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Data for "Tracking C-H activation with orbital resolution"

These are the data displayed in the figures in the main text and in the Supplementary Materials of the manuscript entitled "Tracking C-H activation with orbital resolution".

Wi-Fi (CSI and RSSI) data of six basic knife activities for cooking (chopping, cubing, French cutting, julienning, mincing, and slicing)

To gather the dataset, we asked two participants to perform six basic knife activities. The layout of the system experiment is provided in Fig. 4. As it illustrates, we put the receiver on the right side and the ESP32 transceiver on the left side of the performing area. The performing area is a cutting board (30 x 46 cm) in this experiment. Each participant performs each activity five times in the performing area. The data is recorded using a customized version of ESP32-CSI-tool [38] on the laptop that helps us to record and save each data in a separate file. After recording all 60 data entries, we used Python code to extract the clean data from all generated text by the tool. The clean data is stored in a database and creates the dataset.

opencc-zeroDec 2022View details →

When death comes: Linking predator-prey activity patterns to timing of mortality to understand predation risk

The assumption that activity and foraging are risky for prey underlies many predator-prey theories and has led to the use of predator-prey activity overlap as a proxy of predation risk. However, the simultaneous measures of prey and predator activity along with timing of predation required to test this assumption have not been available. Here, we used accelerometry data on snowshoe hares (Lepus americanus) and Canada lynx (Lynx canadensis) to determine activity patterns of prey and predators and match these to precise timing of predation. Surprisingly, we found that lynx kills of hares were as likely to occur during the day when hares were inactive as at night when hares were active. We also found that activity rates of hares were not related to the chance of predation at daily and weekly scales, whereas lynx activity rates positively affected the diel pattern of lynx predation on hares and their weekly kill rates of hares. Our findings suggest that predator-prey diel activity overlap may not always be a good proxy of predation risk, and highlight a need for examining the link between predation and spatiotemporal behavior of predator and prey to improve our understanding of how predator-prey behavioral interactions drive predation risk.

Data associated with studies on the establishment, winter activity, and dispersal of crapemyrtle bark scale

These data files are associated with studies on the establishment, winter activity, and dispersal of crapemyrtle bark scale .

Data set: The opening dynamics of the lateral gate regulates the activity of rhomboid proteases

Dataset: The opening dynamics of the lateral gate regulates the activity of rhomboid proteases Input: MD simulations + docking results

Data from: Nonlinear decoding models enable music reconstruction from human auditory cortex activity

This dataset is associated with the manuscript "Nonlinear decoding models enable music reconstruction from human auditory cortex activity", and provides all preprocessed files necessary to replicate the results. In this study, we recorded intracranial EEG data (specifically, ECoG) in 29 patients with pharmacoresistant epilepsy while they were passively listening to a Pink Floyd song. The present dataset consists of preprocessed neural activity (High-Frequency Activity, 70-150 Hz), electrode coordinates (in MNI template space) and auditory stimulus (raw wave file, and 32- and 128-frequency-bin auditory spectrogram). HFA and both auditory spectrograms have a sampling rate of 100 Hz, and are temporally aligned (duration of 190.72 s). The code we used to preprocess and analyze the data is hosted on GitHub, <a href="https://github.com/ludovicbellier/PF_HFAdecoding">here</a> for the manuscript and <a href="https://github.com/ludovicbellier/PF_HFAdecoding">there</a> for the predictive modeling functions.

opencc-zeroApr 2023View details →

Neuronal activation in the geomagnetic responsive region Cluster N covaries with nocturnal migratory restlessness in white-throated sparrows

Cluster N is a region of the visual forebrain of nocturnally migrating songbirds that supports the geomagnetic compass of nocturnal migrants. Cluster N expresses immediate-early genes (ZENK), indicating neuronal activation. This neuronal activity has only been recorded at night during the migratory season. Night-to-night variation in Cluster N activity in relation to migratory behaviour has not been previously examined. We tested whether Cluster N is activated only when birds are motivated to migrate and presumably engage their magnetic compass. We measured immediate-early gene activation in Cluster N of white-throated sparrows (Zonotrichia albicollis) in three conditions: daytime, nighttime migratory restless, and nighttime resting. Birds in the nighttime migratory restlessness group had significantly greater numbers of ZENK-labelled cells in Cluster N compared to both the daytime and the nighttime resting groups. Additionally, the degree of migratory restlessness was positively correlated with the number of ZENK-labelled cells in the nighttime migratory restless group. Our study adds to the number of species observed to have neural activation in Cluster N and demonstrates for the first time that immediate early gene activation in Cluster N is correlated with the amount of active migratory behaviour displayed across sampled individuals. We conclude that Cluster N is facultatively regulated by the motivation to migrate, together with nocturnal activity, rather than obligatorily active during the migration season.

Allosteric activation of cell wall synthesis during bacterial growth

This repository contains single-molecule FRET data related to this manuscript organized by figure. Note that data that appear both in the main and in the supplementary figures are provided only once, in the relevant main figure folders. Each figure folder contains all relevant datasets, deposited as zipped folders with pre-processed raw trajectories in the .dat format. These trajectories list donor excitation/donor emission (column 1) and donor excitation/acceptor emission (column 2) values as a function of time, and can be visualized and further processed using either custom code or the publicly available ebFRET software (http://ebfret.github.io/).

opencc-zeroMay 2023View details →

Data from: Environmental DNA metabarcoding revealed the impacts of anthropogenic activities on phytoplankton diversity in Dianchi Lake and its three inflow rivers

Phytoplankton diversity is closely related to environmental variables and has been widely used in ecological health assessment of rivers and lakes. Combining the advantages of DNA-based identification and high-throughput sequencing technology, environmental DNA (eDNA) metabarcoding permits a new measurement for biodiversity monitoring in aquatic ecosystems. However, it had rarely been used to explore the variability and similarity of phytoplankton diversity between a lake and its inflow rivers and the effects of environmental variables on phytoplankton. This study utilized eDNA metabarcoding to investigate the spatial distribution of phytoplankton and the impacts of environmental variables on the phytoplankton diversity in Dianchi Lake (one of the most polluted urban lakes in China) and its main inflow rivers (Panlong River, Baoxiang River and Chai River). The OTU table is the original table about phytoplankton taxa. A total of 243 distinct phytoplankton taxa were detected, covering 9 phyla, 30 classes, 84 orders and 132 families, and the taxonomic richness of rivers was higher than that of Dianchi Lake.

opencc-zeroMay 2023View details →

Data for: Passive and active parental food allocation in a songbird

Parent-offspring conflict over food allocation can be modeled using two theoretical frameworks: passive (scramble competition) and active choice (signaling) resolution models. However, differentiating between these models empirically can be challenging. One possibility involves investigating details of decision-making by feeding parents. Different nestling traits, related to competitive prowess or signalling cryptic condition, may interact additively or non-additively as predictors of parental feeding responses. To explore this, we experimentally created even-sized, small broods of pied flycatchers and manipulated nestling cryptic quality, independently of size, by vitamin E supplementation. We explored how interactions between nestling cryptic condition, size, signals, and spatial location predicted food allocation and prey-testing by parents. Parents created the potential for spatial scramble competition between nestlings by feeding from and to a narrow range of nest locations. Heavier supplemented nestlings grew faster and were more likely to access profitable nest locations. However, the most profitable locations were not more contested, and nestling turnover did not vary in relation to spatial predictability or food supply. Postural begging was only predicted by nestling hunger and body mass, but parents did not favor heavier nestlings. This suggests that size-mediated and spatial competition in experimental broods was mild. Pied flycatcher fathers allocated food in response to nestling position and begging order, while mothers seemingly followed an active choice mechanism involving assessment of more complex traits, including postural intensity interacting with order, position, and treatment, and perhaps other stimuli when performing prey-testings. Differences in time constraints may underlie sex differences in food allocation rules.

MEDDOPROF Silver Standard: Predictions for Occupations, Working Statuses and Activities in Clinical Case Reports

MEDDOPROF Silver Standard This repository contains the MEDDOPROF Silver Standard, a collection of clinical case reports of multiple specialties that have been automatically annotated with occupations, working statuses and activities using named entity recognition models trained on the MEDDOPROF corpus. MEDDOPROF and this Silver Standard have been created by the Barcelona Supercomputing Center's NLP for Biomedical Information Analysis. About the MEDDOPROF Corpus <a href="https://temu.bsc.es/meddoprof/">MEDDOPROF</a> is a corpus and shared task focused on the detection and normalization of occupations and related information such as working statuses and non-paid activities in clinical texts in Spanish. All mentions in the corpus have been normalized to SNOMED CT, with occupations also being normalized to the European Skills, Competences, and Occupations classification ESCO. MEDDOPLACE was released as part of the IberLEF 2021 workshop, which in turn was held within the SEPLN 2021 conference. About this Silver Standard The Silver Standard includes 13,357 documents and a total of 5,568,844 tokens. The documents belong to over 10 different medical specialties, including occupational health, oncology, radiology, infectology, dermatology, psichiatry and more. The corpus includes three different labels: PROFESION (occupation), SITUACION-LABORAL (working status) and ACTIVIDAD (activity/hobby). There is a total of 4,332 predictions (1,325 unique), with the most common label being PROFESION with 3,599 predictions (1,181 unique), followed by SITUACION-LABORAL with 682 (180 unique) and ACTIVIDAD with 51 (44 unique). The annotations are presented in .ann format, which is the format used by the annotation tool brat. For more information, please check the attached README file. Citation If you use this Silver Standard or any MEDDOPROF materials, please cite the task's overview paper: Lima-López, Salvador, Eulàlia Farré-Maduell, Antonio Miranda-Escalada, Vicent Brivá-Iglesias, & Martin Krallinger. “NLP applied to occupational health: MEDDOPROF shared task at IberLEF 2021 on automatic recognition, classification and normalization of professions and occupations from medical texts.” Procesamiento del Lenguaje Natural [Online], 67 (2021): 243-256. License This work is licensed under a Creative Commons Attribution 4.0 International License. Contact If you have any questions or suggestions, please contact us at: - Salvador Lima-López (<salvador [dot] limalopez [at] gmail [dot] com>) - Martin Krallinger (<krallinger [dot] martin [at] gmail [dot] com>) Acknowledgements MEDDOPROF was promoted by the Spanish government's 2020 Proyectos de I+D+i RTI Tipo A (AI4ProfHealth - DESCIFRANDO EL PAPEL DE LAS PROFESIONES EN LA SALUD DE LOS PACIENTES A TRAVES DE LA MINERIA DE TEXTOS (PID2020-119266RA-I00)). Related Links - MEDDOPROF website: <a href="https://temu.bsc.es/meddoprof/">https://temu.bsc.es/meddoprof/</a> - MEDDOPROF Gold Standard: <a href="https://doi.org/10.5281/zenodo.5070540">https://doi.org/10.5281/zenodo.5070540</a> - MEDDOPROF Annotation Guidelines: <a href="https://doi.org/10.5281/zenodo.4694675">https://doi.org/10.5281/zenodo.4694675</a>

opencc-by-4.0Mar 2023View details →

A Comparison of Passive and Active Dust Sampling Methods for Measuring Airborne MRSA in Pig Farms

Study Abstract: Authors: Anne Rittscher, Abel A. Vlasblom, Birgitta Duim, Peter Scherpenisse, Isabella van Schothorst, Inge M. Wouters, Liese Van Gompel, Lidwien A.M. Smit      Methicillin resistant strains of Staphylococcus aureus (MRSA) are resistant to most b-lactam antibiotics. Pigs are an important reservoir of livestock associated MRSA (LA-MRSA), which is genetically distinct from both hospital and community acquired MRSA. Occupational exposure to pigs on farms can lead to LA-MRSA carriage by workers. There is a growing body of research on MRSA found in the farm environment, the airborne route of transmission, and its implication on human health. This study aims to compare two sampling methods used to measure airborne MRSA in the farm environment; passive dust sampling with electrostatic dust fall collectors (EDCs), and active inhalable dust sampling using stationary air pumps with Teflon filters. Paired dust samples using  EDCs and GSP samplers, totaling 87 samples, were taken from seven Dutch pig farms, in multiple compartments housing pigs of varying ages. Total nucleic acids of both types of dust samples were extracted and targets indicating MRSA (femA, nuc, mecA) and total bacterial count (16S rRNA) were quantified using quantitative Real Time PCRs. MRSA could be measured in all stationary pump samples and in 94% of the EDCs, additionally MRSA was present on every farm sampled. There was a strong positive relationship between the paired MRSA levels found in EDCs and those measured on filters (Normalized by 16S rRNA; Pearson’s correlation coefficient r=0.94, Not Normalized; Pearson’s correlation coefficient r=0.84). This study suggests that EDCs can be used as an affordable and easily standardized method for quantifying airborne MRSA levels in the pig farm setting.

Data and supplementary information: Effects of lithium on locomotor activity and circadian rhythm of honey bees

Data and supplementary files for publication:Erdem, B., Arslan, O.C., Sevin, S. Gozen, A. G., Agosto-Rivera, J. L., Tugrul, G., & Alemdar, H. (2023). Effects of lithium on locomotor activity and circadian rhythm of honey bees. Scientific Reports, 13, 19861. https://doi.org/10.1038/s41598-023-46777-7 AcuteExp_Dark_ActivityData.xlsx - Total LMA counts of acute experiment in dark condition.AcuteExp_Light_ActivityData.xlsx - Total LMA counts of acute experiment in light condition.ChronicExp_ActivityData.xlsx - Total LMA counts of the chronic experiment.ChronicExp_MortalityData.xlsx - Mortality data of the chronic experiment.ChronicExp_PeriodRhytmData.xlsx - Defines rhythmic and arrhythmic individuals and the circadian periods (h) of the rhythmic individuals in chronic experiment.LD_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the 12 h light / 12 h dark condition.DD_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the constant dark condition.LL_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the constant light condition. In the double-plotted actograms, NR indicates "non-rhythmic" individuals.

opencc-zeroDec 2022View details →

Limiting scaring activities reduces economic costs associated with foraging barnacle geese: results from an individual-based model

<ol> <li>With increasing numbers of large grazing birds on agricultural grassland, conflict with farmers is rising. One management approach to alleviate conflict allows foraging on dedicated agricultural land (accommodation areas) and nature reserves, combined with scaring on remaining agricultural land. Here, we examine the cost-effectiveness of these measures by studying the influence on barnacle goose distribution and associated economic damage.</li> <li>We present an individual/agent-based model of barnacle geese (Branta leucopsis) foraging on grasslands in Fryslân, the Netherlands. The model is parameterized using field observations and GPS-tracks and allows simulation of management scenarios, differing in scaring probability and accommodation area size, with different potential management costs. </li> <li>Our model shows that, while yield loss decreases with higher scaring probabilities, costs of damage appraisal increase because geese graze on more fields. With small accommodation areas, achieving high scaring probabilities takes more effort and could result in goose population decline. Total management costs are lowest without scaring activity. </li> <li> Synthesis and applications: Considering costs of active scaring and the need to maintain the barnacle goose population in a favourable conservation status, our model suggests that the most cost-effective scenario is to prevent disturbance of geese. A high scaring probability could be beneficial if applied in small areas, for example around sensitive crops or airfields. Scaring in large areas could result in costs outweighing benefits and a declining barnacle goose population.</li> </ol>

Signs of grassroot activities

Signs of grassroot activities with respect to direct publishing, peer review services, and diamond journal initiatives at Dutch universities; results of a mini tour of university web sites and preprint statistics. For direct publishing, a.k.a. preprint publishing, there seemed to be no readily available statistics on the internet. As <a href="https://www.dimensions.ai/">Dimensions</a> includes preprints, CWTS colleague Ludo Waltman could compile statistics on journal articles that were published as preprints first. The result is presented on page 2. For peer review services I consulted the web site of <a href="https://peercommunityin.org/">Peer Community In</a>, currently the most robust service in this domain with 1900 reviewers, covering 16 disciplines. I selected the reviewers from the Netherlands and made a breakdown by the Dutch universities. The result is presented on pages 3 and 4. For Dutch initiatives in diamond journals I consulted <a href="https://openjournals.nl/">Openjournals.nl</a> and generated the list shown on page 5.

Raw data for: Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity

This repository contains raw data and code related to "Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity" by Goretzki et al. Included are molecular dynamics parameter files, initial structures after system equilibration, production trajectories, and final structures of simulations of: 1. coarse-grained IDRs on membrane, and force and position data for restrained c-termini. Trajectories are subsampled with one frame every 50 ns. 2. The tetrameric TRPV4 core in a POPC in atomistic resolution. Trajectories are sampled with one frame every 1 ns.  3. The isolated ARD in solution in atomistic resolution. Trajectories are subsampled with one frame every 1 ns. Contact information: Name: Stefan L. Schaefer Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany Email: stefan.schaefer@biophys.mpg.de Name: Ainara Claveras Cabezudo Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany Email: ainara.claveras@biophys.mpg.de

Accident rate per year in plumbing activity in construction sector in two companies in Colombia

Dataset of 100 occupational accidents applied to the plumbing activity in two companies with 300 workers of the construction sector, were analyzed. The data were obtained of 2005 to 2022 year. The dataset is a accident database labor administered by Occupational Health and Safety coordinators and it use was approved by the two companies. The kind of occupational accident can be seen in Sheet2(2).

opencc-by-4.0Nov 2019View details →

Figure 1 in A PROTOCOL FOR RECORDING BEHAVIORAL ACTIVITY DURING LONGEVITY STUDIES OF ADULT CHIRONOMIDAE Abstract

Figure 1. Photograph of cardboard box used to organize numbered vials during longevity studies.

Code and Data for the paper "Active smelling in the American cockroach"

Code and Data used in the paper "Active smelling in the american cockroach" by Antoine Hoffmann and Einat Couzin-Fuchs. Code author: Antoine Hoffmann The file structure indicated in the R scripts needs to be replicated for the code to work as is.