Find research datasets worth reusing

opencc-zeroDec 2012View details →

Data from: Individual-based measurements of light intensity provide new insights into the effects of artificial light at night on daily rhythms of urban-dwelling songbirds

1. The growing interest in the effects of light pollution on daily and seasonal cycles of animals has led to a boost of research in recent years. In birds, it has been hypothesized that artificial light at night can affect daily aspects of behaviour, but one caveat is the lack of knowledge about the light intensity that wild animals, such as birds, are exposed to during the night. 2. Organisms have naturally evolved daily rhythms to adapt to the 24-h cycle of day and night, thus, it is important to investigate the potential shifts in daily cycles due to global anthropogenic processes such as urbanization. 3. We captured adult male European blackbirds (Turdus merula) in one rural forest and two urban sites differing in the degree of anthropogenic disturbance. We tagged these birds with light loggers and simultaneously recorded changes in activity status (active/non-active) through an automated telemetry system. We first analysed the relationship between light at night, weather conditions and date with daily activity onset and end. We then compared activity, light at night exposure and noise levels between weekdays and weekends. 4. Onset of daily activity was significantly advanced in both urban sites compared to the rural population, while end of daily activity did not vary either among sites. Birds exposed to higher amounts of light in the late night showed earlier onset of activity in the morning, but light at night did not influence end of daily activity. Light exposure at night and onset/end of daily activity timing was not different between weekdays and weekends, but all noise variables were. A strong seasonal effect was detected in both urban and rural populations, such as birds tended to be active earlier in the morning and later in the evening (relative to civil twilight) in the early breeding season than at later stages. 5. Our results point at artificial light at night as a major driver of change in timing of daily activity. Future research should focus on the costs and benefits of altered daily rhythmicity in birds thriving in urban areas.

opencc-by-4.0Jun 2024View details →

Data for Less predictable global rhythms in human than wildlife contributions to soundscapes

Dataset to the article: Somervuo, P., Roslin, T., Fisher, B.L. et al. Human contributions to global soundscapes are less predictable than the acoustic rhythms of wildlife. Nat Ecol Evol (2025). https://doi.org/10.1038/s41559-025-02786-5

Historical tree phenology data reveal the seasonal rhythms of the Congo Basin rainforest

Tropical forest phenology directly affects regional carbon cycles, but the relation between species-specific and whole-canopy phenology remains largely uncharacterized. We present a unique dataset of historical tropical tree phenology collected in the central Congo Basin, before large-scale impacts of human-induced climate change. Historical data was recovered from a phenological study carried out between 1937 and 1956 in the central Congo Basin at the Yangambi Research Station (N00°48’, E24°29’) in what is now the Democratic Republic of Congo (DRC). The data were retrieved from the archives of the INERA (Institut National pour l'Etude et la Recherche Agronomique) herbarium at the Yangambi Research Station. Ground-based phenological observations of local tropical trees were made four times each month on a rotating schedule (resolution of 7.2 days on average) from 1937 until 1956 by the forestry division of the INEAC (Institut National pour l'Étude Agronomique du Congo). The sampling protocol was recovered at the State Archives of Belgium, including details on the observation methods, the observational routes and the training and schedules of the observers. Canopy leaf senescence was defined as a distinct period during which leaves fall and trees remain bare, while canopy turnover was defined as a period during which leaf-fall comes in peaks with concomitant flushes of new leaves (INEAC archives). Summarised data sheets of these long-term observations were digitized using 12 MP resolution cameras. The hand-written notes and annotations depicting phenophases during the observational period were digitized to binary data (yes or no phenophase event at each time-step) through an online citizen science project ‘Jungle Rhythms’ (Hufkens & Kearsley 2023, https://www.zooniverse.org/projects/khufkens/jungle-rhythms).  A selection of species found in the historical forest inventories (Pierlot 1966) are presented, representing 96.0% of the basal area within these inventories. The phenological data comprises 668 individuals covering 140 species (representing 112 genus and 38 families) for a total of 5011 individual observation years (overview of species in Supplementary Table S1). We did not include individuals that were only identified to genus-level. This data accompanies the publication ‘Kearsley, E., Verbeeck, H., Stoffelen, P., Janssens, S. B., Yakusu, E. K., Kosmala, M., De Mil, T., Bauters, M., Kitima, E. R., Ndiapo, J. M., Chuda, A. L., Richardson, A. D., Wingate, L., Ilondea, B. A., Beeckman, H., van den Bulcke, J., Boeckx, P., & Hufkens, K. (2024). Historical tree phenology data reveal the seasonal rhythms of the Congo Basin rainforest. Plant-Environment Interactions, 5, e10136. https://doi.org/10.1002/pei3.10136’. Reference Pierlot, R. (1966). Structure et composition de forêts denses d’Afrique Centrale, spécialement celles du Kivu. Academie Royale des Sciences d’Outre-Mer. Classe des Sciences naturelles et medicales. N.S. XVI-4, Bruxelles, p. 367.

Uncoupling of Behavioral and Metabolic Twenty-Four-Hour Rhythms in Reindeer (Current Biology, Meier et al. 2024): Pre-Processed metabolomics data

Pre-processed metabolomics data (peak picking, peak alignment, integration and annotation using XCMS) obtained from untargeted UPLC-MS measurements of reindeer blood plasma.

Uncoupling of Behavioral and Metabolic Twenty-Four-Hour Rhythms in Reindeer (Current Biology, Meier et al. 2024): Actigraphy data

Raw reindeer actigraphy data collected and analysed in the course of the study "Uncoupling of Behavioral and Metabolic Twenty-Four-Hour Rhythms in Reindeer" (Current Biology, Meier et al. 2024). Details on data processing and plotting can be found in the published article. Further information and codes can be requested from the first author Sara A. Meier.

Uncoupling of Behavioral and Metabolic Twenty-Four-Hour Rhythms in Reindeer (Current Biology, Meier et al. 2024): Metabolomics analysis tables: Annotation list, pathway analysis outputs, target list for targeted peak exstraction and MS/MS spectra of annotated features

Metabolomics analysis tables: Annotation list, pathway analysis outputs, target list for targeted peak exstraction and MS/MS spectra of annotated features

Uncoupling of Behavioral and Metabolic Twenty-Four-Hour Rhythms in Reindeer (Current Biology, Meier et al. 2024): Raw EEG data and Metabolomics and Sleep Correlation

Raw EEG measured from reindeer (Rangifer tarandus tarandus) used in the paper "Uncoupling of Behavioral and Metabolic Twenty-Four-Hour Rhythms in Reindeer" (Current Biology, Meier et al. 2024)

opencc-zeroMar 2024View details →

Data from: Optimal sampling interval for characterisation of the circadian rhythm of body temperature in homeothermic animals using periodogram and cosinor analysis

Core body temperature (Tc) is a critical aspect of homeostasis in birds and mammals and is increasingly used as a biomarker of the fitness of an animal to its environment. Periodogram and cosinor analysis can be used to estimate the characteristics of the circadian rhythm of Tc from data obtained on loggers that have limited memory capacity and battery life. This data set contains five days of core body temperature, measured by loggers implanted into the abdominal cavity, in nine species of birds and mammals.

opencc-by-4.0Nov 2021View details →

Rest-activity daily rhythm and physical activity levels after hip and knee joint replacement: the role of actigraphy in orthopedic clinical practice.

Elective hip and knee joint replacement for osteoarthritis are cost-effective surgical procedures requiring specific rehabilitation programs. Actigraphy is widely used in both research and clinical practice to study activity patterns with great accuracy and validity but it has never been utilized in orthopedic patients. Therefore, the aim of this study was to objectively assess, through actigraphy, physical activity (PA) levels and rest-activity daily rhythm (RAR) in patients undergoing hip or knee joint replacement and hospitalized for ten days after surgery. Twenty subjects (11 males and 9 females; age: 62.68 ± 10.39 years old; BMI: 29.03 ± 3.92 kg/m2) wore the Actiwatch 2 actigraph (Philips Respironics, Portland, OR) to record both PA levels and RAR for 11 consecutive days and data on subjective scores of pain, by a visual analog scale (VAS), and functional and clinical scores were collected. The following time-points were considered for the statistical analysis: pre-surgery (PRE), the first (POST1), the fourth (POST4) and the tenth (POST10) day after surgery. RAR were processed with the population mean cosinor to describe the rhythm's characteristics (acrophase, amplitude and MESOR) while data on actigraphy-based PA, VAS, and functional clinical scores were compared among PRE, POST1, POST4 and POST 10 with the RM-ANOVA or the non-parametric Friedman test. The day after surgery the subjects had a flattened RAR compared to the other conditions: lower values were detected in POST1 compared to both PRE, POST4 and POST10 for MESOR (p < .0001; η2p = .71, large) and amplitude (p < .0001; η2p = .63, large) while RAR's acrophase (p < .0001; η2p = .61, large) was delayed in PRE (16:45) compared to POST1 (12:42), POST4 (14:38), and POST10 (14:38). PA levels were significantly lower at POST 1 (76.7 ± 33.4) compared to PRE (192.3 ± 91.5; p < .0001 and ES: 1.68, large), POST4 (137.9 ± 45.9; p < .0001 and ES: 1.54, large), and POST10 (131.2 ± 54.3; p < .0001 and ES: 1.21, large) whereas VAS and functional clinical values significantly improved at POST10. Hip and knee joint replacement negatively influenced RAR and PA the first day after surgery but a progressive improvement in the circadian pattern of rest-activity cycle, PA levels, VAS and functional ability was recorded from POST4 to POST10. Actigraphy has the ability to collect real-life data without interfering with clinical practice and give clinicians a new measure of performance that is currently not available. This tool could allow to identify patients with disrupted circadian rhythm and reduced PA in the peri-operative period in orthopedic surgery, and timely intervene on these subjects with personalized rehabilitative intervention.

opencc-by-4.0May 2022View details →

Modified version of the Physionet database "MIT Normal Sinus Rhythm" as Machine Learning dataset

ECGs from the MIT-NSR database with some modifications to make them more suitable as playground data set for machine learning. <ul> <li>all 18 ECGs are trimmed to approx. 50000 heart beats from a region without recording errors</li> <li>scaled to a range -1 to 1 (non-linear/tanh)</li> <li>heart beats annotation as time series with value 1.0 at the point of the annotated beat and 0.0 for all other times</li> <li>additional heart beat column smoothed by applying a gaussian filter</li> <li>provided as csv with columns "time in sec", "channel 1", "channel 2", "beat" and  "smooth"</li> <li>an example that uses the dataset to implement heart-beat detection can be found here: <a href="https://github.com/KnetML/NNHelferlein.jl/blob/main/examples/62-ECG-tagger.ipynb">Heart beat detection with Peephole LSTM</a>.</li> </ul> Original data set description: MIT-BIH Normal Sinus Rhythm Database George Moody, Published: Aug. 3, 1999. Version: 1.0.0 This database includes 18 long-term ECG recordings of subjects referred to the Arrhythmia Laboratory at Boston's Beth Israel Hospital (now the Beth Israel Deaconess Medical Center). Subjects included in this database were found to have had no significant arrhythmias; they include 5 men, aged 26 to 45, and 13 women, aged 20 to 50. DOI: <a href="https://doi.org/10.13026/C2NK5R">https://doi.org/10.13026/C2NK5R</a> Link: <a href="https://www.physionet.org/content/nsrdb/1.0.0/">https://www.physionet.org/content/nsrdb/1.0.0/</a> Ref: Goldberger, A., Amaral, L., Glass, L., Hausdorff, J., Ivanov, P. C., Mark, R., ... & Stanley, H. E. (2000). PhysioBank, PhysioToolkit, and PhysioNet: Components of a new research resource for complex physiologic signals. Circulation [Online]. 101 (23), pp. e215–e220.

opencc-zeroDec 2021View details →

Endogenous rhythm shift and adaptation to the tidal environment in the freshwater snail

Organisms have an endogenous timekeeping system to coordinate their biological processes with environmental cycles, allowing adaptation to external rhythmic changes in their environment. Modification of biological clocks could contribute to range expansion in a novel rhythmic environment. We hypothesized that populations of freshwater species near estuaries have acquired a circatidal rhythm to synchronize with the tidal cycle. Here, we compared the locomotion activity and gene expression rhythms of the freshwater snail Semisulcospira reiniana between individuals inhabiting freshwater and brackish-water areas. Individuals inhabiting brackish-water areas exhibited a rhythmic activity pattern coordinated with the tidal cycle under both field and laboratory conditions. Individuals inhabiting upstream freshwater areas showed a nocturnal activity pattern. The proportion of circadian oscillating genes was greater in freshwater than in brackish-water individuals, while that of circatidal oscillating genes was greater in brackish-water than in freshwater individuals. Interestingly, expression of 16 genes exhibited circadian and circatidal rhythms in freshwater and brackish-water individuals, respectively. Additionally, transcriptome-wide population genetic analyses supported our assumption that these two populations are genetically almost identical. These findings suggest that the slight divergence contributed to the shift in the timekeeping system, and that endogenous rhythms could differ in their periods between freshwater and brackish-water populations. Our results provide evidence of the evolution of endogenous rhythm via range expansion to novel rhythmic environment in a single species.

opencc-by-4.0May 2022View details →

Phase separation of competing memories along the human hippocampal theta rhythm.

Data set for Phase separation of competing memories along the human hippocampal theta rhythm.

opencc-by-4.0May 2022View details →

Data for "Syntactic modulation of rhythm in Australian pied butcherbird song"

Australian pied butcherbird song data necessary for reproducing results in "Syntactic modulation of rhythm in Australian pied butcherbird song".  Code to reproduce results are found in: https://github.com/xingjeffrey/syntax_rhythm_pbb All WAV files in this data repository have been transformed into .pickle format to respect the wishes of the author who contributed the field recordings. The WAV files were only involved in generating spectrograms for computation/manual annotations, and are not absolutely necessary for reproducing the statistical analyses of this study. If needed, the .pickle files corresponding to the WAV files may be used to generate waveforms of the analyzed Australian pied butcherbird songs. If you have any concerns or questions, contact the corresponding author (Jeffrey Xing) at j8xing@ucsd.edu

opencc-by-4.0Mar 2019View details →

MAST rhythm dataset

The MASTrhythm dataset is a collection of 3721 audio files cropped from recordings of conservatory entrance examinations in Turkey (summer 2015 and summer 2016). (see the previous version with audio data here: <a href="https://zenodo.org/record/2620357#.Y1ZOVXVBwW0">https://zenodo.org/record/2620357#.Y1ZOVXVBwW0</a> ) This version of the dataset includes new annotation files.  4 level grades re-collected by blind-random-listening: A new set of grades were collected using an annotation tool that randomly plays audio recordings and ask the annotator to pick a grade from the set of grades: 1-Completely Off, 2-Major Mistakes, 3-Minor Mistakes, and 4-Perfect. The assessments were done by three individuals who specialized in music or have a musical background; the first annotator is a professor of musicology who has taken part as a jury member in many entrance exam auditions, the second and third annotator are music conservatory students of graduate-level programs. A rubric was explicitly defined and used for grading: If only one or two notes were wrong (missing, added, or played in a different rhythmic position), while the rhythmic accents were executed perfectly and without any delay or hurry, this type of error is considered as a "3-minor mistake"; If two-three notes were wrong, and were belonging to any form of hesitation with poorly executed accents, such performances were graded as a "2-major mistake". Any performance with more than three wrong strokes/durations was considered "1-completely off". The 4-level grades are shared in the format of text files: annotator#.txt Naming convention: The dataset is composed of audio files. All other information is coded in the file names: 'ref': reference recording, 'per': performance recording, 'fail': performance graded as 'fail', 'pass': performance graded as 'pass' There exists 40 distinct rhythmic patterns. The ID for the melody makes up the first part of the file name. Examples: '51_rhy1_per101559_fail.m4a': Rhythmic pattern ID: '51_rhy1', this is a candidate performance recording (candidate ID: 101559) graded as fail '55_rhy2_ref280758.m4a': Rhythmic pattern ID: '55_rhy2', this is a reference recording (performed by a jury member) for candidate with ID: 280758. Acknowledgement: This new version of the dataset has been curated within the TUBITAK (The Scientific and Technological Research Council of Turkey) funded research project 1001-121E198 targeting development of automatic assessment tools for music performances.

opencc-by-4.0Apr 2019View details →

MAST rhythm re-annotated subset

In the work described in the paper <a href="http://archives.ismir.net/ismir2019/paper/000052.pdf">A dataset of rhythmic pattern reproductions and baseline automatic assessment system</a><a href="https://ismir2019.ewi.tudelft.nl/?q=accepted-papers"> (ISMIR, 2019)</a>, Falcão et al. applied efforts on annotating a subset of the full <a href="https://zenodo.org/record/2620357#.XKLB39szZuQ">MAST rhythm dataset</a> with grades for a subset of performances. Out of a total of 1040 student submissions comprised by the original dataset, 80 performances (equally distributed between 20 references) were graded by annotators using a custom annotation tool. During this process annotators could play each (reference, performance) pair as many times as desired before deciding on one of the available assessments: 4-Perfect, 3-Minor errors, 2-Major errors, 1-Completely off. Naming convention This dataset is a collection of audio files, onset features and user-annotated data. Audio files are stored into the Only Performances and Only References folders, together with some extra files containing their original onsets, quantized onsets and scaling parameters (for more information regarding this auxiliary data, please check the paper). An indexed list of files (listreferences and listperformances) is also stored in each of these folders in order to allow for mapping between audio files and auxiliary data. Example: <ul> <li>The 10th line in Only Performances/MAST Onsets [Performances] contains the pure onsets for the 10th audio file listed in the Only Performances/listperformances file ('55_rhy2_per138459_pass.wav')</li> </ul> Also, in order to check the reference which relates to a specific performance, one must also look for audio file names in the list of files: the i-eth audio file listed in Only Performances/listperformances is a specific performance whose reference is defined by the i-eth line of Only References/listreferences. Example: <ul> <li>The 10th audio file listed in Only Performances/listperformances file ('55_rhy2_per138459_pass.wav') is a performance whose reference is stored in the 10th line of Only References/listreferences (55_rhy2_ref162559.wav)</li> </ul> Such convention is also applied to the folder that contains the annotations (Performances Annotations). Each one of the annotator_X.txt file lists the grades assigned by the X-ith annotator, and the mapping between the assessments and their referred performances is indexed in listfiles.txt

opencc-zeroJul 2021View details →

Characterizing the modern light environment and its influence on circadian rhythms

Humans have largely supplanted natural light cycles with a variety of electric light sources and schedules misaligned with day-night cycles. Circadian disruption has been linked to a number of disease processes, but the extent of circadian disruption among the population is unknown. In this study, we measured light exposure and wrist temperature among residents of an urban area during each of the four seasons, as well as light illuminance in nearby outdoor locations. Daily light exposure was significantly lower for individuals, compared to outdoor light sensors, across all four seasons. There was also little seasonal variation in the realized photoperiod experienced by individuals, with the only significant difference occurring between winter and summer. We tested the hypothesis that differential light exposure impacts circadian phase timing, detected via the wrist temperature rhythm. To determine the influence of light exposure on circadian rhythms, we modeled the impact of morning and nighttime light exposure on the timing of the maximum wrist temperature. We found that morning and nighttime light exposure had significant but opposing impacts on maximum wrist temperature timing. Our results demonstrate that, within the range of exposure seen in everyday life, nighttime light can delay the onset of the maximum wrist temperature, while morning light can lead to earlier onset. Our results demonstrate that humans are minimizing natural seasonal differences in light exposure, and that circadian shifts and disruptions may be a more regular occurrence in the general population than is currently recognized.

opennotspecifiedJul 2002View details →

FIG. 2 in Larval release rhythms of four species (family Grapsidae and Ocypodidae) of intertidal crabs on a coastal at in western central Taiwan

FIG. 2. Daily larval release patterns of Parasesarma tripectinis, Perisesarma bidens, Hemigrapsus penicillatus and Baruna sinensis. Closed and open circles represent new and full moon phases, respectively. n 5sample size.

opennotspecifiedJul 2002View details →

FIG. 1. Evening high and low tidal heights during 3 in Larval release rhythms of four species (family Grapsidae and Ocypodidae) of intertidal crabs on a coastal at in western central Taiwan

FIG. 1. Evening high and low tidal heights during 3 August to 30 September 1994. Closed and open circles represent new and full moon phases, respectively.

opennotspecifiedJul 2002View details →

FIG. 4 in Larval release rhythms of four species (family Grapsidae and Ocypodidae) of intertidal crabs on a coastal at in western central Taiwan

FIG. 4. Deviation of the larval release timing of Parasesarma tripectinis, Perisesarma bidens, Hemigrapsus penicillatus and Baruna sinensis, from the time of high slack tide. n 5 sample size.