cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25439/rmt.12665651.v4
title: Machine learning models and predictions for a nucleophilic substitution reaction in ionic liquids

description: Machine learning models were built based on published data for a nucleophilic substitution chemical reaction in ionic liquid-acetonitrile solvents. Models were built relating the rate constant of the reaction to the chemical structure of the ionic liquids.<br><b>Publication title</b>: Towards accurate predictions of the rate constants of organic processes in mixtures containing ionic liquids<br><b>Abstract: </b>The ability to tailor the constituent ions in ionic liquids (ILs) is highly advantageous as it provides access to solvents with a range of physicochemical properties. However, this benefit also leads to large compositional spaces that need to be explored to optimise systems, often involving time consuming experimental work. The use of machine learning methods is an effective way to gain insight based on existing data, to develop structure-property relationships and to allow the prediction of ionic liquid properties. Here we have applied machine learning models to experimentally determined rate constants of a representative organic process (the reaction of pyridine with benzyl bromide) in IL-acetonitrile mixtures. Multiple linear regression (MLREM) and artificial neural networks (BRANNLP) were both able to model the data well. The MLREM model was able to identify the structural features on the cations and anions that had the greatest effect on the rate constant. Secondly, predictive MLREM and BRANNLP models were developed from the full initial set of rate constant data. From these models, a large number of predictions (&gt;9000) of rate constant were made for mixtures of different ionic liquids, at different proportions of ionic liquid and molecular solvent, at different temperatures. A selection of these predictions were tested experimentally, including through the preparation of novel ionic liquids, with overall good agreement between the predicted and experimental data. This study highlights the benefits of using machine learning methods on kinetic data in ionic liquid mixtures to enable the development of rigorous structure-property relationships across multiple variables simultaneously, and to predict properties of new ILs and experimental conditions.
DOI: 10.5281/zenodo.4505518
title: Challenging programs for modular verification

description: Challenging programs for modular verification
DOI: 10.5281/zenodo.4505517
title: Challenging programs for modular verification

description: Challenging programs for modular verification
DOI: 10.6084/m9.figshare.13709953
title: Association between the nucleosome footprint profile of plasma cell-free DNA and response to neoadjuvant chemotherapy for breast cancer

description: Gene expression signatures have been used to predict the outcome of chemotherapy for breast cancer. The nucleosome footprint of cell-free DNA (cfDNA) carries gene expression information of the original tissues and thus may be used to predict the response to chemotherapy. Here we carried out the nucleosome positioning on cfDNA from breast cancer patients and healthy individuals and two cancer cell lines and MDA-MB-231 using low-coverage whole-genome sequencing (LCWGS) method.
DOI: 10.6084/m9.figshare.13709953.v1
title: Association between the nucleosome footprint profile of plasma cell-free DNA and response to neoadjuvant chemotherapy for breast cancer

description: Gene expression signatures have been used to predict the outcome of chemotherapy for breast cancer. The nucleosome footprint of cell-free DNA (cfDNA) carries gene expression information of the original tissues and thus may be used to predict the response to chemotherapy. Here we carried out the nucleosome positioning on cfDNA from breast cancer patients and healthy individuals and two cancer cell lines and MDA-MB-231 using low-coverage whole-genome sequencing (LCWGS) method.
DOI: 10.6084/m9.figshare.11965542
title: HIF-1 regulates energy metabolism of Tibetan chicken brain during embryo development under hypoxia

description: this is the source materilas of a paper related to hypoxia adaptation
DOI: 10.6084/m9.figshare.11965542.v1
title: HIF-1 regulates energy metabolism of Tibetan chicken brain during embryo development under hypoxia

description: this is the source materilas of a paper related to hypoxia adaptation
DOI: 10.25919/8vh1-nz53
title: Parkes observations for project P1050 semester 2020OCTS_10

description: This is a request for observing time for the timing campaign of new pulsar discoveries and follow-up of expected new potential pulsars from the re-processing of the low-latitude Galactic plane section of the HTRU survey (P630). We have now completed the first pass re-processing of the 62 % of the survey with GPU based coherent acceleration search and template bank search pipelines, and have discovered 51 previously unknown pulsars. Interesting science can usually only be derived from a new pulsar after confirmation and a follow-up timing campaign is carried out. One year of initial timing is the minimum timespan required to fully characterise any newly-discovered pulsars, essential for deriving pulsar parameters such as the characteristic age, magnetic field strength, spin-down rate, as well as to detect any unexpected behaviour of the pulsar which might result from emission instabilities. This timing project is necessary for following up on any interesting pulsar systems discovered from the HTRU Galactic plane survey. Since all of the pulsars on the observing list here have been confirmed in the current 2020APRS semester, the follow-up timing will produce completely new and exciting results. In addition, this timing project will enable a large-scale examination of the Galactic plane pulsar population, exploring the true boundaries of pulsar parameter space in the galactic plane.
DOI: 10.5281/zenodo.4498564
title: bsafdi/XMM_BSO_DATA: Instrument Responses

description: A repository containing the instrument responses for the analysis used in 2102.02207. The remainder of the data can be found on the paper's github, along with additional supplementary data. The response files are stored in the h5py format. TThere are two files, <code>XMM-BSO-dataset-MOS.hdf5</code> and <code>XMM-BSO-dataset-PN.hdf5</code>, which store the MOS and PN data, respectively. Within each file there are 30 rings, accessed with keys <code>ring_[1-30]</code>. The instrument response is provided with key <code>dtr</code> in [cm^2]. Additional information may be found in the github README.
DOI: 10.5281/zenodo.4498563
title: bsafdi/XMM_BSO_DATA: Instrument Responses

description: A repository containing the instrument responses for the analysis used in 2102.02207. The remainder of the data can be found on the paper's github, along with additional supplementary data. The response files are stored in the h5py format. TThere are two files, <code>XMM-BSO-dataset-MOS.hdf5</code> and <code>XMM-BSO-dataset-PN.hdf5</code>, which store the MOS and PN data, respectively. Within each file there are 30 rings, accessed with keys <code>ring_[1-30]</code>. The instrument response is provided with key <code>dtr</code> in [cm^2]. Additional information may be found in the github README.
DOI: 10.25345/c5jr4k
title: MassIVE MSV000086809 - High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip
title: Development and evaluation of nested nanowell (N2) chip in single-cell proteomics. The newly designed chip helps to improve the sensitivity and robustness of the tandem mass tag labeling approach by sizing down wells.
DOI: 10.5281/zenodo.4504922
title: A High-Accuracy GNSS Dataset of Ground Truth Points Collected within Îles-de-Boucherville National Park, Quebec, Canada

description: This dataset contains high accuracy (&lt; 10 cm error) GNSS ground truth measurements of the invasive reed <em>Phragmites australis </em>subsp. <em>australis </em>within Îles-de-Boucherville National Park (Quebec, Canada). The park, which has extensive stands of <em>P. australis </em>throughout the area, is one of the five study sites for the Canadian Biodiversity Airborne Observatory (CABO). The data were originally collected to serve as training and validation data for airborne hyperspectral imagery acquired in 2019 to assist with the detection and mapping of <em>P. australis </em>within the park, as no previous ground truth data had been collected at this site with such accurate measurements. In total, 320 ground truth points were collected, representing 158 locations where <em>P. australis</em> was present and 162 locations where it was absent. Auxiliary data includes detailed field notes and field photographs that provide context for each point, as well as a shapefile (.shp) containing all 320 points.
DOI: 10.6084/m9.figshare.13718386
title: Ribosomal protein database of Klebsiella oxytoca

description: This work presents the ribosomal protein database of <i>Klebsiella oxytoca</i>.<i> </i>Original data for the work came from the annotated proteome data of the bacterium downloaded from UniProt. Using an in-house MATLAB ribosomal protein database analysis software, the original proteome data file was parsed to extract protein name and amino acid sequence of all ribosomal proteins in the species. The database also includes calculated variables such as number of residues, molecular weight, and nucleotide sequence. Overall, the presented database could serve as a ribosomal protein mass fingerprint for use in microbial identification, or it could be used in fundamental studies seeking to uncover new insights into ribosomal protein biology.
DOI: 10.6084/m9.figshare.13718386.v1
title: Ribosomal protein database of Klebsiella oxytoca

description: This work presents the ribosomal protein database of <i>Klebsiella oxytoca</i>.<i> </i>Original data for the work came from the annotated proteome data of the bacterium downloaded from UniProt. Using an in-house MATLAB ribosomal protein database analysis software, the original proteome data file was parsed to extract protein name and amino acid sequence of all ribosomal proteins in the species. The database also includes calculated variables such as number of residues, molecular weight, and nucleotide sequence. Overall, the presented database could serve as a ribosomal protein mass fingerprint for use in microbial identification, or it could be used in fundamental studies seeking to uncover new insights into ribosomal protein biology.
DOI: 10.5281/zenodo.4505623
title: Data set for integrative modeling of the doublecortin - microtubule interaction

description: Data set for integrative modeling of the doublecortin - microtubule interaction.
DOI: 10.6073/pasta/ea971f57d961b6b488a1f5f14744536c
title: APT01 Daily precipitation amounts measured at multiple sites across konza prairie

description: Data set contains daily records of precipitation on 10 raingauges at 10 sites on Konza Prairie. Two sites (020A and 002C; SE) have 7-day clocks (one revolution per week), 7 have 24-hour clocks (one revolution per day), and the Headquarters raingauge generates daily data and 15 minute data. The Headquarters raingauge generates data year round. The remaining rain gauges are operated from April 1 to October 31. Precipitation amounts are recorded in mm. As of 2011, the HQ 1 (7-day clock) and HQ 2 (24-hour clock) raingauges have been discontinued and replaced with an Ott Pluvio2 rainguage that began data generation March 2010.
DOI: 10.5517/ccdc.csd.cc25ljy8
title: CCDC 2013820: Experimental Crystal Structure Determination

description: Related Article: Asuka Takahashi, Masaki Mishima, Kotohiro Nomura, Akiko Inagaki|2021|Organometallics|40|98|doi:10.1021/acs.organomet.0c00684
DOI: 10.5517/ccdc.csd.cc26mjm0
title: CCDC 2044562: Experimental Crystal Structure Determination

description: Related Article: Jan Pecak, Sarah Fleissner, Luis F. Veiros, Ernst Pittenauer, Berthold Stöger, Karl Kirchner|2021|Organometallics|40|278|doi:10.1021/acs.organomet.0c00755
DOI: 10.5517/ccdc.csd.cc26mjn1
title: CCDC 2044563: Experimental Crystal Structure Determination

description: Related Article: Jan Pecak, Sarah Fleissner, Luis F. Veiros, Ernst Pittenauer, Berthold Stöger, Karl Kirchner|2021|Organometallics|40|278|doi:10.1021/acs.organomet.0c00755
DOI: 10.6073/pasta/f3cfdb13b79f0bc8568df18c778bbeeb
title: ASD02 Stream discharge measured at the flumes on watershed N04D at Konza Prairie

description: Stream discharge is measured on a catchment (N04D), with 4-year fire return interval and grazed by bison since 1992. Measurements are taken at 5 minute intervals at a triangular throated flume. The prairie streams are 3rd-order and are intermittent. Daily and stormflow discharge records are available.
DOI: 10.6073/pasta/2108321f17b04da3ea2664cd67827483
title: High-frequency measurements of chlorophyll fluorescence, characterizing F.I.Z. bias.

description: This dataset consists of high-frequency measurements of chlorophyll a fluorescence (Fchl), collected as part of manipulative experiments conducted in Lake George, NY. Experiments were set up to test for the potential of phototactic zooplankton to interfere with Fchl measurements. To test for any bias associated with fluorometer interference by zooplankton (FIZ), fluorometers were placed in the shallows of Lake George, and collected data under various treatment conditions. It was found that excitation light from fluorometers triggered a positive phototactic response during nighttime hours, biasing Fchl data by as much as 31x. Full results gleaned from this dataset can be found in: Moriarty, V.W., Lucius, M.A., Johnston, K.E., Borrelli, J.J., Mattes, B.M., Pezzuoli, A.R., Watson, C.D., Eichler, L.W. and Relyea, R.A. (2021), Fluorometer optical path interference via zooplankton phototaxis: Implications for high‐frequency data collection. Limnol Oceanogr Methods. https://doi.org/10.1002/lom3.10411
DOI: 10.6073/pasta/797b3d5b31883f2119ad493952ba2b2d
title: ASD04 Stream discharge measured at the flumes on watershed N20B at Konza Prairie

description: Stream discharge is measured on a catchment (N20B), with 20-year fire return interval and grazed by bison since 1992. Measurements are taken at 5 minute intervals at a triangular throated flume. The prairie streams are 3rd-order and are intermittent. Daily and stormflow discharge records are available.
DOI: 10.25439/rmt.12705056
title: Lysozyme conformational changes with ionic liquids – FTIR, fluorescence, SAXS and crystallography study

description: SAXS experiments were carried out at the SAXS/WAXS beamline at the Australian Synchrotron, Melbourne, Australia. The setup had an automated well plate system, where each sample and blank solvent was drawn into the same capillary to enable accurate buffer subtraction. Ten successive frames of 1 s exposure were collected for each sample under flow. This system has been designed for weakly-scattering protein samples and reduces protein damage through minimizing X-ray radiation dose per molecule. Lysozyme samples were equilibrated for 1 hour before measurement, and 50 μL of each sample were loaded into the 96-well plate used for the automated sampling setup. The q-range for all the SAXS experiments was 0.006 to 0.53 Å−1. Scatterbrain 2.82 was used for SAXS data processing, and Chromixs, DAMMIN and SREFLEX of the ATSAS software package were used for SAXS data analysis. SAXS patterns are presented as the average of the measurements after careful blank subtraction of the corresponding solvent. The radius of gyration (Rg) for lysozyme was calculated from the Guinier approximation through the ATSAS package. The distance distribution function P(r) and the maximum diameter (Dmax) were also obtained using the ATSAS software. CRYSOL was used to screen different lysozyme crystal structures (PDB ID 1dpw, 1dpx, 1lkr, 1lks, 1uco, 3a8z, 3ru5, 3wul, 3wum, 3wun and 193l), and 1dpw was selected as the closest match to the SAXS patterns. The discrepancies χ2 values of the initial structure with the SAXS patterns were provided, while the best refined models in different ILs were selected based on the χ2 values. <br>
DOI: 10.25439/rmt.12705056.v2
title: Lysozyme conformational changes with ionic liquids – FTIR, fluorescence, SAXS and crystallography study

description: SAXS experiments were carried out at the SAXS/WAXS beamline at the Australian Synchrotron, Melbourne, Australia. The setup had an automated well plate system, where each sample and blank solvent was drawn into the same capillary to enable accurate buffer subtraction. Ten successive frames of 1 s exposure were collected for each sample under flow. This system has been designed for weakly-scattering protein samples and reduces protein damage through minimizing X-ray radiation dose per molecule. Lysozyme samples were equilibrated for 1 hour before measurement, and 50 μL of each sample were loaded into the 96-well plate used for the automated sampling setup. The q-range for all the SAXS experiments was 0.006 to 0.53 Å−1. Scatterbrain 2.82 was used for SAXS data processing, and Chromixs, DAMMIN and SREFLEX of the ATSAS software package were used for SAXS data analysis. SAXS patterns are presented as the average of the measurements after careful blank subtraction of the corresponding solvent. The radius of gyration (Rg) for lysozyme was calculated from the Guinier approximation through the ATSAS package. The distance distribution function P(r) and the maximum diameter (Dmax) were also obtained using the ATSAS software. CRYSOL was used to screen different lysozyme crystal structures (PDB ID 1dpw, 1dpx, 1lkr, 1lks, 1uco, 3a8z, 3ru5, 3wul, 3wum, 3wun and 193l), and 1dpw was selected as the closest match to the SAXS patterns. The discrepancies χ2 values of the initial structure with the SAXS patterns were provided, while the best refined models in different ILs were selected based on the χ2 values. <br>
DOI: 10.25439/rmt.12705056.v1
title: Lysozyme conformational changes with ionic liquids – FTIR, fluorescence, SAXS and crystallography study

description: SAXS experiments were carried out at the SAXS/WAXS beamline at the Australian Synchrotron, Melbourne, Australia. The setup had an automated well plate system, where each sample and blank solvent was drawn into the same capillary to enable accurate buffer subtraction. Ten successive frames of 1 s exposure were collected for each sample under flow. This system has been designed for weakly-scattering protein samples and reduces protein damage through minimizing X-ray radiation dose per molecule. Lysozyme samples were equilibrated for 1 hour before measurement, and 50 μL of each sample were loaded into the 96-well plate used for the automated sampling setup. The q-range for all the SAXS experiments was 0.006 to 0.53 Å−1. Scatterbrain 2.82 was used for SAXS data processing, and Chromixs, DAMMIN and SREFLEX of the ATSAS software package were used for SAXS data analysis. SAXS patterns are presented as the average of the measurements after careful blank subtraction of the corresponding solvent. The radius of gyration (Rg) for lysozyme was calculated from the Guinier approximation through the ATSAS package. The distance distribution function P(r) and the maximum diameter (Dmax) were also obtained using the ATSAS software. CRYSOL was used to screen different lysozyme crystal structures (PDB ID 1dpw, 1dpx, 1lkr, 1lks, 1uco, 3a8z, 3ru5, 3wul, 3wum, 3wun and 193l), and 1dpw was selected as the closest match to the SAXS patterns. The discrepancies χ2 values of the initial structure with the SAXS patterns were provided, while the best refined models in different ILs were selected based on the χ2 values. <br>
DOI: 10.6073/pasta/8cef44aa9387e401bafe803fc4b2459e
title: ASD05 Stream discharge measured at the flumes on watershed N01B at Konza Prairie

description: Stream discharge is measured on a catchment (N01B), with 1-year fire return interval and grazed by bison since 1992. Measurements are taken at 5 minute intervals at a triangular throated flume. The prairie streams are 3rd-order and are intermittent. Daily and stormflow discharge records are available.
DOI: 10.6073/pasta/1cea8de5c604e54cb263da73e635ab5d
title: ASD06 Stream discharge measured at the flumes on watershed N02B at Konza Prairie

description: Stream discharge is measured on a catchment (N02B), with 2-year fire return interval and grazed by bison since 1992. Measurements are taken at 5 minute intervals at a triangular throated flume. The prairie streams are 3rd-order and are intermittent. Daily and stormflow discharge records are available.
DOI: 10.6084/m9.figshare.12803105.v3
title: Quantified life

description: <b>Source</b>Data are scraped from a simple Fitbit that tracked steps and sleep (one individual person listed here). Aggregated to day.<br><b>Meta-data</b>simple_date is m/m/d format.<br>year is year listed only.<br>steps are total daily steps.<br>mins_asleep is the total time asleep each night.<br>efficiency is the Fitbit estimate sleep efficiency based on total time in bed, total time awake versus sleep, and number of times restless.<br>lagged_sleep are the minutes asleep lagged by one day (ie from the night before)<br>lagged_efficiency is the efficiency in the sleep from the night before<br><br>
DOI: 10.17025/1764127
title: Photoelectrochemically Self Improving Si/GaN Photocathode: Figure 1b Raw Data

description: Accelerated CA testing on bare epilayer Si/GaN photocathode at constant bias of -0.6 V vs RHE under 3.5 sun illumination for 150 hours in 0.5 M H2SO4 (pH=0.4)
DOI: 10.17025/1764132
title: Photoelectrochemically Self Improving Si/GaN Photocathode: Figure 1c Raw Data

description: Intermittent chronoamperometry (CA) testing was performed on Si/GaN photocathode in hourly manner. The LSV scan at 0 hour, 1 hour CA, 2 hours CA, 3 hours CA, 4 hours CA, 6 hours CA, 8 hours CA and 10 hours CA were recorded to track the changes of the photoelectrochemica (PEC) performance of the photocathode. The scan range was set to be 0V vs open circuit voltage (Eoc) to -0.7V vs RHE. Test was performed under one sun illumination in 0.5M H2SO4 (pH=0.4).
DOI: 10.17025/1764133
title: Photoelectrochemically Self Improving Si/GaN Photocathode: Figure 1d Raw Data

description: Fig1d results were obtained using a 3-electrode configuration with IrOx as the counter electrode and saturated calomel electrode as the reference electrode. Two Si/GaN photocathodes were compared. Sample #1 (named as S#1) was the as-received sample, and sample #2 (named as S#2) was CA tested for 4 hours under same testing conditions described in Fig.1a. The PEC performance (J-V curve) was recorded for both samples. Then a photodeposition of Pt was performed on both samples, each loading time was set to be 5 minutes, then the J-V curve was recorded to track the changes of the performance. The Pt photodeposition was stopped until the J-V curve won't shift (the maximum onset potential was achieved). The results show that, S#1 needs at least 20 minutes of Pt photodeposition to achieve its best PEC performance while S#2, which is after CA testing, only needs 5 minutes of Pt photodeposition to achieve its best PEC performance.
DOI: 10.17025/1764154
title: Photoelectrochemically Self Improving Si/GaN Photocathode: Figure 2b Raw Data

description: Photoconductive atomic force microscopy (PC-AFM) measurements were conducted on Si/GaN samples. PeakForce TUNA mode was used to acquire the morphology and current simultaneously. A PtIr conductive probe with spring constant of 2.8 Nm-1 was used for the scanning. A white light source was used to illuminate the surface during the acquisition. Line scan extracting the topography and photocurrent from a as-received Si/GaN sample. The topography mapping is 2 × 2 µm2. The sample bias was 0.4V and this photoconductive AFM measurement was performed under white light front illumination with an angle.