</p> <p>Version2 (v2) has updated reaction recipe.</p>
The process of HDAC11 Assay Development: time-course study follow-up
<p>A follow-up to check the increased fluorescence signals at 0 min of the HDAC11 reaction with its substrate was performed. </p> <p>Version2 (v2) is updated with the reaction recipe.</p>
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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.