cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10829212
title: Data generated for the manuscript: "Increased 'selfness' in the tumor emerges as a possible immune scuplting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA"

description: This submission has processed data generated for the manuscript: "Increased 'selfness' in the tumor emerges as a possible immune scuplting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA".

The `data` folder contains processed information for the Human Protein Atlas (HPA) and The Cancer Genome Atlas (TCGA) datasets. The HPA data is found in `data/hpa` and contains gene ranks used to compute the thymus-likeness score (TLS) and files where the TLS has been calculated for the HPA tissues. The TCGA data can be found in `data/proc`, where individual RDS files have been given for each analyzed cohort. These RDS files contain the results of the cutoff scanning procedure mentioned in the manuscript and account for the bulk of the data generated for this study. RDS files can be loaded using the `readRDS` function in an R session. Other information used to create plots is in the `data` folder.

The `plots` folder contain the result of plotting the entireity of the cutoff scanning procedure. The manuscript only contains plots for the 28 cohorts where a significant difference in terms of immune difference is observed, and that too, only the final heuristic plots. The `plots/tcga/immuneres` folder has plots at different levels: (i) single cell category/single deconvolution method with permutation tests (ii) single cell category/multiple deconvolution methods and (iii) significant cell categories/representative deconvolution method. Only (iii) is present in the manuscript. Overall, this folder should contain ~2000 plots.

The code used to generate this study is deposited at: https://gitlab.com/narencs179/thymus-like-score
DOI: 10.5281/zenodo.10639316
title: Example data for: Pitfalls in diagnosing temperature extremes

description: Pre-calculated extreme frequencies for ERA5 using a 31 day running window for the 90th percentile. The accompanying code is at: https://github.com/lukasbrunner/running_window_bias
DOI: 10.5281/zenodo.10639317
title: Example data for: Pitfalls in diagnosing temperature extremes

description: Pre-calculated extreme frequencies for ERA5 using a 31 day running window for the 90th percentile. The accompanying code is at: https://github.com/lukasbrunner/running_window_bias
DOI: 10.18419/darus-3316/1
title: sheet new.png

description: :unav
DOI: 10.18419/darus-3316/2
title: kineticSep22.dts

description: :unav
DOI: 10.18419/darus-3316/3
title: CR30-30min-2hourtest.dat

description: :unav
DOI: 10.18419/darus-3316/4
title: DLS210201-CR39kinetic.dts

description: :unav
DOI: 10.5281/zenodo.10829207
title: Programmable multi-photon quantum interference in a single spatial mode -- Data and code for simulations

description: Description of the data and file structure

This Dataset contains data files with experimental results for the manuscript "Programmable multi-photon quantum interference in a single spatial mode" (pre-print version at https://arxiv.org/abs/2305.11157).

The CSV files contain the measured output distributions of our time-bin interferometer, for the various experiments we run. In the first column is the number of counts detected and in the following columns the corresponding output modes. The counts were detected by post-processing the time-tags of the recorded single photon events (a detailed explanation can be found in the Supplementary Informations of the paper).The number of counts is reported for all possible combinations of output modes in order to reconstruct the entire output distribution of collisionless events.

The text file contains the data points of the time-bin HOM histogram shown in the paper.

 

Code/Software

We also provide the Jupyter Notebook (LoopExperiment.ipynb) we used to simulate the experiments, developed by Dr. Tobias Guggemos.

The Loop-based architecture is a photonic experiment, that allows scalable implementation of Boson Sampling and arbitrary unitaries on a photonic platform. It can be implemented as a single, sequenced or nested architecture.

We use the python framework Perceval to simulate our experiments. We simulate the conversion of the time-bin encoded setup as path encoded photonic qubits.

More details can be found in the Notebook.
DOI: 10.5281/zenodo.10829208
title: Programmable multi-photon quantum interference in a single spatial mode -- Data and code for simulations

description: Description of the data and file structure

This Dataset contains data files with experimental results for the manuscript "Programmable multi-photon quantum interference in a single spatial mode" (pre-print version at https://arxiv.org/abs/2305.11157).

The CSV files contain the measured output distributions of our time-bin interferometer, for the various experiments we run. In the first column is the number of counts detected and in the following columns the corresponding output modes. The counts were detected by post-processing the time-tags of the recorded single photon events (a detailed explanation can be found in the Supplementary Informations of the paper).The number of counts is reported for all possible combinations of output modes in order to reconstruct the entire output distribution of collisionless events.

The text file contains the data points of the time-bin HOM histogram shown in the paper.

 

Code/Software

We also provide the Jupyter Notebook (LoopExperiment.ipynb) we used to simulate the experiments, developed by Dr. Tobias Guggemos.

The Loop-based architecture is a photonic experiment, that allows scalable implementation of Boson Sampling and arbitrary unitaries on a photonic platform. It can be implemented as a single, sequenced or nested architecture.

We use the python framework Perceval to simulate our experiments. We simulate the conversion of the time-bin encoded setup as path encoded photonic qubits.

More details can be found in the Notebook.
DOI: 10.18419/darus-3316/5
title: S5EuLSVlight.txt

description: :unav
DOI: 10.18419/darus-3316/6
title: S76EuLSVlightafterca1.txt

description: :unav
DOI: 10.18419/darus-3316/7
title: Eu reduction CA figure 5.opju

description: :unav
DOI: 10.18419/darus-3316/8
title: kineticOct8-1.dts

description: :unav
DOI: 10.18419/darus-3316/9
title: DLS-24-09-2020.xlsx

description: :unav
DOI: 10.18419/darus-3316/10
title: CR52Jan070007.ibw

description: :unav
DOI: 10.18419/darus-3316/11
title: CR30-1p5h-2hourtest.dat

description: :unav
DOI: 10.18419/darus-3316/12
title: kineticSep24-1.dts

description: :unav
DOI: 10.18419/darus-3316/13
title: COF_20coatings0006.ibw

description: :unav
DOI: 10.18419/darus-3316/14
title: Figure 2.png

description: :unav
DOI: 10.18419/darus-3316/15
title: CR39-30min-DEC18-1htest.raw

description: :unav
DOI: 10.18419/darus-3316/16
title: CR13-5 h-2nd-2hourtest-1.dat

description: :unav
DOI: 10.18419/darus-3316/17
title: S5EuLSVdarkafterca-2.txt

description: :unav
DOI: 10.18419/darus-3316/18
title: CR13-2p5 h-2hourtest.dat

description: :unav
DOI: 10.18419/darus-3316/19
title: A1_0001-zoomin_20210811.dm3

description: :unav
DOI: 10.18419/darus-3316/20
title: F12-RHE-HERLSV.tab

description: :unav
DOI: 10.18419/darus-3316/21
title: Figure 6.tif

description: :unav
DOI: 10.18419/darus-3316/22
title: CR13-2p5h-2hourtest.raw

description: :unav
DOI: 10.18419/darus-3316/23
title: DLS210203-CR39after2day.dts

description: :unav
DOI: 10.18419/darus-3316/24
title: YAO-4_new.jpg

description: :unav
DOI: 10.48324/dandi.000939/0.240318.1020
title: Large-scale recordings of head-direction cells in mouse postsubiculum

description: 64-channel linear probe recordings from mouse postsubiculum (dorsal presubiculum) - a region in which most excitatory cells are narrowly tuned to the animal's head-direction.  Dataset (upload in progress) includes one recording session per mouse (N = 31 mice, 42 - 185 units per recording). All sessions include a square open field exploration epoch and two sleep epochs. Some sessions additionally include a triangular open field epoch or an optogenetic stimulation epoch. 

Each NWB file contains: timestamps of detected units, mean waveforms, LFP,  animal position and head-direction,  sleep scoring (REM/NREM), accelerometer data. 

Data used in Duszkiewicz et al, 2024 (DOI: 10.1038/s41593-024-01588-5). Collected by Adrian J. Duszkiewicz and Sofia Skromne Carrasco in Peyrache lab. 

Full dataset in Matlab format (including ADN recordings) and code to reproduce figures in the article can be found at:
https://doi.org/10.6084/m9.figshare.24921252
DOI: 10.18419/darus-3316/25
title: CR30-5h-2hourtest_SE.ipynb

description: :unav
DOI: 10.18419/darus-3316/26
title: LSV.opju

description: :unav
DOI: 10.18419/darus-3316/28
title: DLS-07-10-2020.xlsx

description: :unav
DOI: 10.18419/darus-3316/29
title: P3.tab

description: :unav
DOI: 10.18419/darus-3316/30
title: kineticOct6-1.dts

description: :unav
DOI: 10.18419/darus-3316/31
title: S5EuLSVdarkafterca-1.txt

description: :unav
DOI: 10.18419/darus-3316/32
title: DLS-22-09-2020.xlsx

description: :unav
DOI: 10.18419/darus-3316/33
title: Figure 5.cdr

description: :unav
DOI: 10.18419/darus-3316/34
title: CR39-30min-DEC18-1htest.dat

description: :unav
DOI: 10.18419/darus-3316/35
title: CR13-1h-2nd-2hourtest_SE.ipynb

description: :unav
DOI: 10.18419/darus-3316/36
title: CR44inmarker0004.ibw

description: :unav
DOI: 10.18419/darus-3316/37
title: CR30-1p5h-2hourtest.raw

description: :unav
DOI: 10.18419/darus-3316/38
title: reaction kinetics crystallinity FWHM.opju

description: :unav
DOI: 10.18419/darus-3316/39
title: blender-new1.png

description: :unav
DOI: 10.18419/darus-3316/40
title: CR30-30min-2hourtest.dat

description: :unav
DOI: 10.18419/darus-3316/41
title: kineticSep22.dts

description: :unav
DOI: 10.18419/darus-3316/42
title: DLS210201-CR39kinetic.dts

description: :unav
DOI: 10.18419/darus-3316/43
title: S11EuLSVlight.txt

description: :unav
DOI: 10.18419/darus-3316/44
title: DLS-08-10-2020.xlsx

description: :unav
DOI: 10.18419/darus-3316/45
title: 20coatings31.tif

description: :unav
DOI: 10.18419/darus-3316/46
title: CR13-10min-2nd-2hourtest_SE.ipynb

description: :unav
DOI: 10.18419/darus-3316/47
title: Figure 2.tif

description: :unav
DOI: 10.18419/darus-3316/48
title: F12-V-HERLSV.tab

description: :unav
DOI: 10.18419/darus-3316/49
title: YL-CR13_N2_77K_2020_12_06_10_22_42.qps

description: :unav
DOI: 10.18419/darus-3316/50
title: Figure 4 kinetics.cdr

description: :unav
DOI: 10.18419/darus-3316/51
title: reaction kinetics DLS-05-10-2020-b2.opju

description: :unav
DOI: 10.18419/darus-3316/52
title: CR13-10 min-2nd-2hourtest.raw

description: :unav
DOI: 10.18419/darus-3316/53
title: Figure 3.cdr

description: :unav
DOI: 10.18419/darus-3316/54
title: F12light.tab

description: :unav
DOI: 10.18419/darus-3316/55
title: YAO-1_new.jpg

description: :unav
DOI: 10.18419/darus-3316/56
title: S11EuLSVlightafterca.txt

description: :unav
DOI: 10.18419/darus-3316/57
title: S76EuCA.txt

description: :unav
DOI: 10.18419/darus-3316/58
title: S11EuLSVdarkafterca.txt

description: :unav
DOI: 10.18419/darus-3316/59
title: DLS-06-10-2020.xlsx

description: :unav
DOI: 10.18419/darus-3316/60
title: F12CA.tab

description: :unav
DOI: 10.18419/darus-3316/61
title: CR39-1h-1hourtest_SE.ipynb

description: :unav
DOI: 10.18419/darus-3316/62
title: S5CA-1.txt

description: :unav
DOI: 10.18419/darus-3316/63
title: DLS.opju

description: :unav
DOI: 10.18419/darus-3316/64
title: DLS210203-CR39after3day.dts

description: :unav
DOI: 10.18419/darus-3316/66
title: 20coatings36.tif

description: :unav
DOI: 10.18419/darus-3316/68
title: CR39-2p5 h-DEC18-1htest.raw

description: :unav
DOI: 10.18419/darus-3316/69
title: A3_0007-zoomin_1.dm3

description: :unav
DOI: 10.18419/darus-3316/70
title: figure 3.cdxml

description: :unav
DOI: 10.18419/darus-3316/71
title: 200910S5.ipynb

description: :unav
DOI: 10.18419/darus-3316/72
title: CR13-30 min-2nd-2hourtest.dat

description: :unav
DOI: 10.18419/darus-3316/73
title: CR30-2p5h-2hourtest.raw

description: :unav
DOI: 10.18419/darus-3316/75
title: CR13-5 h-2nd-2hourtest-1.raw

description: :unav
DOI: 10.18419/darus-3316/77
title: S76EuLSVdarkafterca.txt

description: :unav
DOI: 10.18419/darus-3316/78
title: CR13-5h-2nd-2hourtest_SE.ipynb

description: :unav
DOI: 10.18419/darus-3316/79
title: Sphere new -1.png

description: :unav
DOI: 10.18419/darus-3316/80
title: IFFT of FFT of A1_0001-zoomin_20210811.dm3

description: :unav
DOI: 10.18419/darus-3316/81
title: Figure 2_R1.tif

description: :unav
DOI: 10.18419/darus-3316/82
title: F12dark_afterca.tab

description: :unav
DOI: 10.18419/darus-3316/83
title: CR30-2p5h-2hourtest_SE.ipynb

description: :unav
DOI: 10.18419/darus-3316/85
title: CR39-2p5 h-DEC18-1htest.dat

description: :unav
DOI: 10.18419/darus-3316/86
title: spherefilm12.tif

description: :unav
DOI: 10.18419/darus-3316/87
title: Figure 6.cdr

description: :unav
DOI: 10.18419/darus-3316/88
title: DLS-01-02-2021.xlsx

description: :unav
DOI: 10.18419/darus-3316/89
title: DLS-23-09-2020.xlsx

description: :unav
DOI: 10.18419/darus-3316/90
title: CR39-5h-2-Jan13-1htest.raw

description: :unav
DOI: 10.18419/darus-3316/91
title: CR30-1h-2hourtest_SE.ipynb

description: :unav
DOI: 10.18419/darus-3316/92
title: sheet new.png

description: :unav
DOI: 10.18419/darus-3316/93
title: spherefilm01.tif

description: :unav
DOI: 10.18419/darus-3316/94
title: 210223F12HER.ipynb

description: :unav
DOI: 10.18419/darus-3316/95
title: fig for scheme.bmp

description: :unav
DOI: 10.18419/darus-3316/96
title: S5EuLSVlight.txt

description: :unav
DOI: 10.18419/darus-3316/97
title: S76EuLSVlightafterca1.txt

description: :unav
DOI: 10.18419/darus-3316/98
title: Eu reduction CA figure 5.opju

description: :unav
DOI: 10.18419/darus-3316/99
title: kineticOct8-1.dts

description: :unav
DOI: 10.18419/darus-3316/100
title: DLS-24-09-2020.xlsx

description: :unav
DOI: 10.18419/darus-3316/101
title: CR52Jan070007.ibw

description: :unav
DOI: 10.18419/darus-3316/102
title: CR30-1p5h-2hourtest.dat

description: :unav
DOI: 10.18419/darus-3316/103
title: kineticSep24-1.dts

description: :unav
DOI: 10.18419/darus-3316/104
title: COF_20coatings0006.ibw

description: :unav
DOI: 10.18419/darus-3316/105
title: Figure 2.png

description: :unav
DOI: 10.18419/darus-3316/106
title: CR39-30min-DEC18-1htest.raw

description: :unav
DOI: 10.18419/darus-3316/107
title: CR13-5 h-2nd-2hourtest-1.dat

description: :unav
DOI: 10.18419/darus-3316/108
title: S5EuLSVdarkafterca-2.txt

description: :unav
DOI: 10.18419/darus-3316/109
title: CR13-2p5 h-2hourtest.dat

description: :unav
DOI: 10.18419/darus-3316/110
title: A1_0001-zoomin_20210811.dm3

description: :unav
DOI: 10.18419/darus-3316/111
title: F12-RHE-HERLSV.tab

description: :unav
DOI: 10.18419/darus-3316/112
title: Figure 6.tif

description: :unav
DOI: 10.18419/darus-3316/113
title: CR13-2p5h-2hourtest.raw

description: :unav
DOI: 10.18419/darus-3316/114
title: DLS210203-CR39after2day.dts

description: :unav
DOI: 10.18419/darus-3316/115
title: YAO-4_new.jpg

description: :unav
DOI: 10.18419/darus-3316/116
title: CR30-5h-2hourtest_SE.ipynb

description: :unav
DOI: 10.18419/darus-3316/117
title: LSV.opju

description: :unav
DOI: 10.18419/darus-3316/119
title: DLS-07-10-2020.xlsx

description: :unav
DOI: 10.18419/darus-3316/120
title: P3.tab

description: :unav
DOI: 10.18419/darus-3316/121
title: kineticOct6-1.dts

description: :unav
DOI: 10.18419/darus-3316/122
title: S5EuLSVdarkafterca-1.txt

description: :unav
DOI: 10.18419/darus-3316/123
title: DLS-22-09-2020.xlsx

description: :unav
DOI: 10.18419/darus-3316/124
title: Figure 5.cdr

description: :unav
DOI: 10.18419/darus-3316/125
title: CR39-30min-DEC18-1htest.dat

description: :unav
DOI: 10.18419/darus-3316/126
title: CR13-1h-2nd-2hourtest_SE.ipynb

description: :unav
DOI: 10.18419/darus-3316/127
title: CR44inmarker0004.ibw

description: :unav
DOI: 10.18419/darus-3316/128
title: CR30-1p5h-2hourtest.raw

description: :unav
DOI: 10.18419/darus-3316/129
title: reaction kinetics crystallinity FWHM.opju

description: :unav
DOI: 10.21942/uva.25428238
title: BiTSI

description: Dataset used in the paper "Sentiment-Driven Speculation in Financial Markets with Heterogeneous Beliefs: a Machine Learning approach" by Tommaso Di Francesco and Cars Hommes. It contains the BiTSI index, a sentiment index obtained by scraping Twitter for all posts containing the term "Bitcoin" from November 1, 2019, to December 30, 2022. Ohter data are daily Bitcoin Price and the Risk-free rate proxied by the  Market Yield on U.S. Treasury Securities at 1-Year Constant Maturity.
DOI: 10.21942/uva.25428238.v1
title: BiTSI

description: Dataset used in the paper "Sentiment-Driven Speculation in Financial Markets with Heterogeneous Beliefs: a Machine Learning approach" by Tommaso Di Francesco and Cars Hommes. It contains the BiTSI index, a sentiment index obtained by scraping Twitter for all posts containing the term "Bitcoin" from November 1, 2019, to December 30, 2022. Ohter data are daily Bitcoin Price and the Risk-free rate proxied by the  Market Yield on U.S. Treasury Securities at 1-Year Constant Maturity.
DOI: 10.18419/darus-3316/130
title: blender-new1.png

description: :unav
DOI: 10.18419/darus-3348/1
title: SBA-15_N2_M2_analysis-adsorption-branch.txt

description: :unav
DOI: 10.18419/darus-3348/2
title: SBA-15_sa_Particle8b.dm3

description: :unav
DOI: 10.18419/darus-3348/3
title: SBA-15_Particle2.dm3

description: :unav
DOI: 10.18419/darus-3348/4
title: OMS_TLCT_N2_M3_raw-data.qps

description: :unav
DOI: 10.18419/darus-3348/5
title: MCM-41_N2_M1_analysis-desorption-branch.txt

description: :unav
DOI: 10.18419/darus-3348/6
title: SBA-15_N2_M1_analysis-desorption-branch.txt

description: :unav
DOI: 10.18419/darus-3348/7
title: OMS_TLCT_Particle4.tif

description: :unav
DOI: 10.18419/darus-3348/8
title: OMS_TLCT_N2_M2_analysis-desorption-branch.txt

description: :unav
DOI: 10.18419/darus-3348/9
title: OMS_TLCT_Particle5b.dm3

description: :unav
DOI: 10.18419/darus-3348/10
title: SBA-15_Particle4.dm3

description: :unav
DOI: 10.18419/darus-3348/11
title: OMS_TLCT_deconvoluted.pdh

description: :unav
DOI: 10.18419/darus-3348/12
title: Overview_SBA-15_Particle1-2-3.dm3

description: :unav
DOI: 10.18419/darus-3348/13
title: OMS_TLCT_Particle1f.dm3

description: :unav
DOI: 10.18419/darus-3348/14
title: MCM-41_N2_M2_raw-data.RAW

description: :unav
DOI: 10.18419/darus-3348/15
title: MCM-41_Particle6a.dm3

description: :unav
DOI: 10.18419/darus-3348/16
title: MCM-41_Particle7.dm3

description: :unav
DOI: 10.18419/darus-3348/17
title: SBA-15_Particle5.dm3

description: :unav
DOI: 10.18419/darus-3348/18
title: Overview_SBA-15_Particle6-7-8-9.dm3

description: :unav
DOI: 10.18419/darus-3348/19
title: MCM-41_Particle3.tif

description: :unav
DOI: 10.18419/darus-3348/20
title: SBA-15_sa_Particle2.tif

description: :unav
DOI: 10.18419/darus-3348/21
title: SBA-15_sa_Particle3.tif

description: :unav
DOI: 10.18419/darus-3348/22
title: MCM-41_Particle3.dm3

description: :unav
DOI: 10.18419/darus-3348/23
title: SBA-15_N2_M1_analysis-adsorption-branch.txt

description: :unav
DOI: 10.18419/darus-3348/24
title: SBA-15_sa_Particle1.dm3

description: :unav
DOI: 10.18419/darus-3348/25
title: OMS_TLCT_Particle2b.tif

description: :unav
DOI: 10.18419/darus-3348/26
title: OMS_TLCT_Particle1d.dm3

description: :unav
DOI: 10.5281/zenodo.10820337
title: KoestlerEtAlEpigeneticsAndChromatin2024_STEDdata

description: Folder 1 contains the raw STED microscopy data in tiff format and the rois used for the measurements in ImageJ/Fiji.
File 2 contains the measurements of the Histone peak distances along fibres displaying H3K4me3 or H3K27me3 for peak detection tolerance 0.17 and 1.0 as used for Figure 5ABC.
Folder 3 contains the intensity measurements of pan-Histones, H3K4me3 and H3K27me3 along the chromatin fibres as used for Figure 5ABDE.
DOI: 10.5281/zenodo.10820338
title: KoestlerEtAlEpigeneticsAndChromatin2024_STEDdata

description: Folder 1 contains the raw STED microscopy data in tiff format and the rois used for the measurements in ImageJ/Fiji.
File 2 contains the measurements of the Histone peak distances along fibres displaying H3K4me3 or H3K27me3 for peak detection tolerance 0.17 and 1.0 as used for Figure 5ABC.
Folder 3 contains the intensity measurements of pan-Histones, H3K4me3 and H3K27me3 along the chromatin fibres as used for Figure 5ABDE.
DOI: 10.18419/darus-3348/27
title: OMS_TLCT_Particle1b.tif

description: :unav
DOI: 10.18419/darus-3348/28
title: SBA-15_sa.pdh

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DOI: 10.18419/darus-3348/29
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