cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.1411210
title: Fantom5 Transcribed Enhancers In Mm10

description: <strong>Overview</strong>

Transcribed enhancers were identified and their expression was quantified across all human FANTOM5 libraries, following the re-aligned FANTOM5 CAGE data upon mm10 (GRCm38) (obtained from http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v1/basic/), and decomposition-based peak identification (obtained from https://zenodo.org/record/545682#.WPuNy1Pyv2Q) by Kawaji, Hideya.

<strong>Description</strong>

Transcribed enhancers were called based on bidirectional balanced RNA signatures as per Andersson et al (2014). Enhancers were only identified distal to known exons (+/-100bp region from boundaries) and transcription start sites (+/-300bp), defined by GENCODE vM7 annotation. In total, 44,138 enhancers were identified across 1,068 libraries and the expression was quantified. For details regarding the identification of transcribed enhancers from CAGE data, please see Andersson et al (2014) and blog post.

Due to varying noise levels across FANTOM5 libraries and the intrinsic low expression levels of transcribed enhancers, library-specific noise levels were estimated to define of robust set of enhancers in each sample. In summary, for each library, expression was quantified in randomly sampled genomic regions distal to assembly gaps, DNase hypersensitive sites (ENCODE), known exons and gene TSSs (GENCODE vM7) to create a genomic background expression distribution. For each library, we called an enhancer active (used) if its expression was above the 99.9th quantile of the library’s genomic background expression distribution. The robust set of enhancers consist of those significantly expressed in at least one library.

While this approach ensures less permissive enhancer calling in noisy libraries, for some libraries the noise threshold is zero meaning that a single CAGE tag is sufficient for calling an enhancer active. Furthermore, the possibility of detecting enhancer transcription is affected by sequencing depth, so the number of active enhancers per library might not be biologically meaningful to compare when sequencing depths differ.

<strong>Data files</strong><br>
Each predicted enhancer is described in BED12 format with two blocks denoting the merged regions of transcription initiation on the minus and plus strands. The thickStart and thickEnd columns denote the inferred mid position between blocks of transcription initiation events. Expression and usage matrices are tab delimited and the first row gives the FANTOM5 CNhs IDs and the first column the enhancer ID (same as column 4 in BED file). Usage matrices contain zeroes and ones (0:not used, 1:used).


	enhancers (BED12 format)
	enhancer expression matrix (tab delimited, first row: CNhs IDs, first column: enhancer ID (coordinate))
	binary enhancer usage matrix (0:not used, 1:used, tab delimited, first row: CNhs IDs, first column: enhancer ID (coordinate))
DOI: 10.17632/cfsfb28zzn.2
title: Dataset for Corrosion Science Paper 2018

description: Excel pages with the processed data for the Figures included in paper.
DOI: 10.17632/mk8cjzjhd2.1
title: Tanshinone IIA attenuates TNF‐α induced PTX3 expression and monocyte adhesion to endothelial cells through the p38/NF‐κB pathway

description: Original figure-Western blotting
DOI: 10.17632/shfsd2z354.1
title: The BRCT domains of the BRCA1 and BARD1 tumor suppressors differentially regulate homology-directed repair and stalled fork protection. Billing et al
DOI: 10.5281/zenodo.1217817
title: Data For "The Hydrodynamic Response Of The Sediment-Water Interface To Coherent Turbulent Motions"

description: The data provided can be used to reproduce the figures presented in the manuscript titled "The hydrodynamic response of the sediment-water interface to coherent turbulent motions" submitted to Geophysical Research Letters.
DOI: 10.5281/zenodo.1217818
title: Data For "The Hydrodynamic Response Of The Sediment-Water Interface To Coherent Turbulent Motions"

description: The data provided can be used to reproduce the figures presented in the manuscript titled "The hydrodynamic response of the sediment-water interface to coherent turbulent motions" submitted to Geophysical Research Letters.
DOI: 10.17632/485swhn5tc.1
title: Regulation of neuroregeneration by long noncoding RNAs

description: Source data for panels in Ben-Tov Perry et al.
DOI: 10.17632/kszngyhpmt.1
title: Historical Data For Simulation_February-April

description: Historical production data
DOI: 10.17632/vdjz8vnnf7.1
title: Tanshinone IIA attenuates TNF‐α induced PTX3 expression and monocyte adhesion to endothelial cells through the p38/NF‐κB pathway

description: statistical data
DOI: 10.17632/w8jv9ngnsk.2
title: Proteomics explains client specificity of the human TRAP complex in ER protein import

description: In mammalian cells, one-third of all polypeptides are transported into/across the ER-membrane via the Sec61-channel. While the Sec61-complex facilitates translocation of all polypeptides with amino-terminal signal peptides (sp) or transmembrane helices, the Sec61-associated TRAP-complex supports translocation of only a subset, i.e. in a substrate-specific manner. To characterize TRAP-dependent precursors, we combined siRNA-mediated TRAP depletion in human cells, label-free quantitative proteomics, and differential expression analysis. The results were validated by western blotting and quantitative RT-PCR as well as under conditions of over-production of TRAP-dependent precursors and their mutated variants in the presence or absence of MG132, a proteasome inhibitor. Sp analysis of TRAP-clients revealed above-average glycine-plus-proline content as the distinguishing feature. Thus, TRAP acts as an sp-receptor on the ER-membrane’s cytosolic face for precursor polypeptides with high glycine-plus-proline content in their sp and triggers substrate-specific (and regulated) opening of the Sec61-channel by its interaction with the ER-lumenal hinge of Sec61α. The work is about to be published under the title Proteomics reveals signal peptide features determining the client specificity in human TRAP-dependent ER protein import by Duy Nguyen, Regine Stutz, Stefan Schorr, Sven Lang, Stefan Pfeffer, Hudson H. Freeze, Friedrich Förster, Volkhard Helms1 Johanna Dudek & Richard Zimmermann Here we present the original western blot data plus additional SP and TMH analyses, which are presented in a pptx figure and a xlsx table, respectively . Additional physicochemical properties of TRAP clients with SP or TMH. In addition to the hydrophobicity score and glycine/proline (GP) content, we determined the ΔGapp values of SP sequences (a) and transmembrane helices (TMH) (b) with the ΔGapp predictor for TM helix insertion (http://dgpred.cbr.su.se) and plotted these values against the relative count (Density). Glycine and glycine plus proline content of human signal peptides. We used custom scripts to compute the glycine (G) and glycine plus proline (GP) content of human SP sequences from UniProtKB entries. GP content was calculated as the total fraction of glycine and proline in the respective sequence. Notably, 1382 SP of a total of 3513 have a GP content of &gt; 15%, the proposed threshold for TRAP involvement and, therefore, potential regulation by phosphorylation and/or calcium binding by TRAP subunit α.
DOI: 10.5281/zenodo.1411979
title: Nonhuman Primate Reaching With Multichannel Sensorimotor Cortex Electrophysiology: Broadband For Indy_20161014_04

description: This dataset supplements https://doi.org/10.5281/zenodo.583331 .<br>
<br>
<strong>General description.</strong> These data consist of extracellular neural recordings ("broadband") from primate subject "Indy", session identifier "indy_20161014_04".

<strong>Filtering. </strong>The data are sampled at 24414.0625 Hz and are unfiltered, except for an anti-aliasing filter built-in to the recording amplifier: a 4th order low-pass with a roll-off of 24 dB per octave at 7.5 kHz, operating at the sampling rate.

<strong>File format.</strong> The data are contained in an HDF5 formatted file, organized according to the Neurodata Without Borders (NWB) version 1.0.6 specification.

<strong>Datasets. </strong>A few of the relevant dataset paths are listed here for convenience. In the below, <em>n</em> refers to the number of recording channels and <em>k</em> refers to the number of samples.


	"/acquisition/timeseries/broadband/data" - k x n
	
		The broadband neural recordings.
	
	
	"/acquisition/timeseries/broadband/data/conversion" (scalar attribute)
	
		When multiplied by each sample converts the data into units of volts.
	
	
	"/acquisition/timeseries/broadband/timestamps" - k x 1
	
		Timestamps for each sample, seconds.
	
	
	"/general/extracellular_ephys/electrode_map" - n x 3
	
		The relative coordinates of each electrode contact (x, y, z), meters.
	
	


Please refer to the master dataset for further information.
description: This research was supported by the Congressionally Directed Medical Research Program (W81XWH-14-1-0510). JEO was supported by fellowship #2978 from the Paralyzed Veterans of America. JGM was supported by a fellowship from the Swartz Foundation.
DOI: 10.7298/x4r78cc1
title: Data supplement to: Near-field model for a high-momentum negatively buoyant line source within a three-dimensional hydrostatic lake model
DOI: 10.17632/y2b9sjnd88.1
title: Relating frontrunner retailers’ carbon and energy intensity to policy, strategy and building practice

description: The tables present retrieved data concerning the energy intensity (EI) and carbon intensity (CI) of the highest revenue retailers. Benchmarks were calculated for food and non-food retailers, applying the statistic function "Q1" for EI and CI "best practice" reference levels, where frontrunner retailers can be found.
DOI: 10.17632/4hwy8rz7vh.1
title: Data for: Experimental chronic traffic noise exposure alters adult and nestling corticosterone levels, and reduces nestling body condition in a free-living bird

description: Data set (sheet 1) and explanations (sheet 2) for experimental tests of traffic noise on tree swallow corticosterone levels (in adults and nestlings), parental feeding behavior, and nestling body condition.
DOI: 10.5281/zenodo.1410856
title: Ev Data Monitoring

description: Electric Vehicle (EV) data collected by Emotion, expert Italian company specialized in the sector of electric mobility, partner of SOFIE project.

These data were collected using a particular OBD device connected on each EV. OBD communicates using a TCP/IP system.

Data shown in this dataset were updated every 10 seconds.
DOI: 10.5281/zenodo.1410857
title: Ev Data Monitoring

description: Electric Vehicle (EV) data collected by Emotion, expert Italian company specialized in the sector of electric mobility, partner of SOFIE project.

These data were collected using a particular OBD device connected on each EV. OBD communicates using a TCP/IP system.

Data shown in this dataset were updated every 10 seconds.
DOI: 10.17632/wtwhbtmypc.1
title: Data for: A new temperature-dependent strategy to modulate the epidermal growth factor receptor

description: This dataset contains the DNA constructs of EGFR-ELPs and raw/processed data support the temperature-dependent activation and internalization of EGFR-ELPs.
DOI: 10.17632/zz6sgk6syg.1
title: Robot-Assisted Gait training versus Conventional Therapy in Severe Multiple Sclerosis patients
DOI: 10.17632/c79z6gz9rm.1
title: Development of Annotated Bangla Speech Corpora

description: This dataset contains Bangla read speech corpora which can be used for phonetic research and developing speech applications. Several criteria were maintained in the corpora development process that includes considering the phonetic and prosodic features during text selection. On the other hand, a specification was maintained in the recording phase as the speaking style is a vital part in speech applications. We also concentrated on proper text normalization, pronunciation, aligning, and labeling. The labeling was done manually – in the present endeavor sentence level labeling (annotation) was completed by maintaining a specification so that it could be expanded in future.
DOI: 10.17632/v2rpgbvhfr.2
title: PGC-1α Controls Skeletal Stem Cell Fate and Bone-Fat Balance in Osteoporosis and Skeletal Aging by Inducing TAZ

description: Provided here are the raw images and results for relevant data associated with the correction regarding the below manuscript: PGC-1α Controls Skeletal Stem Cell Fate and Bone-Fat Balance in Osteoporosis and Skeletal Aging by Inducing TAZ. Cell Stem Cell. 2018 Aug 2;23(2):193-209.e5. doi: 10.1016/j.stem.2018.06.009.
DOI: 10.5281/zenodo.1222171
title: Contribution Of Allelic Imbalance To Colorectal Cancer

description: <strong>Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge, and unbiased CRISPR-Cas9 knockout and activation screens identified altogether 79 genes within AI peaks regulating cell growth. Genetic and functional data implicates loss of TP53 as a sufficient driver of AI. The WGS highlights an influence of copy number aberrations on the rate of detected somatic point mutations. Importantly, the data reveal several associations between AI target genes, suggesting a role for a network of lineage-determining transcription factors in colorectal tumorigenesis. Overall, the results unravel the contribution of AI in colorectal cancer and provide a plausible explanation why so few genes are commonly affected by point mutations in cancers.</strong>
description: This work was supported by grants from the Jane and Aatos Erkko Foundation, Academy of Finland (Finnish Center of Excellence Program 2012–2017, 250345), the Finnish Cancer Society, the Finnish Cancer Foundation, the Paulo Foundation,  K. Albin Johanssons stiftelse, Päivikki and Sakari Sohlberg Foundation, Cancer Society of Finland, the State Research Funding, Integrated Life Science Doctoral Program (ILS), University of Helsinki, the Sigrid Juselius Foundation and SYSCOL (an EU FP7 Collaborative Project, 258236), the Novo Nordic Foundation (NNF14OC0012747), the Danish Cancer Society (R107-A7035 and R133-A8520), the Danish Council for Independent Research | Medical Science (DFF - 4183-00619), the Nordic Information for Action eScience Center (NIASC); a Nordic Center of Excellence financed by NordForsk (Project number 62721) and Nordic biobank-based study of causes and biomarkers of cancer: Pilot study financed by NordForsk 07 BM 11/424. We acknowledge the computational resources provided by the ELIXIR node hosted at CSC - IT Center for Science funded by the Academy of Finland (grants 271642, 263164) and the Ministry of Education and Culture, Finland. The Danish Cancer Biobank is acknowledged for biological material. We also acknowledge the support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council, and Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure.
description: {"references": ["Palin et.al. Contribution of allelic imbalance to colorectal cancer (2018) Nature Communications"]}
DOI: 10.5281/zenodo.1222172
title: Contribution Of Allelic Imbalance To Colorectal Cancer

description: <strong>Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge, and unbiased CRISPR-Cas9 knockout and activation screens identified altogether 79 genes within AI peaks regulating cell growth. Genetic and functional data implicates loss of TP53 as a sufficient driver of AI. The WGS highlights an influence of copy number aberrations on the rate of detected somatic point mutations. Importantly, the data reveal several associations between AI target genes, suggesting a role for a network of lineage-determining transcription factors in colorectal tumorigenesis. Overall, the results unravel the contribution of AI in colorectal cancer and provide a plausible explanation why so few genes are commonly affected by point mutations in cancers.</strong>
description: This work was supported by grants from the Jane and Aatos Erkko Foundation, Academy of Finland (Finnish Center of Excellence Program 2012–2017, 250345), the Finnish Cancer Society, the Finnish Cancer Foundation, the Paulo Foundation,  K. Albin Johanssons stiftelse, Päivikki and Sakari Sohlberg Foundation, Cancer Society of Finland, the State Research Funding, Integrated Life Science Doctoral Program (ILS), University of Helsinki, the Sigrid Juselius Foundation and SYSCOL (an EU FP7 Collaborative Project, 258236), the Novo Nordic Foundation (NNF14OC0012747), the Danish Cancer Society (R107-A7035 and R133-A8520), the Danish Council for Independent Research | Medical Science (DFF - 4183-00619), the Nordic Information for Action eScience Center (NIASC); a Nordic Center of Excellence financed by NordForsk (Project number 62721) and Nordic biobank-based study of causes and biomarkers of cancer: Pilot study financed by NordForsk 07 BM 11/424. We acknowledge the computational resources provided by the ELIXIR node hosted at CSC - IT Center for Science funded by the Academy of Finland (grants 271642, 263164) and the Ministry of Education and Culture, Finland. The Danish Cancer Biobank is acknowledged for biological material. We also acknowledge the support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council, and Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure.
description: {"references": ["Palin et.al. Contribution of allelic imbalance to colorectal cancer (2018) Nature Communications"]}
DOI: 10.17632/62kyt6cfp7.2
title: data for SiO2 aerogel–incorporated geopolymer insulation materials
DOI: 10.17632/8m599n5mk5.1
title: Dataset on Parabolic Dish Cooker in Omu-Aran, Kwara State.

description: The Date presents the Solar Irradiance, Ambient Temperatures, Absorber Plate Temperatures, Chamber Temperatures and Water Temperatures of a Parabolic Dish Cooker. The experimental investigations were carried out in Landmark University Engineering Workshop, Omu-Aran, Kwara State, Nigeria from June, 2017 to April, 2018. Parabolic Dish Cooker  Aperture diameter of the parabolic solar reflector=0.86m  Aperture area of the parabolic solar reflector = 0.581mm2  Focal Length of the solar parabolic reflector = 0.42cm  Rim Angle of the solar parabolic reflector = 54.2degree  Surface area of the parabolic reflector = 1.04mm2  Absorber Area for the parabola = 0.05mm2  Concentrating ratio = 12.0 Campbell Scientific LTD Pyranometer of ET106 weather station
DOI: 10.17632/gwdfwzsf6k.1
title: Data on Parabolic Dish Cooker

description: This data presents Solar Radiation, Ambient Temperatures, Chamber Temperatures, Water Temperatures and Absorber Temperatures for a Parabolic Dish Cooker. The specification of the Parabolic Dish Cooker are as follows:  Aperture diameter of the parabolic solar reflector=0.86m  Aperture area of the parabolic solar reflector = 0.58mm2  Focal Length of the solar parabolic reflector = 0.42cm  Rim Angle of the solar parabolic reflector = degree  Surface area of the parabolic reflector = 1.04mm2  Absorber Area for the parabola = 0.05mm2  Concentrating ratio = 12.0 Campbell Scientific LTD Pyranometer of ET106 weather station The experimental investigations were carried out in Landmark University Engineering Workshop, Omu-Aran, Kwara State, North Central Nigeria from June, 2017 to April, 2018.
DOI: 10.17632/mkwpbt5xz6.1
title: Clinical dataset of patients undergoing surgery with and without preoperatively usage of the ACS NSQIP Surgical Risk Calculator

description: This study investigated if postoperative complications could be reduced when using a Surgical Risk Calculator before surgery. Therefore two study groups were compared. The first study group (named Group Vorher) was operated in 2012 / 2013 without the preoperative usage of a Surgical Risk Calculator and contained 1040 patients. The comparison group (named Group Nachher), however, was operated in 2014 / 2015 using the Surgical Risk Calculator preoperativeley and contained overall 1065 patients. To compare the two study groups patients were matched via Propensity Score Matching using characteristics like age, sex, oncological intervention and American Society of Anesthesiologists Physical Status Classification. The actual occurred complications were graded via Clavien-Dindo Classification of Surgical Complications. Additionally, the results of the ACS NSQIP Surgical Risk Calculator for both study groups were compared. Two tables show an overview of all patients data before the propensity score matching. Patients that were not included in the matching are marked with three stars in the tables (***). After the matching 956 patients remained in each group. The third table shows an overview of the performed surgeries sorted by OPS-Code (Operation and Procedure Code) including only patients after the Propensity Score Matching.
DOI: 10.5281/zenodo.1134208
title: Raw Diffraction Images Of Smggds-558 And Farnesylated Rhoa Complex

description: Diffraction images of SmgGDS-558 and farnesylated RhoA complex (PDB code: 5ZHX).<br>
<br>
Small and large wedge (1, 5, 180, 360, .. degrees per crystal) datasets were collected from beamlines BL41XU and BL44XU at SPring-8 and BL1A at Photon Factory. PILATUS3 6M (BL41XU), MX300-HS (BL44XU), and EIGER X 4M (BL1A) detectors were used at wavelengths of 0.9 and 1.0 Å.

The crystals belonged to space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> with unit cell parameters a=93.3, b=181.8, c=205.3 Å.<br>
<br>
Electron density maps from various combinations of datasets were evaluated through KAMO, and finally data from 20161010_BL44XU/kozo0001 were merged and used for structural refinement at 3.5 Å resolution.<br>
<br>
Note that the master.h5 files were modified; see<br>
https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md
DOI: 10.5281/zenodo.1134209
title: Raw Diffraction Images Of Smggds-558 And Farnesylated Rhoa Complex

description: Diffraction images of SmgGDS-558 and farnesylated RhoA complex (PDB code: 5ZHX).<br>
<br>
Small and large wedge (1, 5, 180, 360, .. degrees per crystal) datasets were collected from beamlines BL41XU and BL44XU at SPring-8 and BL1A at Photon Factory. PILATUS3 6M (BL41XU), MX300-HS (BL44XU), and EIGER X 4M (BL1A) detectors were used at wavelengths of 0.9 and 1.0 Å.

The crystals belonged to space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> with unit cell parameters a=93.3, b=181.8, c=205.3 Å.<br>
<br>
Electron density maps from various combinations of datasets were evaluated through KAMO, and finally data from 20161010_BL44XU/kozo0001 were merged and used for structural refinement at 3.5 Å resolution.<br>
<br>
Note that the master.h5 files were modified; see<br>
https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md