Find research datasets worth reusing

opencc-by-4.0Jan 2021View details →

Data set for "Cell-type-specific nicotinic input disinhibits mouse barrel cortex during active sensing"

Data set for: Gasselin C, Hohl B, Vernet A, Crochet C, Petersen CCH (2021) Cell-type-specific nicotinic input disinhibits mouse barrel cortex during active sensing. Neuron doi: 10.1016/j.neuron.2020.12.018 There are 2 files in this upload: 1. The file named "2021_Gasselin_Neuron.pdf" is the Open Access pdf of the online publication in Neuron. 2. The file named "Gasselin_data_code.zip" (~9 GB) is a zipped version of a folder "Gasselin_data_code" (~13 GB), which contains the data analysed in the study along with the Matlab code used to generate the published figures. To access the data and the code, first unzip the file. Then add the folder with subfolders to the Matlab path and run the different codes. The current folder must be the main folder (‘Gasselin_data_code’). Each code computes and plots the results used in the corresponding figure. Figures and Tables are saved in the subfolder ‘Figures’. The subfolder ‘Functions’ contains functions called by the main codes. The main folder contains the following codes: Gasselin_Figure1: computes and plots the results for the panels D, E and F of figure 1. Gasselin_Figure2: computes and plots the results for the panels B and C of figure 2. Gasselin_Figure3: computes and plots the results for the panels B, C and D of figure 3. Gasselin_Figure4: computes and plots the results for the panels A, B and C of figure 4. Gasselin_FigureS1: computes and plots the results for the panels A, B and C of figure S1. Gasselin_FigureS2: computes and plots the results for the panels A and B of figure S2.   The subfolder ‘Data’ contains the data structures used for the different figures: data_figure1.mat data_figure2.mat data_figure3.mat data_figure4_MECA.mat data_figure4_Activation.mat data_figure4_Inactivation.mat data_figureS2_Activation.mat data_figureS2_Inactivation.mat data_Axon.mat   The data structures contain the following fields: Mouse_Name : name of the mouse. Mouse_DateOfBirth: date of birth of the mouse (YMD). Mouse_Sex: sex of the mouse (F or M). Mouse_Genotype: genotype of the mouse. Mouse_Drug: experimental condition of the recording (control = ‘No Drug’; blockade of glutamatergic transmission = ‘CNQX_DAPV’; blockade of glutamatergic transmission and nicotinic receptors = ‘CNQX_DAPV_MECA’; blockade of nicotinic receptors only = ‘MECA’). Mouse_Virus: virus injected if any. Cell_Counter; cell recorded in a given mouse. Cell_Type: type of the recorded cell based on 2P imaging. (EXC, VIP, PV, SST, 5HT3aR_non_VIP). Cell_Depth: depth of the recorded cell relative to pia (µm). Cell_TargetedBrainArea: cortical area targeted (C2 column of the barrel cortex = C2). Cell_Fluorescence: expression of the genetically encoded fluorophore (FALSE or TRUE). A neuron recorded in a VIP_IRES_Cre x LSL_tdTomato (cf Mouse_Genotype) with Cell_Fluorescence=TRUE is considered as a VIP neuron (cf Cell_Type). Sweep_Counter: number of the sweep recorded for a given neuron (data were acquired across successive continuous sweeps of 30-60 s). Sweep_Type: experimental condition during that sweep (Only spontaneous whisking onset = ‘Onset’; Whisking onset and whisker stimulus = ‘Onset_Whisker_Stim’ ; Optogenetic stimulation = ‘Opto_Stim’;  Optogenetic activation = ‘Opto_Activation’; Optogenetic inactivation = ‘Opto_Inactivation’;  ). Sweep_Start_Time: time at the beginning of the sweep recording (YMDHms). Sweep_WhiskerAngle: C2 whisker angular position extracted from simultaneous high-speed video filming (deg). Sweep_WhiskerAngle_SamplingRate: sampling rate of the whisker angle trace. Sweep_WhiskingOnset_Time: time of identified whisking onset - excluding any whisker stimulus shortly before or after (s). Sweep_MembranePotential: membrane potential recording (mV) after cutting of the APs. Sweep_MembranePotential_SamplingRate: sampling rate of the membrane potential signal (pt.s-1). Sweep_CurrentInjected: current injected into the cell (pA). Sweep_CurrentInjected_SamplingRate: sampling rate of current signal (pt.s-1). Sweep_WhiskerStim_Name: whisker to which the magnetic stimulus was applied to (C2 or B2&C2). Sweep_WhiskerStim_Time: onset times of the whisker stimulus (s). Sweep_OptoStim_Power: light power applied for optogenetic manipulations (% of the max power). Sweep_OptoStim_Time: onset times of the light pulses for optogenetic manipulations (s). Cell_ID: unique cell identifier (= Mouse_Name+Cell_Counter). SpikeThreshold: spike threshold used to detect APs (mV). Trial_WhiskingOnset: data structure containing the cut signals used to compute averaged responses around whisking onset times. Trial_WhiskerStim: data structure containing the cut signals used to compute averaged responses around whisker stimulus onset times. Trial_WhiskerStim_QuietTrials: data structure containing the cut signals used to compute averaged responses around whisker stimulus onset times for trials without whisker movements. Trial_WhiskerStim_WhiskingTrials: data structure containing the cut signals used to compute averaged responses around whisker stimulus onset times for trials with whisker movements. Trial_Opto: data structure containing the cut signals used to compute averaged responses around optogenetic stimulus onset times. Trial_OptoAndWhisker_QuietTrials: data structure containing the cut signals used to compute averaged responses around whisker stimulus onset times for trials with optogenetic manipulation and no whisker movements. Trial_OptoAndWhisker_WhiskingTrials: data structure containing the cut signals used to compute averaged responses around whisker stimulus onset times for trials with optogenetic manipulation and with whisker movements. Trial_OnlyWhisker_QuietTrials: data structure containing the cut signals used to compute averaged responses around whisker stimulus onset times for trials without optogenetic manipulation and without whisker movements. Trial_OnlyWhisker_WhiskingTrials: data structure containing the cut signals used to compute averaged responses around whisker stimulus onset times for trials without optogenetic manipulation and with whisker movements. Trial_OnlyOpto: data structure containing the cut signals used to compute averaged responses around optogenetic stimulus onset times in trials without whisker stimulus.

opencc-by-4.0Jan 2023View details →

Dynamics of activation in the voltage-sensing domain of Ci-VSP

This dataset contains unbiased molecular dynamics trajectories, stripped of water and lipid coordinates due to size constraints. It also contains full initial and final structures for all trajectories.<h3>Description of the data and file structure</h3>The data are deposited as a .tar.gz file: it can be unpacked by running tar -xzvf traj-data.tar.gz.The trajectories are organized into two groups (group1 and group2), each containing a folder with stripped_trajs as .xtc files, as well as the full starting and ending coordinates (with waters and lipids) as intial_structs and final_structs. The models for the down--, down, up, and up+ states are in models.The parameter file is civsd-amber-top.parm7 and the topology files with and without the waters/lipids are civsd.psf and civsd-pro.psf<h3>Sharing/Access information</h3>Derived data (collective variables computed from the raw trajectories) are available as supplementary information to the accompanying publication.<h3>Code/Software</h3>Analysis of the trajectories can be performed using the MDAnalysis, MDTraj, PyEMMA, scikit-learn, and VMD, softwares along with custom codes written in Python/Jupyter notebooks and tcl. Custom codes are available at <a href="https://github.com/dinner-group/ci-vsd">https://github.com/dinner-group/ci-vsd</a>.

opencc-by-4.0Jan 2022View details →

Data set for "On the Use of Pulsed UV or Visible Light Activated Gas Sensing of Reducing and Oxidising Species with WO3 and WS2 Nanomaterials"

This excel file contains the  raw data gathered with the measurements performed under different conditions of illumination for the different sensors. These data have been exploited in the paper "On the Use of Pulsed UV or Visible Light Activated Gas Sensing of Reducing and Oxidising Species with WO3 and WS2 Nanomaterials" DOI: 10.3390/s21113736

opencc-by-4.0Jun 2022View details →

Data for the publication "Retrieving ice-nucleating particle concentration and ice multiplication factors using active remote sensing validated by in situ observations"

This repository contains the data for the paper: Wieder, J., Ihn, N., Mignani, C., Haarig, M., Bühl, J., Seifert, P., Engelmann, R., Ramelli, F., Kanji, Z. A., Lohmann, U., and Henneberger, J.: Retrieving ice nucleating particle concentration and ice multiplication factors using active remote sensing validated by in situ observations, Atmos. Chem. Phys. Discuss. [preprint], https://doi.org/10.5194/acp-2022-67, in review, 2022. More information can be found in the README files. Note that the scripts to reproduce the figures of the publication are available on request.

opencc-by-4.0Feb 2019View details →

Top view of DR1/DR2 double riffle, each section contains a spawning ground made up of eight gravel-filled trays, a rest area. The "double riffle" was designed to accommodate two groups from 25 to 50 specimens of broodstock in strictly identical conditions. The spawning grounds are equipped with waterproof, motion-sensing cameras with infrared night vision, connected to a 1000 Gb recorder. The diurnal and nocturnal activities of the two groups can therefore be simultaneously recorded over a long period. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Top view of DR1/DR2 double riffle, each section contains a spawning ground made up of eight gravel-filled trays, a rest area. The "double riffle" was designed to accommodate two groups from 25 to 50 specimens of broodstock in strictly identical conditions. The spawning grounds are equipped with waterproof, motion-sensing cameras with infrared night vision, connected to a 1000 Gb recorder. The diurnal and nocturnal activities of the two groups can therefore be simultaneously recorded over a long period.

opencc-by-4.0May 2022View details →

Vibration and IMU Sensing Human Activity Dataset

This dataset contains fine-grained human daily activity data collected by infrastructure vibration sensors and one on-wrist IMU sensor. This dataset is collected from six persons from two domestic homes, in total, there are 12 sub-datasets. For the naming, "p" means person and "l" means location. Each dataset has 11 columns, 1o of them stands for sensors' reading. * Due to the uploading platform, please ignore all files in the folder '__MACOSX', and files whose names start with '._'. These are computer system files, not parts of the shared dataset.  ** If you are going to use this dataset for any publications, we will appreciate you to cite this dataset properly. ************************************************************ The following content is copied from README.txt in the compressed folder: ----------------------- Labels: Keyboard typing 1 Using mouse 2 Handwriting 3 Cutting vegetables 4 Stir-frying vegetables 5 Wiping the table 6 Sweeping floor 7 Using vacuum to vacuum floor: 8 Open and close drawer: 9 None Activity: 10 ----------------------- 11 Columns: 1: Activity label 2: Vibration sensor put on the Living Area floor 3: Vibration sensor put on the Living Area table 4: Vibration sensor put on the Studying Area floor 5: Vibration sensor put on the Studying Area desk 6, 7, 8: Accelerometer X,Y,Z 9, 10, 11: Gyroscope X,Y,Z ----------------------- All signals are zero-meaned. The vibration sensors' sampling rate is roughly around 6500Hz, and the IMU sensors' original sampling rate is roughly around 235Hz. ************************************************************ New in Version 2: - Added extracted features from IMU data and vibration data for reference. - IMU signal is applied with a sliding window of 1.5 seconds with 0.75 seconds overlapping, then the feature is extracted in each window. The feature's description can be found here: https://dl.acm.org/doi/abs/10.1145/3410530.3414320 - The vibration signal is applied with event detection to extract events in the vibration signal. For each event, we normalize it by its energy, then extract 10~490 Hz frequency amplitude as the feature.   Disclaimer: Both event detection and feature extraction are empirical, we don't guarantee it is an optimal one.

opencc-by-4.0Mar 2023View details →

Data for Non-Equilibrium Sensing of Volatile Compounds Using Active and Passive Analyte Delivery

<blockquote> Version 2: Added missing files to <code>sniffing_data.zip</code> </blockquote> See GitHub repository for data processing functions and examples: <a href="https://github.com/soerenbrandt/sniffing-sensor">https://github.com/soerenbrandt/sniffing-sensor</a> Abstract: Sensor technologies have allowed us to outperform the human senses of sight, hearing, and touch; however, the development of artificial noses is significantly behind their biological counterparts. This is largely due to the complexity of natural olfaction, as it incorporates complex fluid dynamics within the nasal anatomy together with the response patterns of hundreds to thousands of unique molecular-scale receptors for odor interpretation. We designed a sensing approach to identify volatiles that exploits time-dependent information from a single sensor (here, the reflectance spectra from a mesoporous one-dimensional photonic crystal) by augmenting and accentuating differences in the non-equilibrium mass-transport dynamics of vapors stemming from their distinct physicochemical properties, thus obviating the need for a large sensor array. By training a machine learning algorithm on the sensor output, we clearly identify polar and nonpolar volatile organic compounds, determine the mixing ratios of binary mixtures, and accurately predict the boiling point, flash point, vapor pressure, and viscosity of several volatile liquids within those used for training as well as compounds unknown to the model. We further implement a bioinspired active sniffing approach, in which the fluid dynamics and patterns of analyte delivery are controlled, enabling an additional modality of differentiation and reducing the duration of data collection and analysis to seconds. These results outline a strategy to build accurate and rapid artificial noses for volatile liquids that can provide useful information on chemicals such as their composition and properties, and can be applied in a variety of fields, including disease diagnosis, hazardous waste management, and healthy building monitoring.

opencc-by-4.0Jun 2023View details →

Data set for "Membrane potential dynamics of excitatory and inhibitory neurons in mouse barrel cortex during active whisker sensing"

Data set for: Kiritani T, Pala A, Gasselin C, Crochet S, Petersen CCH (2023) Membrane potential dynamics of excitatory and inhibitory neurons in mouse barrel cortex during active whisker sensing. PLOS ONE 18: e0287174. doi: 10.1371/journal.pone.0287174 There are 2 files in this upload: 1. The file named "2023_Kiritani_PLOSONE.pdf" is the Open Access pdf of the online publication in PLOS ONE. 2. The file named "Kiritani_data_code.zip" (~5 GB) is a zipped version of a folder "Kiritani_data_code" (~5 GB), which contains the data analysed in the study along with the Matlab codes used to generate the published figures. To access the data and codes, first unzip the file. You need to install the Matlab 'Signal Processing' and 'Curve Fitting' Toolboxes. In Matlab, add the path of the folder 'Kiritani_data_code' and all subfolders. Directly from this folder, you should first run the codes in the folder 'Data_Analysis_Codes', sequentially executing 'Analysis_1.m' through to 'Analysis_9.m'. Note, execution of 'Analysis_9.m' can take a long time (~1 hour on a good desktop PC). You can then run the codes in the folder 'Figure_Plotting_Codes' to generate the figures published in the journal article. In the folder 'Data', you can also find a DataViewer to visualise the data sets, which you can run by executing 'DataViewer.m' directly from the subfolder ‘Data’.

opencc-by-4.0Apr 2020View details →

Fine-Grained Activities of Daily Living Data with Structural Vibration and Electrical Load Sensing

Fine-grained non-intrusive monitoring of activities of daily living (ADL) enables various smart building applications, including ADL pattern assessments for older adults at risk for loss of safety or independence. We utilize structural vibration sensing and electrical load sensing to acquire multiple fine-grained kitchen activities under a lab structure setting. Each file contains the following values: -RawData: time series of data for each channel (vibration on the table, vibration on the floor, load) -Label: manually fine-grained labels of events -Table: detected events start/stop index for vibration sensor on the table -Floor: detected events start/stop index for vibration sensor on the floor -Load: detected events start/stop index for load sensor Label notation: 1 -- operating the kettle 2 -- kettle on 3 -- operating the microwave 4 -- microwave on 5 -- put things on the stove 6 -- operating with stove 7 -- stove on 8 -- operating vacuum 9 -- sweep floor 10 -- walking/step 11 -- miscellaneous 12 -- synchronization signal (knock on the floor) 13 -- vacant 14 -- microwave door open

openmit-licenseJan 2021View details →

Experimental Data for the Paper 'Hierarchical Fusion and Divergent Activation Based Weakly Supervised Learning for Object Detection from Remote Sensing Images'

Experimental Data for the Paper 'Hierarchical Fusion and Divergent Activation Based Weakly Supervised Learning for Object Detection from Remote Sensing Images' In this repository, we provide the implementation of the algorithms developed in the paper 'Hierarchical Fusion and Divergent Activation Based Weakly Supervised Learning for Object Detection from Remote Sensing Images' along with the experimental results, and the methods used for comparison. The goal is to provide the elements needed to validate and reproduce our research work as well as all the tools needed to reach the same conclusions as we did. The data used in our experiments that we have the copyright of [<a href="http://doi.org/10.1109/ACCESS.2020.3019956">A</a>],[<a href="http://doi.org/10.5281/zenodo.3843229">B</a>] is already published <a href="http://doi.org/10.5281/zenodo.3843229">on zenodo</a>. The licences valid for the elements of this repository are discussed under point "3. Licenses" below. 1. Structure The repository contains the following items: <ol> <li>"CODE_AND_RESULTS.zip" with the source codes and results of our method and the comparison methods,</li> <li>"README" - this text here.</li> <li>"LICENSE" - the <a href="https://mit-license.org/">MIT License</a></li> </ol> We now focus on the structure of the file CODE_AND_RESULTS.zip. It contains the following items: <ol> <li>The directory "new_methods" contains the source code and results of the new methods proposed in our paper.</li> <li>The directory "comparison" contains the source code of the two approaches used for comparison: ACoL [<a href="https://doi.org/10.1109/CVPR.2018.00144">A</a>] and DANet [<a href="http://doi.org/10.1109/ICCV.2019.00669">B</a>].</li> <li>The folder "tools_and_metrics" holds additional libraries, software tools, and metrics using in our experiments. </li> <li>"README" - this text here.</li> <li>"LICENSE" - the <a href="https://mit-license.org/">MIT License</a></li> </ol> Inside the folder "new_methods," the following sub-folders are provided: <ol> <li>"data" includes data loading code and code for how organizing the input data of the neural network.</li> <li>"expr" includes training code.</li> <li>"model" includes neural network model, basic network and additional modules, depending on the file name, including improved network, and comparison model.</li> <li>"utils" includes some used library functions and test codes when testing, including image segmentation, searching for the largest connected area and data visualization, etc. Verification on the WSADD dataset is done via test_airplane.py and on the DIOR dataset via val_model.py.</li> </ol> In our experiments, we used two datasets: "WSADD" [<a href="http://doi.org/10.1109/ACCESS.2020.3019956">A</a>],[<a href="http://doi.org/10.5281/zenodo.3843229">B</a>], which is already published <a href="http://doi.org/10.5281/zenodo.3843229">on zenodo</a> under the <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> license. The "<a href="https://doi.org/10.1109/CVPR.2018.00144">DIOR</a>" proposed in [<a href="http://doi.org/10.1016/j.isprsjprs.2019.11.023">C</a>]. 2. References [<a href="http://doi.org/10.1109/ACCESS.2020.3019956">A</a>] Z.-Z. Wu, T. Weise, Y. Wang, Y. Wang, Convolutional neural network based weakly supervised learning for aircraft detection from remote sensing image, IEEE Access 8 (2020) 158097-158106. doi:<a href="http://doi.org/10.1109/ACCESS.2020.3019956">10.1109/ACCESS.2020.3019956</a>.    [<a href="http://doi.org/10.5281/zenodo.3843229">B</a>] Z.-Z. Wu. Weakly Supervised Airplane Detection Dataset: WSADD. May 2020. zenodo.org. doi:<a href="http://doi.org/10.5281/zenodo.3843229">10.5281/zenodo.3843229</a>. [<a href="http://doi.org/10.1016/j.isprsjprs.2019.11.023">C</a>] K. Li, G. Wan, G. Cheng, L. Meng, J. Han, Object detection in optical remote sensing images: A survey and a new benchmark, ISPRS Journal of Photogrammetry and Remote Sensing 159 (2020) 296-307. doi:<a href="http://doi.org/10.1016/j.isprsjprs.2019.11.023">10.1016/j.isprsjprs.2019.11.023</a>.    [<a href="https://doi.org/10.1109/CVPR.2018.00144">D</a>] X. Zhang, Y. Wei, J. Feng, Y. Yang, T. S. Huang, Adversarial complementary learning for weakly supervised object localization, in: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR'18), Jun. 18-22, 2018, Salt Lake City, UT, USA, IEEE Computer Society, 2018, pp. 1325-1334. doi:<a href="https://doi.org/10.1109/CVPR.2018.00144">10.1109/CVPR.2018.00144</a>.    [<a href="http://doi.org/10.1109/ICCV.2019.00669">E</a>] H. Xue, C. Liu, F. Wan, J. Jiao, X. Ji, Q. Ye, DANet: Divergent activation for weakly supervised object localization, in: Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV'19), Oct. 27-Nov. 2, 2019, Seoul, Korea, IEEE, 2019, pp. 6588-6597. doi:<a href="http://doi.org/10.1109/ICCV.2019.00669">10.1109/ICCV.2019.00669</a>. 3. Licenses The following licenses apply for the files and folders in the archive "CODE_AND_RESULTS.zip": <ul> <li>The files in the folder `new_methods` are under the <a href="https://mit-license.org/">MIT License</a>.</li> <li>The files in the folder `comparison/ACoL` have been obtained from https://github.com/xiaomengyc/ACoL, which is under the <a href="https://mit-license.org/">MIT License</a>.</li> <li>We put our code and data under the </li> <li>The files in the folder "comparison/DANet" have been obtained from <a href="https://github.com/xuehaolan/DANet">https://github.com/xuehaolan/DANet</a>, which is an open source project without associated license at the time of this writing. They will therefore remain under the copyright of the user <a href="https://github.com/xuehaolan/">https://github.com/xuehaolan/</a>.</li> <li>The files in the folder "tools_and_metrics/detections_DIOR" are related to the repository <a href="https://github.com/rafaelpadilla/Object-Detection-Metrics">https://github.com/rafaelpadilla/Object-Detection-Metrics</a>, which is under the <a href="https://mit-license.org/">MIT License</a>, and therefore are under the same license.</li> <li>The files in the folder "tools_and_metrics/Nest-pytorch" are based on the repository <a href="https://github.com/ZhouYanzhao/Nest">https://github.com/ZhouYanzhao/Nest</a>, which is under the <a href="https://mit-license.org/">MIT License</a>.</li> <li>The files in the folder "tools_and_metrics/PRM-pytorch" are based on the repository <a href="https://github.com/ZhouYanzhao/PRM">https://github.com/ZhouYanzhao/PRM</a>, which is an open source project without associated license at the time of this writing. They will therefore remain under the copyright of the user <a href="https://github.com/ZhouYanzhao/">https://github.com/ZhouYanzhao/</a>.</li> </ul> The <a href="https://mit-license.org/">MIT License</a> is included here as file "LICENSE". 4. Contact 1. Dr. <a href="http://iao.hfuu.edu.cn/146">Zhize WU</a>, wuzz@hfuu.edu.cn 2. Dr. <a href="http://iao.hfuu.edu.cn/5">Thomas WEISE</a>, tweise@hfuu.edu.cn, tweise@ustc.edu.cn Institute of Applied Optimization,    School of Artificial Intelligence and Big Data,    Hefei University, South Campus 2, Jinxiu Dadao 99,    Hefei Economic and Technological Development Area,    Shushan District, Hefei 230601, Anhui, China

opencc-zeroDec 2019View details →

Data from: Canine sense of quantity: evidence for numerical ratio-dependent activation in parietotemporal cortex

The approximate number system (ANS), which supports the rapid estimation of quantity, emerges early in human development and is widespread across species. Neural evidence from both human and non-human primates suggests the parietal cortex as a primary locus of numerical estimation, but it is unclear whether the numerical competencies observed across non-primate species are subserved by similar neural mechanisms. Moreover, because studies with non-human animals typically involve extensive training, little is known about the spontaneous numerical capacities of non-human animals. To address these questions, we examined the neural underpinnings of number perception using awake canine functional magnetic resonance imaging. Dogs passively viewed dot arrays that varied in ratio and, critically, received no task-relevant training or exposure prior to testing. We found evidence of ratio-dependent activation, which is a key feature of the ANS, in canine parietotemporal cortex in the majority of dogs tested. This finding is suggestive of a neural mechanism for quantity perception that has been conserved across mammalian evolution.

opencc-zeroApr 2024View details →

Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity

Isocitrate Dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2-hydroxyglutarate, disrupting enzymes involved in epigenetics and other processes. A hallmark of IDH1-mutant solid tumors is T cell exclusion, whereas mIDH1 inhibition in preclinical models restores anti-tumor immunity. Here, we define a cell-autonomous mechanism of mIDH1-driven immune evasion. IDH1-mutant solid tumors show striking, selective hypermethylation and silencing of the cytoplasmic dsDNA sensor, CGAS, compromising innate immune signaling. mIDH1 inhibition restores DNA demethylation, derepressing CGAS and transposable element (TE) subclasses. dsDNA produced by TE-reverse transcriptase activates cGAS, triggering viral mimicry and stimulating anti-tumor immunity. Thus, we demonstrate that mIDH1 epigenetically suppresses innate immunity and link endogenous reverse transcriptase activity to the mechanism of action of an FDA-approved oncology drug.

opencc-zeroJun 2024View details →

Data from: Structural basis for activation and allosteric modulation of full-length calcium-sensing receptor

Calcium-sensing receptor (CaSR) is a class C G protein-coupled receptor (GPCR) that plays an important role in calcium homeostasis and parathyroid hormone secretion. Here, we present multiple cryo-electron microscopy structures of full-length CaSR in distinct ligand-bound states. Ligands (Ca2+ and l-tryptophan) bind to the extracellular domain of CaSR and induce large-scale conformational changes, leading to the closure of two heptahelical transmembrane domains (7TMDs) for activation. The positive modulator (evocalcet) and the negative allosteric modulator (NPS-2143) occupy the similar binding pocket in 7TMD. The binding of NPS-2143 causes a considerable rearrangement of two 7TMDs, forming an inactivated TM6/TM6 interface. Moreover, a total of 305 disease-causing missense mutations of CaSR have been mapped to the structure in the active state, creating hotspot maps of five clinical endocrine disorders. Our results provide a structural framework for understanding the activation, allosteric modulation mechanism, and disease therapy for class C GPCRs.

opencc-by-4.0Jun 2024View details →

Accompanying data for the paper "Making Sense of Wildlife Habitat Use on Active Oil Sands Mines: Quasi-experiments, Occupancy Models, Trends Assessments, and Upland Habitat Reclamation"

This data set contains both the raw species detection records and the derived occupancy model data used to assess usage patterns for the nine species of wildlife.  Data have been anonymized by using non-identifying company and lease names. These attributes are not required to reproduce the results in this paper and was done per contractual requirements between LGL Limited and its clients. Data is currently being reviewed by the client and will be shared publicly once final approval has been received.

opencc-by-4.0Sep 2019View details →

Occupancy Sensing and Activity Recognition with Cameras and Wireless Sensors

This dataset contains human activity data from a wireless sensing system, which includes a Doppler motion sensor and a wireless network. The Doppler sensor is a low-cost dual Doppler sensor modified from a commercial-off-the-shelf range-controlled radar, which operates at 5.8 GHz with two directional antennas. The wireless network uses four IEEE 802.15.4 radio nodes (CC2531 from TI) to create a mesh network to measure the RSS between each pair of radio nodes operating on the 16 frequency channels at 2.4 GHz. For the activity experiment, we recruited human subjects to perform 42 trials of four activities  (each one with two minutes duration): (1)  walking in a room (10 trials), (2) sitting in a chair (10 trials), (3) lying on a bed (12 trials), and (4) body turning on a bed (10 trials). For the walking activity, the human subjects walk along different paths at different locations in the room. For the lying on bed activity, we ask human subjects to breathe normally on bed with three orientations facing upwards, right and left. Finally, for the turning on bed case, human subjects turn their bodies from one side to the other on bed with random time intervals. We also recorded two-minute data of the empty room case before and after each human subject trial. Note that each data file name has its corresponding activity in it, so it is pretty self-explanatory.

opencc-by-4.0Jun 2021View details →

Analysis code and quantification for publication "The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes"

Analysis code and input/output files for all quantifications performed for publication entitled "The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes."  All questions on the analyses or code can be directed to han@walterlab.ucsf.edu

opencc-by-4.0Oct 2021View details →

Active sensing in bees through antennal movements is independent of odor molecule (source videos)

Videos of restrained bombus terrestris stimulated by odors to record their antennal movements. The video were used in the following preprint: https://www.biorxiv.org/content/10.1101/2021.09.13.460114v1