cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3623150
title: Function and evolution of B-Raf loop dynamics relevant to cancer recurrence under drug inhibition

description: Oncogenic mutations in the kinase domain of the B-Raf protein have long been associated with cancers involving the RAF-MEK-ERK pathway. One constitutive ERK activating mutation in B-Raf, the V600E (valine to glutamate) replacement occurring adjacent to a site of threonine phosphorylation (T599) occurs in many types of cancer, and in a large percentage of certain cancers, such as melanoma. Because natural ATP binding activity and the V600E mutation are both known to alter the physical behavior of the activation loop in the ATP binding domain, this system is especially amenable to comparative functional analyses using molecular dynamics of drug classes and genetic variants at all-atom resolution. Here, we employ machine learning enabled identification of functionally conserved protein dynamics to compare how disease pertinent molecular variations impact conserved loop dynamics during the binding of four ATP competitive B-Raf inhibitors (sorafenib, vemurafenib, dabrafenib, and PLX7904) that differ in their effectiveness in preventing cancer recurrence. We demonstrate that drug development targeting B-Raf has progressively moved towards ATP competitive inhibitors that demonstrate less tendency to mimic the functional dynamic shifts associated with ATP binding in this domain. We argue this functional dynamic mimicry in first generation B-Raf inhibitors increases the side effect of hyperactivation (i.e. inducing MAPK activation in non-tumorous cells in the absence of secondary mutation). Within the context of the binding interaction of each inhibitor, we compare the functional dynamic impacts of V600E and other sensitizing and drug resistance causing mutations in the activation and P-loops, confirming sites of low mutational tolerance in these two functional regions. Lastly, we investigate V600E sensitivity of B-Raf loop dynamics in an evolutionary context, demonstrating that while it probably shares partial origin with its early evolution in primitive eukaryotes, the functional sensitivity to V600E was secondarily increased during early jawed vertebrate evolution.
DOI: 10.5281/zenodo.3624664
title: KBNLB390007382 - Coutumes et ordonnances du pays et conté de Namur: decretées et authorisées par Sa Majesté le deusieme may seize cens quatre vingt et deux : avec le stil & maniere de proceder au Conseil provincial & és cours subalternes

description: Titel: <em> </em><em>Coutumes et ordonnances du pays et conté de Namur: </em><em>decretées et authorisées par Sa Majesté le deusieme may seize cens quatre vingt et deux : avec le stil & maniere de proceder au Conseil provincial & és cours subalternes</em> Publisher: François Chenu, Place: Namur Year: 1682 Used version: The copy we used for the transcriptions is held at the KB National Library of the Netherlands. Link digitised version of the book: https://books.google.nl/books?id=HyvY76zkEKIC (Main) Language: French. Province: Namur. Font: Roman. Model used: French_18thCentury_Print Version of Transkribus used: v.1.9.1. Other info: Abbyy FineReader v.11 has been used. Link model: For more information on the HTR-model used, please visit: https://lab.kb.nl/dataset/entangled-histories-ordinances-low-countries. Transcription conventions: The abbreviations have been written out into full words. The hyphens at the end of a line have been kept (when there). If you are in need of the original scans of the documents, please contact dataservices@kb.nl. This transcription is part of the dataset created with the ‘Entangled Histories’-project. PI: dr. C.A. Romein;<br> Scientific Programmer: S.F. Veldhoen, MSc;<br> Project Manager: drs. M. de Gruijter.
DOI: 10.5255/ukda-sn-854043
title: Migrants, minorities and engagement in local civil society 2016-2017
DOI: 10.5281/zenodo.3623149
title: Function and evolution of B-Raf loop dynamics relevant to cancer recurrence under drug inhibition

description: Oncogenic mutations in the kinase domain of the B-Raf protein have long been associated with cancers involving the RAF-MEK-ERK pathway. One constitutive ERK activating mutation in B-Raf, the V600E (valine to glutamate) replacement occurring adjacent to a site of threonine phosphorylation (T599) occurs in many types of cancer, and in a large percentage of certain cancers, such as melanoma. Because natural ATP binding activity and the V600E mutation are both known to alter the physical behavior of the activation loop in the ATP binding domain, this system is especially amenable to comparative functional analyses using molecular dynamics of drug classes and genetic variants at all-atom resolution. Here, we employ machine learning enabled identification of functionally conserved protein dynamics to compare how disease pertinent molecular variations impact conserved loop dynamics during the binding of four ATP competitive B-Raf inhibitors (sorafenib, vemurafenib, dabrafenib, and PLX7904) that differ in their effectiveness in preventing cancer recurrence. We demonstrate that drug development targeting B-Raf has progressively moved towards ATP competitive inhibitors that demonstrate less tendency to mimic the functional dynamic shifts associated with ATP binding in this domain. We argue this functional dynamic mimicry in first generation B-Raf inhibitors increases the side effect of hyperactivation (i.e. inducing MAPK activation in non-tumorous cells in the absence of secondary mutation). Within the context of the binding interaction of each inhibitor, we compare the functional dynamic impacts of V600E and other sensitizing and drug resistance causing mutations in the activation and P-loops, confirming sites of low mutational tolerance in these two functional regions. Lastly, we investigate V600E sensitivity of B-Raf loop dynamics in an evolutionary context, demonstrating that while it probably shares partial origin with its early evolution in primitive eukaryotes, the functional sensitivity to V600E was secondarily increased during early jawed vertebrate evolution.
DOI: 10.17632/kntnfm8grc.3
title: The molecular structural diversity of mitochondrial cardiolipins

description: A description of the data is given in: Oemer, G., Lackner, K., Muigg, K., Krumschnabel, G., Watschinger, K., Sailer, S., Lindner, H., Gnaiger, E., Wortmann, S.B., Werner, E.R., et al. (2018). The molecular structural diversity of mitochondrial cardiolipins. Proc. Natl. Acad. Sci. U. S. A. (2018) https://doi.org/10.1073/pnas.1719407115
DOI: 10.17632/k8h5nw39pn.3
title: Development on Chinese Version of Family Ritual Questionnaire

description: Family ritual questionnire (Chinese version) Data_Updated
DOI: 10.17632/k8h5nw39pn.4
title: Development on Chinese Version of Family Ritual Questionnaire

description: Family ritual questionnire (Chinese version) Data_Updated
DOI: 10.5281/zenodo.3609285
title: Supplementary data for human Y-chromosome gene expression analysis

description: Processed data for: AK Godfrey, S Naqvi, L Chmátal, JM Chick, RN Mitchell, SP Gygi, H Skaletsky, DC Page. Quantitative analysis of Y-chromosome gene expression across 36 human tissues. <em>Genome Res</em> (2020). The following six files are provided for reference and for use in future analyses. (1) <strong>gencode.v24.annotation.basic_ccds_nopar.gtf.gz</strong> — transcriptome annotation used in analyses (2) <strong>gtex.ksto.gen24c.prefilt_pass1.genes.est_counts.txt.gz</strong> — genes x samples matrix containing estimated count values output by kallisto for all samples passing initial set of metadata-based filters. (3) <strong>gtex.ksto.gen24c.prefilt_pass1.pcgenes.tpm.txt.gz</strong> — protein-coding genes x samples matrix containing TPM values output by kallisto for all samples passing initial set of metadata-based filters. (4) <strong>gtex.ksto.gen24c.prefilt_pass1.postfilt_pass.pcgenes.tpm.txt.gz </strong>— protein-coding genes x samples matrix containing TPM values output by kallisto for samples passing initial metadata-based filters and expression-outlier filters. (5) <strong>gtex.ksto.gen24c.prefilt_pass1.postfilt_pass.pcgenes.adj_tpm.txt.gz </strong>— protein-coding genes x samples matrix (based on file #4 above) containing TPM values adjusted for RIN, ischemic time, and intronic-read mapping rate. (6) <strong>gtex_metadata_subset.txt</strong> — sample/donor metadata The remaining 24 files contain the input data required to replicate analyses in the manuscript, as detailed at https://github.com/akg8/MSY-expression. HDF5 (`.h5`) files contain individual pandas DataFrame objects with the key `df`. These files can be downloaded individually, or they can be downloaded all at once by downloading the file <strong>msy_expression.all_input_data.zip </strong>(recommended). --- <strong>Version history:</strong> <strong>Version 1</strong> contained just the six listed files above. In <strong>Version 2</strong>, the remaining 24 files needed for reproducing analyses were added. In addition, gtex_metadata_subset.txt was updated with the previously missing column `SEX`. In <strong>Version 3</strong>, a single zipped file msy_expression.all_input_data.zip was added so that all input data for re-analysis can be downloaded more conveniently.
DOI: 10.5281/zenodo.3609286
title: Supplementary data for human Y-chromosome gene expression analysis

description: Processed data for: AK Godfrey, S Naqvi, L Chmátal, JM Chick, RN Mitchell, SP Gygi, DC Page. Non-coding sequence divergence of the human X and Y chromosomes drove male-biased expression of dosage-sensitive regulatory genes. (1) <strong>gencode.v24.annotation.basic_ccds_nopar.gtf.gz</strong> — transcriptome annotation used in analyses (2) <strong>gtex.ksto.gen24c.prefilt_pass1.genes.est_counts.txt.gz</strong> — genes x samples matrix containing estimated count values output by kallisto for all samples passing initial set of metadata-based filters. (3) <strong>gtex.ksto.gen24c.prefilt_pass1.pcgenes.tpm.txt.gz</strong> — protein-coding genes x samples matrix containing TPM values output by kallisto for all samples passing initial set of metadata-based filters. (4) <strong>gtex.ksto.gen24c.prefilt_pass1.postfilt_pass.pcgenes.tpm.txt.gz </strong>— protein-coding genes x samples matrix containing TPM values output by kallisto for samples passing initial metadata-based filters and expression-outlier filters. (5) <strong>gtex.ksto.gen24c.prefilt_pass1.postfilt_pass.pcgenes.adj_tpm.txt.gz </strong>— protein-coding genes x samples matrix (based on file #4 above) containing TPM values adjusted for RIN, ischemic time, and intronic-read mapping rate. (6) <strong>gtex_metadata_subset.txt</strong> — sample/donor metadata
DOI: 10.5281/zenodo.3624881
title: UU1874-44885 - Groot placaet-boeck, vervattende de placaten, ordonnantien ende edicten van de doorluchtige, hoogh mog. heeren Staten Generael der Vereenighde Nederlanden ende vande ed. groot-mog. heeren Staten van Hollandt en West-Vrieslandt, mitsgaders vande ed. mog. heeren Staten van Zeelandt (Volume 2)

description: Titel: <em> </em><em>Groot placaet-boeck, vervattende de placaten, ordonnantien ende edicten van de doorluchtige, hoogh mog. heeren Staten Generael der Vereenighde Nederlanden ende vande ed. groot-mog. heeren Staten van Hollandt en West-Vrieslandt, mitsgaders vande ed. mog. heeren Staten van Zeelandt </em><em> </em><em> </em><em>(Volume </em><em>2</em><em>)</em> Publisher: weduwe ende erfgenamen van wylen Hillebrandt Jacobsz van Wouw Place: ‘s-Gravenhage Year: 1664 Used version: The copy we used for the transcriptions is held at Utrecht University. Link digitised version of the book: http://objects.library.uu.nl/reader/index.php?obj=1874-44885&amp;lan=nl (Main) Language: Dutch. Province: Holland, West-Friesland and Zeeland. Font: Roman. Model used: Dutch_Romanprint_Print Version of Transkribus used: v.1.9.1. Other info: Abbyy FineReader v.11 has been used. Link model: For more information on the HTR-model used, please visit: https://lab.kb.nl/dataset/entangled-histories-ordinances-low-countries. Transcription conventions: The abbreviations have been written out into full words. The hyphens at the end of a line have been kept (when there). If you are in need of the original scans of the documents, please contact dataservices@kb.nl. This transcription is part of the dataset created with the ‘Entangled Histories’-project. PI: dr. C.A. Romein;<br> Scientific Programmer: S.F. Veldhoen, MSc;<br> Project Manager: drs. M. de Gruijter.
DOI: 10.5281/zenodo.3624882
title: UU1874-44885 - Groot placaet-boeck, vervattende de placaten, ordonnantien ende edicten van de doorluchtige, hoogh mog. heeren Staten Generael der Vereenighde Nederlanden ende vande ed. groot-mog. heeren Staten van Hollandt en West-Vrieslandt, mitsgaders vande ed. mog. heeren Staten van Zeelandt (Volume 2)

description: Titel: <em> </em><em>Groot placaet-boeck, vervattende de placaten, ordonnantien ende edicten van de doorluchtige, hoogh mog. heeren Staten Generael der Vereenighde Nederlanden ende vande ed. groot-mog. heeren Staten van Hollandt en West-Vrieslandt, mitsgaders vande ed. mog. heeren Staten van Zeelandt </em><em> </em><em> </em><em>(Volume </em><em>2</em><em>)</em> Publisher: weduwe ende erfgenamen van wylen Hillebrandt Jacobsz van Wouw Place: ‘s-Gravenhage Year: 1664 Used version: The copy we used for the transcriptions is held at Utrecht University. Link digitised version of the book: http://objects.library.uu.nl/reader/index.php?obj=1874-44885&amp;lan=nl (Main) Language: Dutch. Province: Holland, West-Friesland and Zeeland. Font: Roman. Model used: Dutch_Romanprint_Print Version of Transkribus used: v.1.9.1. Other info: Abbyy FineReader v.11 has been used. Link model: For more information on the HTR-model used, please visit: https://lab.kb.nl/dataset/entangled-histories-ordinances-low-countries. Transcription conventions: The abbreviations have been written out into full words. The hyphens at the end of a line have been kept (when there). If you are in need of the original scans of the documents, please contact dataservices@kb.nl. This transcription is part of the dataset created with the ‘Entangled Histories’-project. PI: dr. C.A. Romein;<br> Scientific Programmer: S.F. Veldhoen, MSc;<br> Project Manager: drs. M. de Gruijter.
DOI: 10.17632/kb92kdjtcz.1
title: Review of Text Clustering Methods and Suggested Solutions for Theme Based Clustering of the Quran

description: In the datasets, documents of modern, unedited, and unmarked Arabic texts were utilised, which consisted of a sample of nearly 1,680 documents obtained from various online Arabic resources. The testing dataset comprised of four fields, namely: art, economics, politics, and sports articles. The other dataset collection consisted of 383,872 Arabic documents, which were primarily newswire dispatches as released by the Agency France Press (AFP) between years 1994 and 2000. Standard TREC classes and ground truth were thus established for this collection, whereby 10 classes were thus classified as part of TREC 2001. The last datasets is the Qur'an data, which converted from softcopy to database to contactes with each chapters and verses.
DOI: 10.5519/qd.k36ov0mv
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (941 records)
DOI: 10.17632/4t8c4bmw5p.1
title: Medullary, pontine and mesencephalic pathology in ALS and PLS: the segmental brainstem profile of motor neuron disease

description: Brainstem pathology is a pathognomonic feature of ALS encompassing lower cranial nerve and descending corticospinal tract degeneration. Post mortem studies have highlighted macroscopic brainstem atrophy in ALS since the earliest descriptions of the disease [1, 2], and brainstem involvement is a stage-defining feature of pathological TDP-43 burden [3]. Despite the plethora of recent imaging studies in ALS [4, 5], brainstem alterations are poorly characterised radiologically. The majority of imaging papers in ALS and PLS focus on cortical atrophy patterns [6-9], telencephalic white matter degeneration [8, 10-12], basal ganglia [13-16] and spinal cord pathology [17-19]. The quantitative assessment of brainstem changes in vivo offers the opportunity to assess longitudinal changes [20-22], explore correlations with clinical metrics [23, 24], and define the imaging signatures of specific motor neuron disease phenotypes [25, 26]. In a prospective, single-centre imaging study [27], we have acquired high-resolution imaging data for 100 patients with amyotrophic lateral sclerosis (ALS), 33 patients with primary lateral sclerosis (PLS), 30 patients with frontotemporal dementia (FTD) and 100 healthy controls (HC) using a standardised imaging protocol [13]. ALS patients were scanned longitudinally 4 months apart. T1-weighted imaging data were acquired with a 3D Inversion Recovery prepared Spoiled Gradient Recalled echo (IR-SPGR) pulse sequence on a 3 Tesla MRI system. Following quality control and standard pre-processing steps [15, 28], a Bayesian parcellation algorithm was utilised to segment the brainstem into the medulla oblongata, pons and mesencephalon [29]. Raw volumetric data are presented for each brainstem segment, stratified by study-group membership as supplementary information to our recent research paper. [27] Our data demonstrate that segmental and progressive brainstem pathology can be readily detected in vivo in ALS and our findings also confirm considerable brainstem atrophy in PLS. [13, 30] The interpretation of our volumetric data is aided by the availability of reference data sets from healthy- and disease-controls.
DOI: 10.17632/srvd7d6x6f.1
title: Data for: Geochemistry and lithostratigraphy of the Mugher Mudstone: Insights into the Late Jurassic-Early Cretaceous Clastic sedimentation in Ethiopia and its surroundings
DOI: 10.17632/srvd7d6x6f.2
title: Data for: Geochemistry and lithostratigraphy of the Mugher Mudstone: Insights into the Late Jurassic-Early Cretaceous Clastic sedimentation in Ethiopia and its surroundings
DOI: 10.5281/zenodo.3614030
title: KBNLB080004223 - Derde deel vanden zesden placcaert-boeck van Vlaenderen

description: Titel: <em> </em><em>Derde</em><em> deel vanden zesden placcaert-boeck van Vlaenderen</em> Publisher: Petrus de Goesin en zoonen Place: Gent Year: 1786 Used version: The copy we used for the transcriptions is held at the KB National Library of the Netherlands. Link digitised version of the book: https://books.google.nl/books?vid=KBNL:KBNLB080004223&redir_esc=y (Main) Language: Dutch. Province: Flanders. Font: Roman. Model used: Dutch_Romantype_Print Version of Transkribus used: v.1.9.1. Other info: Abbyy FineReader v.11 has been used. Link model: For more information on the HTR-model used, please visit: https://lab.kb.nl/dataset/entangled-histories-ordinances-low-countries. Transcription conventions: The abbreviations have been written out into full words. The hyphens at the end of a line have been kept (when there). If you are in need of the original scans of the documents, please contact dataservices@kb.nl. This transcription is part of the dataset created with the ‘Entangled Histories’-project. PI: dr. C.A. Romein;<br> Scientific Programmer: S.F. Veldhoen, MSc;<br> Project Manager: drs. M. de Gruijter.
DOI: 10.5281/zenodo.3614031
title: KBNLB080004223 - Derde deel vanden zesden placcaert-boeck van Vlaenderen

description: Titel: <em> </em><em>Derde</em><em> deel vanden zesden placcaert-boeck van Vlaenderen</em> Publisher: Petrus de Goesin en zoonen Place: Gent Year: 1786 Used version: The copy we used for the transcriptions is held at the KB National Library of the Netherlands. Link digitised version of the book: https://books.google.nl/books?vid=KBNL:KBNLB080004223&redir_esc=y (Main) Language: Dutch. Province: Flanders. Font: Roman. Model used: Dutch_Romantype_Print Version of Transkribus used: v.1.9.1. Other info: Abbyy FineReader v.11 has been used. Link model: For more information on the HTR-model used, please visit: https://lab.kb.nl/dataset/entangled-histories-ordinances-low-countries. Transcription conventions: The abbreviations have been written out into full words. The hyphens at the end of a line have been kept (when there). If you are in need of the original scans of the documents, please contact dataservices@kb.nl. This transcription is part of the dataset created with the ‘Entangled Histories’-project. PI: dr. C.A. Romein;<br> Scientific Programmer: S.F. Veldhoen, MSc;<br> Project Manager: drs. M. de Gruijter.
DOI: 10.21227/w7ny-xs54
title: ExoNet: Large-Scale Hierarchical Image Database of Human Locomotion Environments

description: Recent advances in robotic vision and artificial intelligence have enabled researchers to develop environment recognition systems for lower-limb exoskeletons and prostheses. However, insufficient and private training databases have impeded the widespread development and dissemination of image classification algorithms for environment recognition. To address these shortcomings, we have developed “ExoNet”, the first open-source large-scale hierarchical database of high-resolution wearable camera images of human locomotion environments. Unparalleled in both scale and diversity, ExoNet comprises over 5.6 million images of various indoor and outdoor real-world walking environments, collected using a lightweight wearable smartphone camera system throughout summer, autumn, and winter seasons. Approximately 940,000 images in ExoNet were human-annotated using a 12-classs hierarchical classification architecture. Available publicly through IEEE DataPort, ExoNet offers an unprecedented communal platform for training, developing, and comparing image classification algorithms for next-generation environment recognition systems. Beyond the control of robotic lower-limb exoskeletons and prostheses, applications of ExoNet extend to other assistive technologies (e.g., powered wheelchairs) and humanoids and autonomous legged robotics.Reference: Laschowski B, McNally W, Wong A, and McPhee J. (2020). ExoNet: Large-Scale Hierarchical Image Database of Human Locomotion Environments. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. In Preparation.
DOI: 10.17632/2bjcvm5c3n.2
title: Dataset for Carbon sequestartion

description: Avijit Ghosh_IGFRI_GSM
DOI: 10.17632/jz42th6t4t.3
title: Techno stress and Coping strategies

description: Techno Stress and Coping Strategies
DOI: 10.17632/2bjcvm5c3n.1
title: Dataset for Carbon sequestartion

description: Avijit Ghosh_IGFRI_GSM
DOI: 10.17632/92s86j8hny.2
title: Test Validation of Extension-Twisting Coupled Laminates with Matched Orthotropic Stiffness.

description: This dataset contains raw and processed test and simulation data that underpins an experimental validation study for three classes of coupled laminate with matching Extension-Twisting coupling. The designs have matching orthotropic stiffness, in both extension and bending, and have been chosen specifically to investigate the influence of mechanical Extension-Shearing and/or Bending-Twisting on the performance of Extension-Twisting coupled designs under axial tension loads. All designs are Hygro-Thermally Curvature Stable (HTCS) or warp-free. An Electronic Annex to the article is also provided, which contains specimen data and Abaqus input files from which the simulations can be reproduced. Supplementary Note: It was not thought possible that zero Extension-Shearing coupled compliances, a16 and a26, could be achieved in the presence of Bending-Twisting coupled stiffnesses, when matching both Extension-Twisting (and inseparable Shearing-Bending) coupled stiffnesses and orthotropic Extensional and Bending stiffnesses. However, this was due to an oversight whilst interrogating the laminate databases. These designs have therefore been provided in a further supplement to the electronic annex to this article, since they do not affect any of the conclusions drawn.
DOI: 10.17632/4bpbk34pt9.1
title: suicide

description: A study on the psychosocial risk factors of suicidal ideation in college students