cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6010698
title: Comprehensive characterisation of the genomic insertion site of a transgene in highly repetitive, centromeric region of Anopheles mosquitoes

description: The availability of the genomic sequence of the malaria mosquito <em>Anopheles</em> <em>gambiae</em> has sparked in recent years the development of transgenic technologies with the potential to be used as novel tools for vector control. These technologies rely on genome editing that confers features able to affect vector capacity. This can be achieved by either reducing the mosquito population or by making mosquitoes refractory to the parasite infection. Although sophisticated molecular techniques such as those based on AttB/AttP site-specific recombination and CRISPR/Cas9 systems can lead to the integration of transgenes in specific sites of the genome, methods that allow semi-random integration are still in use due to their high efficiency; PiggyBac transposon-mediated integrations fall in this category. Characterization of the insertion site of transgenes in transgenic strains generated via PiggyBac integration can be hampered when the transgene is inserted in regions of the genome rich in repetitive sequences. Here we describe a number of techniques that were used to identify the genomic location of the transgene in a repetitive region in the <em>Anopheles gambiae</em> strain Ag(PMB)1 which was initially reported on Chromosome 3R 36D. Whilst Inverse PCR used in previous analysis was unable to distinguish between multiple genomic locations as potential insertion sites of the transgene, here we demonstrate that the use of FISH identifies clearly the integration of the transgene in a poorly annotated centromeric region of Chromosome 2R 19D. This study emphasises the need for accuracy in sequencing data for the genome of organisms of medical importance such as <em>Anopheles </em>mosquitoes. An effort to further improve reference genomes is of paramount importance to support and facilitate vector control interventions based on genome editing.
DOI: 10.5281/zenodo.6010752
title: EU Alerts/notifications on pesticides content in tea, vegetable and fruits

description: The objective of this dataset is to establish a group of active substances/food products of interest and to know the importance of this risk (occurrence of pesticides) in the food trade between in EU and China. Data include active substances, concentrations, food product, notifying country, date of notification. All food products collected in this dataset come from China. The origin of the data is the RASFF portal.(since 2010 until January 2022). 294 entries have been collected.
DOI: 10.5281/zenodo.6010751
title: EU Alerts/notifications on pesticides content in tea, vegetable and fruits

description: The objective of this dataset is to establish a group of active substances/food products of interest and to know the importance of this risk (occurrence of pesticides) in the food trade between in EU and China. Data include active substances, concentrations, food product, notifying country, date of notification. All food products collected in this dataset come from China. The origin of the data is the RASFF portal.(since 2010 until January 2022). 294 entries have been collected.
DOI: 10.21227/w3j6-br54
title: Dataset of Ruixin Fan

description: This is the dataset for Ruixin Fan
DOI: 10.5519/qd.a6uugkdm
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (46 records)
DOI: 10.6084/m9.figshare.19131416
title: A thermodynamic database of membrane protein-protein complexes and mutants for understanding their binding affinity

description: We developed a database, MPAD (Membrane Protein complex binding Affinity Database), which includes 5436 experimental data from 950 proteins on the binding affinities of membrane protein complexes and their mutants along with sequence, structure, and functional information, membrane specific features, experimental conditions, as well as literature information. The database can be freely accessed at https://web.iitm.ac.in/bioinfo2/mpad.
DOI: 10.6084/m9.figshare.19139591
title: Bolder et al Grad-CAM example.zip from Seasonal variations of serotonin in the visual system of an ant revealed by immunofluorescence and a machine learning approach

description: Zip file containing the machine learning code (R), the Grad-Cam code (python), and a file structure with an example set of images to allow for test runs of the Grad-Cam experiment
DOI: 10.6084/m9.figshare.19139597.v1
title: Bolder et al supplementary data.xlsx from Seasonal variations of serotonin in the visual system of an ant revealed by immunofluorescence and a machine learning approach

description: Excel document containing all measurements of head with, neuropil area, serotonin immunofluorescence, and the results of the machine learning approach for all thre neuropils
DOI: 10.6084/m9.figshare.19139597
title: Bolder et al supplementary data.xlsx from Seasonal variations of serotonin in the visual system of an ant revealed by immunofluorescence and a machine learning approach

description: Excel document containing all measurements of head with, neuropil area, serotonin immunofluorescence, and the results of the machine learning approach for all thre neuropils
DOI: 10.6084/m9.figshare.19131416.v2
title: A thermodynamic database of membrane protein-protein complexes and mutants for understanding their binding affinity

description: We developed a database, MPAD (Membrane Protein complex binding Affinity Database), which includes 5436 experimental data from 950 proteins on the binding affinities of membrane protein complexes and their mutants along with sequence, structure, and functional information, membrane specific features, experimental conditions, as well as literature information. The database can be freely accessed at https://web.iitm.ac.in/bioinfo2/mpad.
DOI: 10.5281/zenodo.5028649
title: MALDI-TOF Spectra for Zooarcheology by Mass Spectrometry (ZooMS) for Borić et al. (2021)

description: This dataset contains MALDI-TOF spectral data in .mzML format for zooarcheology by mass spectrometry (ZooMS) samples referenced in Borić et al. (2021). Folder names correspond to the ZooMS sample names referenced in the article. Files in the same folder are technical replicates.
DOI: 10.5281/zenodo.5028648
title: MALDI-TOF Spectra for Zooarcheology by Mass Spectrometry (ZooMS) for Borić et al. (2021)

description: This dataset contains MALDI-TOF spectral data in .mzML format for zooarcheology by mass spectrometry (ZooMS) samples referenced in Borić et al. (2021). Folder names correspond to the ZooMS sample names referenced in the article. Files in the same folder are technical replicates.
DOI: 10.5281/zenodo.5040049
title: MALDI-TOF-MS spectra of modern Australian marsupials for ZooMS (Zooarchaeology by Mass Spectrometry)

description: MALDI-TOF-MS spectra of extracted collagen from modern Australian marsupials. These spectra were used to develop peptide markers for Zooarchaeology by Mass Spectrometry (ZooMS). All spectra are uploaded in .mzml format. One sample per species was also analyzed with LC-MS/MS (indicated in the metadata file). The LC-MS/MS data is available at PXD027107 through MassIVE (doi:10.25345/C5TC2H). Information about the species and sample numbers can be found in the metadata file.
DOI: 10.5281/zenodo.5040048
title: MALDI-TOF-MS spectra of modern Australian marsupials for ZooMS (Zooarchaeology by Mass Spectrometry)

description: MALDI-TOF-MS spectra of extracted collagen from modern Australian marsupials. These spectra were used to develop peptide markers for Zooarchaeology by Mass Spectrometry (ZooMS). All spectra are uploaded in .mzml format. One sample per species was also analyzed with LC-MS/MS (indicated in the metadata file). The LC-MS/MS data is available at PXD027107 through MassIVE (doi:10.25345/C5TC2H). Information about the species and sample numbers can be found in the metadata file.
DOI: 10.5281/zenodo.5040055
title: MALDI-TOF-MS spectra of archaeological bone fragments from Bandicoot Bay, Barrow Island (Australia) for ZooMS (Zooarchaeology by Mass Spectrometry)

description: MALDI-TOF-MS spectra for archaeological bone fragments from Bandicoot Bay, Barrow Island, Western Australia. All spectra are uploaded in .mzml format.
DOI: 10.5281/zenodo.5040054
title: MALDI-TOF-MS spectra of archaeological bone fragments from Bandicoot Bay, Barrow Island (Australia) for ZooMS (Zooarchaeology by Mass Spectrometry)

description: MALDI-TOF-MS spectra for archaeological bone fragments from Bandicoot Bay, Barrow Island, Western Australia. All spectra are uploaded in .mzml format.
DOI: 10.3886/e100510
title: MacArthur Mental Health Court Study

description: The MacArthur Mental Health Court (MHC) project is a longitudinal study examining the effectiveness of these specialty courts in reducing recidivism, reducing the number of jail days and stays, and increasing access to community mental health and substance use treatment. The study included four data collection sites (two in CA, one in MN, and one in IN), two samples (newly enrolled MHC clients and a comparison sample of offenders with mental illness in the traditional criminal justice system), two interview time points (baseline and 6-month follow-up), and the collection of objective criminal justice and court data up to 18 months post-enrollment in the MHC/post-arrest. This comprehensive project was funded by the John D. and Catherine T. MacArthur Network on Community Mandated Treatment, led by Professor John Monahan, and was conducted by Policy Research Associates (Principal Investigator: Dr. Henry J. Steadman).
description: Presence of Common Scales: Several Likert scales were used.<br>Colorado Symptoms Inventory<br>Insight and Treatment Attitudes Questionnaire
description: There were two samples: MHC and TAU (treatment as usual) samples.<br>The MHC sample were newly enrolled clients in the four participating courts who provided informed consent to participate.<br>The TAU sample were newly arrested offenders with mental health problems in the jails of the same four cities as the courts, who also provided informed consent. In addition, the TAU sample had to be eligible for the MHC (criteria relating to criminal charges and mental health) but could not have been referred to, or rejected from the MHC. <br><br><br>
description: Newly enrolled mental health court (MHC) participants in four locations<br>Newly arrested offenders with mental health issues in four locations<br><br><br>.
description: face-to-face interview; Survey data at baseline (entry into MHC or criminal justice system)<br>Survey data at 6-month follow-up<br>Administrative data from courts
DOI: 10.3886/e100510v2
title: MacArthur Mental Health Court Study

description: The MacArthur Mental Health Court (MHC) project is a longitudinal study examining the effectiveness of these specialty courts in reducing recidivism, reducing the number of jail days and stays, and increasing access to community mental health and substance use treatment. The study included four data collection sites (two in CA, one in MN, and one in IN), two samples (newly enrolled MHC clients and a comparison sample of offenders with mental illness in the traditional criminal justice system), two interview time points (baseline and 6-month follow-up), and the collection of objective criminal justice and court data up to 18 months post-enrollment in the MHC/post-arrest. This comprehensive project was funded by the John D. and Catherine T. MacArthur Network on Community Mandated Treatment, led by Professor John Monahan, and was conducted by Policy Research Associates (Principal Investigator: Dr. Henry J. Steadman).
description: Presence of Common Scales: Several Likert scales were used.<br>Colorado Symptoms Inventory<br>Insight and Treatment Attitudes Questionnaire
description: There were two samples: MHC and TAU (treatment as usual) samples.<br>The MHC sample were newly enrolled clients in the four participating courts who provided informed consent to participate.<br>The TAU sample were newly arrested offenders with mental health problems in the jails of the same four cities as the courts, who also provided informed consent. In addition, the TAU sample had to be eligible for the MHC (criteria relating to criminal charges and mental health) but could not have been referred to, or rejected from the MHC. <br><br><br>
description: Newly enrolled mental health court (MHC) participants in four locations<br>Newly arrested offenders with mental health issues in four locations<br><br><br>.
description: face-to-face interview; Survey data at baseline (entry into MHC or criminal justice system)<br>Survey data at 6-month follow-up<br>Administrative data from courts
DOI: 10.6084/m9.figshare.19139600
title: Data extraction (After recalculate the HRs).xlsx

description: To use morbidity data to analyze possible dose-response relationships, it is necessary to have the following information for each SUA concentration category: assigned average or median SUA levels, deaths, follow-up person-years, adjusted HRs and 95% CIs. When the HRs and 95% CIs reported in the original study were not based on the lowest SUA group as the reference, we recalculated the relevant HRs and 95% CIs using the lowest dose group as the reference.
DOI: 10.6084/m9.figshare.19139600.v1
title: Data extraction (After recalculate the HRs).xlsx

description: To use morbidity data to analyze possible dose-response relationships, it is necessary to have the following information for each SUA concentration category: assigned average or median SUA levels, deaths, follow-up person-years, adjusted HRs and 95% CIs. When the HRs and 95% CIs reported in the original study were not based on the lowest SUA group as the reference, we recalculated the relevant HRs and 95% CIs using the lowest dose group as the reference.
DOI: 10.6084/m9.figshare.19139492
title: Data extraction (Before recalculate the HRs).xlsx

description: The original information was extracted including the first author, year of publication, national/region where the research was conducted, study design, number of center, sample size, number of all-cause and cardiovascular deaths, follow-up duration, mean or median of SUA concentration, multi-factorial adjusted HRs and its 95% confidence intervals (CIs) of all-cause mortality or cardiovascular mortality.
DOI: 10.6084/m9.figshare.19139492.v1
title: Data extraction (Before recalculate the HRs).xlsx

description: The original information was extracted including the first author, year of publication, national/region where the research was conducted, study design, number of center, sample size, number of all-cause and cardiovascular deaths, follow-up duration, mean or median of SUA concentration, multi-factorial adjusted HRs and its 95% confidence intervals (CIs) of all-cause mortality or cardiovascular mortality.
DOI: 10.5281/zenodo.5021376
title: Canopy temperature is regulated by ecosystem structural traits and captures the ecohydrologic dynamics of a semiarid mixed conifer forest site

description: The data have been used in a published article in the Journal of Geophysical Research: Biogeosciences, titled "Canopy temperature is regulated by ecosystem structural traits and captures the ecohydrologic dynamics of a semiarid mixed conifer forest site". Please check out the published article for more information about the data.<br> <br> Javadian, M., Smith, W. K., Lee, K., Knowles, J. F., Scott, R. L., Fisher, J. B., et al. (2022). Canopy temperature is regulated by ecosystem structural traits and captures the ecohydrologic dynamics of a semiarid mixed conifer forest site. <em>Journal of Geophysical Research: Biogeosciences</em>, 127, e2021JG006617. https://doi.org/10.1029/2021JG006617<br> <br> There are 5 folders in the main folder as follows:<br> <br> 1."EC_Tower" : The flux tower data over US-MtB eddy covariance site from Jan 2020 to May 2021.<br> 2. "FLIR_Thermometer": The vertical temperature profiles on Nov, 14, 2020.<br> 3."PRI": The photochemical reflectance index (PRI) from Jan 2020 to Feb 2021.<br> 4. "Tree_Sap_Flow": Tree sap flow data from Jan 2020 to May 2021.<br> 5. "UAS": Unmanned Aircraft Systems (UAS) images
DOI: 10.5281/zenodo.5021375
title: Canopy temperature is regulated by ecosystem structural traits and captures the ecohydrologic dynamics of a semiarid mixed conifer forest site

description: The data have been used in a published article in the Journal of Geophysical Research: Biogeosciences, titled "Canopy temperature is regulated by ecosystem structural traits and captures the ecohydrologic dynamics of a semiarid mixed conifer forest site". Please check out the published article for more information about the data.<br> <br> Javadian, M., Smith, W. K., Lee, K., Knowles, J. F., Scott, R. L., Fisher, J. B., et al. (2022). Canopy temperature is regulated by ecosystem structural traits and captures the ecohydrologic dynamics of a semiarid mixed conifer forest site. <em>Journal of Geophysical Research: Biogeosciences</em>, 127, e2021JG006617. https://doi.org/10.1029/2021JG006617<br> <br> There are 5 folders in the main folder as follows:<br> <br> 1."EC_Tower" : The flux tower data over US-MtB eddy covariance site from Jan 2020 to May 2021.<br> 2. "FLIR_Thermometer": The vertical temperature profiles on Nov, 14, 2020.<br> 3."PRI": The photochemical reflectance index (PRI) from Jan 2020 to Feb 2021.<br> 4. "Tree_Sap_Flow": Tree sap flow data from Jan 2020 to May 2021.<br> 5. "UAS": Unmanned Aircraft Systems (UAS) images
DOI: 10.6084/m9.figshare.19096781.v1
title: WAMRI component C Test results

description: Contiene los resultados de una serie de test sobre el componente C en WAMRI<br>
DOI: 10.34740/kaggle/dsv/3157424
title: Review mechanisms labour market discrimination
DOI: 10.5281/zenodo.6011020
title: Hybrid gridded demographic data for the world, 1950-2020 0.25˚ resolution

description: This is a hybrid gridded dataset of demographic data for the world, given as 5-year population bands at a 0.25 degree grid resolution. This dataset combines the NASA SEDAC Gridded Population of the World version 4 (GPWv4) with the ISIMIP Histsoc gridded population data and the United Nations World Population Program (WPP) demographic modelling data. Demographic fractions are given for the time period covered by the UN WPP model (1950-2050) while demographic totals are given for the time period covered by the combination of GPWv4 and Histsoc (1950-2020). More detailed can be found on the page of the original version (https://doi.org/10.5281/zenodo.3768003). This release increases the resolution to 0.25˚ and is explicitly designed to match with the grid definition of the ERA5 climate reanalysis dataset. For pre-2000 population data, the ISIMIP Histsoc data was upscaled from it's native 0.5˚ resolution.
DOI: 10.17037/data.00002761
title: Search strategy for "Quantifying the effectiveness and health co-benefits of climate change mitigation actions across sectors: a protocol for an umbrella review"

description: The search strategy was constructed for an umbrella review of systematic reviews, synthesising modelled and empirical evidence on such actions on climate change mitigation and health across all sectors and disciplines. The umbrella review is undertaken as a part of the Pathfinder Initiative (https://www.lshtm.ac.uk/research/centres-projects-groups/pathfinder-initiative)
DOI: 10.5281/zenodo.5972932
title: Can DyeCycling break the photobleaching limit in single-molecule FRET?

description: <strong>Abstract. </strong>Biomolecular systems, such as proteins, crucially rely on dynamic processes at the nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that control biomolecular systems. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique to observe in real-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural states. Currently, this technique is fundamentally limited by irreversible photobleaching, causing the untimely end of the experiment and thus, a prohibitively narrow temporal bandwidth of ≤ 3 orders of magnitude. Here, we introduce <em>‘DyeCycling’</em>, a measurement scheme with which we aim to break the photobleaching limit in single-molecule FRET. We introduce the concept of spontaneous dye replacement by simulations, and as an experimental proof-of-concept, we demonstrate the intermittent observation of a single biomolecule for one hour with a time resolution of milliseconds. Theoretically, DyeCycling can provide &gt;100-fold more information per single molecule than conventional smFRET. We discuss the experimental implementation of DyeCycling, its current and fundamental limitations, and specific biological use cases. Given its general simplicity and versatility, DyeCycling has the potential to revolutionize the field of time-resolved smFRET, where it may serve to unravel a wealth of biomolecular dynamics by bridging from milliseconds to the hour range.
DOI: 10.5281/zenodo.5972931
title: Can DyeCycling break the photobleaching limit in single-molecule FRET?

description: <strong>Abstract. </strong>Biomolecular systems, such as proteins, crucially rely on dynamic processes at the nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that control biomolecular systems. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique to observe in real-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural states. Currently, this technique is fundamentally limited by irreversible photobleaching, causing the untimely end of the experiment and thus, a prohibitively narrow temporal bandwidth of ≤ 3 orders of magnitude. Here, we introduce <em>‘DyeCycling’</em>, a measurement scheme with which we aim to break the photobleaching limit in single-molecule FRET. We introduce the concept of spontaneous dye replacement by simulations, and as an experimental proof-of-concept, we demonstrate the intermittent observation of a single biomolecule for one hour with a time resolution of milliseconds. Theoretically, DyeCycling can provide &gt;100-fold more information per single molecule than conventional smFRET. We discuss the experimental implementation of DyeCycling, its current and fundamental limitations, and specific biological use cases. Given its general simplicity and versatility, DyeCycling has the potential to revolutionize the field of time-resolved smFRET, where it may serve to unravel a wealth of biomolecular dynamics by bridging from milliseconds to the hour range.
DOI: 10.6084/m9.figshare.16727251.v1
title: A Survey on How Test Flakiness Affects Developers and What Support They Need To Address It

description: Replication Dataset for the research paper "A Survey on How Test Flakiness Affects Developers and What Support They Need To Address It", which was presented at the 15th IEEE International Conference on Software Testing, Verification and Validation (ICST) 2022
DOI: 10.5445/ir/1000142811
title: Graphite lubrication of highly loaded contacts: humidity-dependent friction and structural transition to turbostratic carbon
DOI: 10.6084/m9.figshare.19096781.v3
title: WAMRI component C Test results

description: Contiene los resultados de una serie de test sobre el componente C en WAMRI<br>
DOI: 10.6084/m9.figshare.19096781.v2
title: WAMRI component C Test results

description: Contiene los resultados de una serie de test sobre el componente C en WAMRI<br>
DOI: 10.6084/m9.figshare.12455996
title: TableS1

description: Data related to the paper Giant Viruses Encode Actin-Related Proteins
DOI: 10.6084/m9.figshare.12455996.v1
title: TableS1

description: Data related to the paper Giant Viruses Encode Actin-Related Proteins
DOI: 10.6084/m9.figshare.14501487
title: 06_family_predictions_using_SiLiX

description: Data related to the paper Giant Viruses Encode Actin-Related Proteins<br><br>