cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.2677922
title: Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen

description: <strong>Motivation: </strong>As a proxy for diseased cells, a cell line cannot be thought of as a perfect model. Many diseases feature an important molecular heterogeneity. Consequently, a drug may be effective against one molecular subtype of a disease, but less so against another. To characterise drugs with respect to their effect not only on one cell line but on a consensus of several is therefore a promising strategy to streamline the drug discovery process.

<strong>Results: </strong>The contribution of this paper is twofold. First, we investigate whether we can predict MOA at the molecular level without optimisation of the MOA classes to the screen specificities. To this end, we benchmark a set of algorithms within a conventional pipeline, and evaluate their MOA prediction performance according to a statistically rigorous framework. Second, we extend this conventional pipeline to the simultaneous analysis of multiple cell lines, each with potentially different morphological baselines. For this, we propose multitask autoencoders, including a domain-adaptive model used to construct domain-invariant feature representations across cell lines. We apply these methods to a pilot screen of two triple negative breast cancer cell lines as models for two different molecular subtypes of the disease.
DOI: 10.5281/zenodo.2677923
title: Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen

description: <strong>Motivation: </strong>As a proxy for diseased cells, a cell line cannot be thought of as a perfect model. Many diseases feature an important molecular heterogeneity. Consequently, a drug may be effective against one molecular subtype of a disease, but less so against another. To characterise drugs with respect to their effect not only on one cell line but on a consensus of several is therefore a promising strategy to streamline the drug discovery process.

<strong>Results: </strong>The contribution of this paper is twofold. First, we investigate whether we can predict MOA at the molecular level without optimisation of the MOA classes to the screen specificities. To this end, we benchmark a set of algorithms within a conventional pipeline, and evaluate their MOA prediction performance according to a statistically rigorous framework. Second, we extend this conventional pipeline to the simultaneous analysis of multiple cell lines, each with potentially different morphological baselines. For this, we propose multitask autoencoders, including a domain-adaptive model used to construct domain-invariant feature representations across cell lines. We apply these methods to a pilot screen of two triple negative breast cancer cell lines as models for two different molecular subtypes of the disease.
DOI: 10.6080/k0571975
title: Data collection curated with an application ontology describes the methods and
 results upon performing an ex-vivo voltage-clamp assay on outer hair cells of the mammalian cochlea.
title: CRCNS.org ear-1

description: This data collection describes the electrical properties of outer hair cells isolated from the mammalian cochlea of the domestic guinea pig.  This data was obtained by performing whole-cell patch clamp voltage clamp assay on cells and monitoring the electrical admittance during a DC voltage ramp.  The membrane capacitance was then calculated at each membrane potential from this admittance, and the voltage-independent and voltage-dependent membrane capacitance was determined upon further analysis.  In some case the DC conductance was also measured by interrogation of the cell with voltage-step function which was calculated from the change in the mean steady-state current with respect to DC voltage.  The data collection contains results from 89 cells isolated from the domestic guinea pig.
This data was originally stored in MATLAB in an unstructured format.  Each recording form a cell was described by 82 fields with the struct format and the collection was stored as an array of structures.  This data has now been curated by a collaboration between the scientist and data architect and is now described with a variant of the Ontology of Biological Investigation (OBI) coined OBI based Inner Ear Electrophysiology (OBI_IEE)).  The data has been transformed to the non-proprietary format:  Hierarchical Data Format version 5 (HDF5) format where this application ontology was mirrored to provide the metadata and nested data architecture within HDF5.  Each digital specimen is displayed in a tree configuration (like directories in a computer) and consists of six main branches based on the ontology classes.  
The curation and archiving of the data set is described in
1.Farrell B, Bengtson J. Ontology based data architecture to promote data sharing in electrophysiology. In: P.  Jaiswal LC, M. A. Haendel, C. J. Mungall editor. Proceedings of the 9th International Conference on Biological Ontology (ICBO); August 7-10, 2018; Corvallis, Oregon, USA2018. http://ceur-ws.org/Vol-2285/ 
2.Farrell, B and J. Bengtson.  2019. Scientist and data architect collaborate to curate and archive an inner ear electrophysiology data collection.  Submitted for publication
The experimental methods and results are described in 
3.Corbitt C, Farinelli F, Brownell WE, Farrell B. Tonotopic relationships reveal the charge density varies along the lateral wall of outer hair cells. Biophys J. 2012 2012/06/20/;102(12):2715-24. PubMed PMID: 22735521. 
4.Paper that describe some new scientific findings from this data collection are being submitted concurrently with paper number (2) above.
DOI: 10.17036/researchdata.aston.ac.uk.00000425
title: PyScale: A software package for property analysis of nucleotide sequences
DOI: 10.5281/zenodo.2652191
title: Thermal regimes, but not mean temperatures, drive patterns of rapid climate adaptation at a continent-scale: evidence from the introduced European earwig across North America

description: Full data set + R script
DOI: 10.5281/zenodo.2652192
title: Thermal regimes, but not mean temperatures, drive patterns of rapid climate adaptation at a continent-scale: evidence from the introduced European earwig across North America

description: Full data set + R script
DOI: 10.17632/jcyw474zwr.1
title: Data for: Inactivation of Shiga-toxin-producing Escherichia coli, Salmonella enterica and Natural Microflora on Tempered Wheat Grains by Atmospheric Cold Plasma

description: Microbial inactivation on wheat grains treated with atmospheric cold plasma
DOI: 10.17632/bpr22bcm9d.1
title: Data for: Pseudo-projection approach to reconstruct locations of point-like scatterers by Lame parameters and mass densities in an elastic half-space

description: These are source code as well as the data to obtain the results presented in the article.
DOI: 10.17632/8jcbgvxmd7.1
title: Data for: New method for evaluating winter air quality: PM2.5 assessment using Community Multi-Scale Air Quality Modeling (CMAQ) in Xi'an

description: Data sets for "New method for evaluating winter air quality: PM2.5 assessment using Community Multi-Scale Air Quality Modeling (CMAQ) in Xi’an".
DOI: 10.17632/nnnpg784tf.1
title: Data for: New method for evaluating winter air quality: PM2.5 assessment using Community Multi-Scale Air Quality Modeling (CMAQ) in Xi'an

description: Datasets for ATMENV-D-18-00359R3
DOI: 10.5258/soton/d0911
title: Optical ruler dataset

description: Dataset for "Detecting nanometric displacements with optical ruler metrology" published in Science.
DOI: 10.5281/zenodo.2683855
title: Reference data for MITOS

description: Reference data for MITOS. Contains

- fasta databases for the BLAST searches (RefSeq release 39)

- automatically covariance models for ncRNA searches (for tRNAs the models are taken from MiTFi http://dx.doi.org/10.1093/nar/gkv746)

As described in http://dx.doi.org/10.1016/j.ympev.2012.08.023
DOI: 10.5281/zenodo.2683856
title: Reference data for MITOS

description: Reference data for MITOS. Contains

- fasta databases for the BLAST searches (RefSeq release 39)

- automatically covariance models for ncRNA searches (for tRNAs the models are taken from MiTFi http://dx.doi.org/10.1093/nar/gkv746)

As described in http://dx.doi.org/10.1016/j.ympev.2012.08.023
DOI: 10.17037/data.00001114
title: Read / ICD-10 Code List - Cancer

description: Read and mapped ICD-10 codes for Cancer sites of interest and exclusive criteria (exposure).
DOI: 10.17037/data.00001117
title: Exposure Code List - Cardiovascular disease (ICD-10)

description: ICD-10 codes for cardiovascular diseases of interest and general codes used in all CVD covariate. Based on CALIBER approach.
DOI: 10.17037/data.00001119
title: Exposure Code List - Revascularisation (OPCS)

description: OPCS codes for Revascularisation. Based on CALIBER approach.
DOI: 10.17037/data.00001120
title: Covariate Code List - Smoking status

description: Read codes for smoking status with categorisation.
DOI: 10.17037/data.00001122
title: Covariate Code List - Diabetes

description: Read codes for diabetes with categorisation. Based on CALIBER approach.
DOI: 10.17037/data.00001124
title: Covariate Code List - Statins

description: Product codes for Statins based on British National Formulary (BNF) codes, drug substance and product names.
DOI: 10.17632/nbpwttjhht.1
title: Data for: To hide or to feed: an evaluation of personality traits in the sand bubbler crab, Dotilla wichmanni, when responding to human disturbance

description: Foraging and risk-taking responses of sand bubbler crab, Dotilla wichmanni, to human disturbance.
DOI: 10.17632/nkx7z2zfmn.1
title: Presidential election

description: Data of the study on redistributive behavior in the 2017 French presidential election
DOI: 10.17037/data.00001121
title: Covariate Code List - Alcohol status

description: Read codes for alcohol status with categorisation (see Supplementary table A1).
DOI: 10.17037/data.00001123
title: Covariate Code List - Diabetes drugs

description: Product codes for diabetes drugs with categorisation.
DOI: 10.17037/data.00001125
title: Covariate Code List - Beta blockers

description: Product codes for beta blockers based on British National Formulary (BNF) codes, drug substance and product names
DOI: 10.17037/data.00001126
title: Covariate Code List - ACE inhibitors

description: Product codes for ACE inhibitors (Angiotensin-converting enzyme) based on British National Formulary (BNF) codes, drug substance and product names.
DOI: 10.17037/data.00001127
title: Covariate Code List - ARBs

description: Product codes for Angiotensin II Receptor Blockers (ARBs) based on British National Formulary (BNF) codes, drug substance and product names.
DOI: 10.17037/data.00001128
title: Covariate Code List - NSAIDs

description: Product codes for Nonsteroidal anti-inflammatory drugs (NSAIDs)  based on British National Formulary (BNF) codes, drug substance and product names.
DOI: 10.17037/data.00001132
title: Covariate Code List - Lupus

description: Read codes for Systemic lupus erythematosus, including localised and unspecified.
DOI: 10.17037/data.00001130
title: Covariate Code List - Hysterectomy

description: Read codes for hysterectomy
DOI: 10.17037/data.00001133
title: Covariate Code List - Sclerosis

description: Read codes for sclerosis. Search strategy developed from https://doi.org/10.1136/annrheumdis-2012-202007.
DOI: 10.17037/data.00001134
title: Covariate Code List - COPD

description: Read codes for Chronic Obstructive Pulmonary Disorder (COPD).
DOI: 10.17037/data.00001135
title: Covariate Code List - Migraine

description: Read codes for migraine. Strategy broadly based on QRisk3 definition.
DOI: 10.17037/data.00001136
title: Covariate Code List - Serum creatinine

description: Read codes indicating serum creatinine/renal function testing.
DOI: 10.17037/data.00001137
title: Covariate Code List - Chronic liver disease

description: Read codes for chronic liver disease.
DOI: 10.17632/sc7hmvcmjf.1
title: Data for: Not the usual suspects: Critical indicators in a dollarized country’s Financial Stress Index
DOI: 10.5281/zenodo.2682546
title: Raw simulation data of response of the PATE particle telescope to electrons

description: The dataset consists of multiple files, one incident energy per file. The electron distribution is spherically symmetric, the simulated particles are radiated from the inner surface of a sphere with a radius of 10 cm which encloses the entire telescope assembly. The initial angular distribution of the electrons is Lambertian uniform. 

<strong>File naming schema</strong>: e_MONO_{ENERGY, MeV}_MeV_{COUNT, pcs}_count_{SERIAL NUMBER}.dat 

For example, a file with a serial number <strong>665</strong> which contains data for <strong>2.4E+8</strong> simulated electrons with <strong>70 keV</strong> energy is named "e_MONO_<strong>00.07</strong>_MeV_<strong>240000000</strong>_count_<strong>665</strong>.dat"

<strong>The data structure is the following:</strong>

Each line represents a detected particle. The detection means that a particle (including secondaries) deposited at least 50 keV at least in one of the sensitive silicon volumes. From the particle telescope view, there is no means to distinguish between particle flavors at the time of ionization and readout, thus no secondaries are treated separately.

The particle record has 11 fields with signed decimal floating point values. The fields are separated by a single tab character ('\t'). There is no tab at the end of the line, the line ending is UNIX ('\n')

The first eight floats are deposited energies in the sensitive silicon volumes of the detectors in the detector stack of the PATE instrument. They come in the following order: D1a D1b D1c D2a D2b D3 AC1 AC2. The next is the angle between the telescope axis and the incident particle momentum as seen by the D1 plate, or <strong>-888.0</strong> in case D1 has less than 50 keV of deposited energy. The next field is the angle between the telescope axis and the incident particle momentum at the starting point. <strong>All angles are in degrees</strong>. The last field is redundant, it contains the incident particle energy in <strong>MeV</strong>.

<strong>Example:</strong>

0       0       0.050963        0       0       0       0       0       12.728  8.9272  0.055

This line represents a 55 keV particle detection, which has deposited 50.963 keV in the D1c detector. The particle was shot at 8.9272 degrees to the telescope axis, at the time it crossed the border of the sensitive volume it had a momentum direction at 12.728 degrees to the telescope axis.
DOI: 10.5281/zenodo.2682547
title: Raw simulation data of response of the PATE particle telescope to electrons

description: The dataset consists of multiple files, one incident energy per file. The electron distribution is spherically symmetric, the simulated particles are radiated from the inner surface of a sphere with a radius of 10 cm which encloses the entire telescope assembly. The initial angular distribution of the electrons is Lambertian uniform. 

<strong>File naming schema</strong>: e_MONO_{ENERGY, MeV}_MeV_{COUNT, pcs}_count_{SERIAL NUMBER}.dat 

For example, a file with a serial number <strong>665</strong> which contains data for <strong>2.4E+8</strong> simulated electrons with <strong>70 keV</strong> energy is named "e_MONO_<strong>00.07</strong>_MeV_<strong>240000000</strong>_count_<strong>665</strong>.dat"

<strong>The data structure is the following:</strong>

Each line represents a detected particle. The detection means that a particle (including secondaries) deposited at least 50 keV at least in one of the sensitive silicon volumes. From the particle telescope view, there is no means to distinguish between particle flavors at the time of ionization and readout, thus no secondaries are treated separately.

The particle record has 11 fields with signed decimal floating point values. The fields are separated by a single tab character ('\t'). There is no tab at the end of the line, the line ending is UNIX ('\n')

The first eight floats are deposited energies in the sensitive silicon volumes of the detectors in the detector stack of the PATE instrument. They come in the following order: D1a D1b D1c D2a D2b D3 AC1 AC2. The next is the angle between the telescope axis and the incident particle momentum as seen by the D1 plate, or <strong>-888.0</strong> in case D1 has less than 50 keV of deposited energy. The next field is the angle between the telescope axis and the incident particle momentum at the starting point. <strong>All angles are in degrees</strong>. The last field is redundant, it contains the incident particle energy in <strong>MeV</strong>.

<strong>Example:</strong>

0       0       0.050963        0       0       0       0       0       12.728  8.9272  0.055

This line represents a 55 keV particle detection, which has deposited 50.963 keV in the D1c detector. The particle was shot at 8.9272 degrees to the telescope axis, at the time it crossed the border of the sensitive volume it had a momentum direction at 12.728 degrees to the telescope axis.
DOI: 10.17037/data.00001138
title: Covariate Code List - Immunosuppressive disease

description: Read codes for transplant, HIV and immunosuppression
DOI: 10.17632/x95kz52rv9.1
title: Data for: Adaptive Partitioning of the tRNA Interaction Interface by Aminoacyl-tRNA-Synthetases

description: Supplementary data for Collins-Hed and Ardell (2019), including atINFLAT.py python script
DOI: 10.17037/data.00001139
title: Covariate Code List - Immunosuppressive drugs

description: Product codes for immunosuppressive drugs.
DOI: 10.17037/data.00001140
title: Covariate Code List - Obstructive sleep apnoea

description: Read codes for obstructive sleep apnoea
DOI: 10.17037/data.00001142
title: Covariate Code List - Severe mental illness

description: Read codes for severe mental illness. Strategy broadly based on QOF defintion / codes for schizophrenia, bipolar, moderate / severe and depression; also includes psychosis and psychoses)
DOI: 10.17037/data.00001141
title: Covariate Code List - Coeliac disease

description: Read codes for Coeliac disease.
DOI: 10.17632/yckxs3r7j2.1
title: Data for: FANCM, RAD1, CHEK1 and TP53I3 Act as BRCA-like Tumor Suppressors and are Mutated in Hereditary Ovarian Cancer

description: Data from functional analysis
DOI: 10.17632/8hmdp3k4hp.1
title: Data for: Manipulations to between-person contextual interference through mismatched practice of golf putting skills

description: These are excel files showing individual means for each pre-test, practice and retention block where relevant, for all measures detailed in the manuscript.
DOI: 10.15129/286a189f-07be-466c-8cca-bb0de1a8bdc0
title: Lung Cancer Stigma: A Concept with consequences for patients

description: The data file contains all the data collected from the participants within this study. Data was collected using hard copy questionnaires from 201 patients diagnosed with lung cancer. For anonymity, the column 'postcode' is blank in the data set uploaded to this repository. 

Access to the dataset is restricted due to ethical constraints
DOI: 10.17632/jtrn48kw3y.1
title: Data for: Geochemical characteristics and potential biogeochemical effect of water-soluble ions in atmospheric aerosols over the western boundary regions of Pacific Ocean
DOI: 10.4119/unibi/2934028
title: MovVis: A movement visualization toolbox for Matlab and Octave

description: MovVis creates videos and animated gifs of input movement data. MovVis can display movements in any speed. MovVis has three options for aligning multiple movements. MovVis can display movements on a chosen background image. MovVis can display movements with desired visual attributes.
DOI: 10.21227/rxjz-rc23
title: Demands for bus ridesharing in Shanghai, China

description: This is the dataset used in the experiment of paper "Bus-Pooling: A Large-Scale Bus Ridesharing Service". The dataset contains 4,891,984 trajectory data from 4,000 Shanghai taxis from one day (Feb 20, 2007), and 66,369 trips are extracted from the trajectory data. The 100 groups of coordinate sets containing three coordinates as experimental samples are used to compare the effectiveness and efficiency of location-allocation algorithms. Each set of coordinates is the pickup and delivery point randomly extracted from 66,369 trips.
DOI: 10.17632/sgn5w9rdt9.1
title: Data for: The redistribution of B concentration and its isotopes during low-grade metamorphism: Observations in metapelites from the Central Range, Taiwan

description: The minerology and B isotopic ratios of metapelites along a contineous profile of prograding metamorphism.
DOI: 10.5281/zenodo.2677926
title: Genomes plasmids MDR B. fragilis ONT sequence read files in fastq format

description: Supporting data for the manuscript <em>Complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids.</em>

Oxford Nanopore reads demultiplexed with Deepbinner v0.2.0 and base-called (with demultiplexing) using Albacore v2.3.3. Barcodes and adapters were removed with Porechop v0.2.4 with the --discard_middle option.

Data from each isolate was produced from two runs per isolate. Data for the individual runs are included here. They can easily be concatenated eg with cat. Runs are named TVS_01,. TVS_02, TVS_03 and TVS_04.

Fast5 (only demultiplexed with deepbinner and basecalled with albacore) as well as illumina reads and genome assemblies can be found via the NCBI bioproject accessions:

Isolates, NCBI bioproject accession no:

CCUG4856T, PRJNA525024

BFO17, PRJNA244943

BFO18, PRJNA244944

S01, PRJNA244942

BFO42, PRJNA253771

BFO67, PRJNA254401

BFO85, PRJNA254455

 

<strong>md5sum's (also found in the file md5.md5):</strong>

135d0570a1e49e25c8fde59f321cca68  BFO17_TVS_03_99377.barcode02_trimmed.fastq.gz<br>
3c6ca800a1f735937c0cffccd263fb82  BFO18_TVS_01_97673.barcode03_trimmed.fastq.gz<br>
dc37823950f529d3a859b7a7c514af8c  BFO18_TVS_03_99377.barcode03_trimmed.fastq.gz<br>
abd707404f9ebbc38652e45ed378ca21  BFO42_TVS_02.barcode10_trimmed.fastq.gz<br>
9761e9ab082e276624c5778dcbeaffd2  BFO42_TVS_04.barcode10_trimmed.fastq.gz<br>
ffc27009c0f7fead1af84ce045dbe5f3  BFO67_TVS_02.barcode09_trimmed.fastq.gz<br>
06c363a7feeeb88f9d195b3769b37f2b  BFO67_TVS_04.barcode09_trimmed.fastq.gz<br>
5553c95cc98f4b9d4cfb38c4f8f8f037  BFO85_TVS_02.barcode08_trimmed.fastq.gz<br>
b1a8013cba7a079cee6d3bdd6cd97ff2  BFO85_TVS_04.barcode08_trimmed.fastq.gz<br>
8169225219a5fb20935d5f0304aa80c5  CCUG4856T_TVS_01_97673.barcode01_trimmed.fastq.gz<br>
a509b0ae912a798a91e677795198c1c6  CCUG5846T_TVS_03_99377.barcode01_trimmed.fastq.gz<br>
8a9d2eb8b626a6e87ed267d31aa220e3  S01_TVS_01_97673.barcode04_trimmed.fastq.gz<br>
69e239a17becc25a4f103dfc3bf5886a  S01_TVS_03_99377.barcode04_trimmed.fastq.gz