cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7805865
title: Gamma-hemolysin components: computational strategies for LukF-Hlg2 dimer reconstruction on a model membrane

description: Project files provided as supporting information to the manuscript “Gamma-Hemolysin Components: Computational Strategies for LukF-Hlg2 Dimer Reconstruction on a Model Membrane”. The data set contains the following folders: LukF_Hlg2_distance: files with the minimum distance between LukF and Hlg2 as a function of time for the simulated replica (Fig. S1); files with the minimum distance between each LukF residue and the Hlg2 monomer and vice versa, averaged over the last 600 ns of simulation in the replica where the spontaneous dimerization is observed (fig. S5). HADDOCK_dimer_crystal_pore_displacement: files with the displacement between Hlg2 residues in the HADDOCK model dimer and the same dimer in the crystal pore, after alignment on the LukF monomer (for both the HADDOCK model in presence and in absence of the LukF N-ter) (Fig. S13) interface_area: files with the interface area between the LukF and the Hlg2 monomers in the replica where the spontaneous dimerization on the membrane is observed, as a function of time (total interface and contribution of LukF and Hlg2 rim domains) (Fig. S4) angles: files with the histograms of the angle between LukF and the axis perpendicular to the membrane, for the simulation of the single LukF monomer and for that capturing the spontaneous dimerization on the membrane (Fig. 4); file with the angle between the LukF and the Hlg2 axis as a function of time in the replica where the spontaneous dimerization is observed (Fig. S6) HADDOCK_scores: files with the HADDOCK scores of the predicted LukF-Hlg2 dimers and their RMSD values computed with respect to the same dimer in the crystal pore. The data are reported for the four top-scored models of each cluster ( for both the HADDOCK models in the presence and in the absence of the LukF N-ter) (Fig. 5). RMSD: files with the RMSD as a function of time for the LukF and the Hlg2 monomers in the replica where the spontaneous dimerization on the membrane is observed (Fig. 2, Fig. S2, Fig. S3) RMSF: files with the RMSF of the LukF and the Hlg2 residues in the replica where the spontaneous dimerization on the membrane is observed and in the simulations of the single monomers (Fig. 2) interaction_persistences: files with H-bond (side chain + backbone and backbone only atoms) salt-bridge, and hydrophobic contact persistence matrices for the single LukF monomer simulated alone (299 x 299) and for the LukF-Hlg2 dimer (299+280 x 299+280) (Fig. 4, Fig. S7 + interactions reported in the manuscript) distance_protein_membrane: files with the minimum distance between each monomer and the membrane, in the last 200ns of the simulation of spontaneous dimerization on the membrane (Figure S9). distance_residues_interface: files with the distance between functionally relevant residues measured along the simulation of the HADDOCK dimer in the absence of LukF N-terminus (Figure S14).
DOI: 10.5517/ccdc.csd.cc28b14t
title: CCDC 2095015: Experimental Crystal Structure Determination

description: Related Article: Jeffery Yarger|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dglk1
title: CCDC 2218563: Experimental Crystal Structure Determination

description: Related Article: Simon K. Edin, Ola F. Wendt|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dgll2
title: CCDC 2218564: Experimental Crystal Structure Determination

description: Related Article: Simon K. Edin, Ola F. Wendt|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dcht3
title: CCDC 2215595: Experimental Crystal Structure Determination

description: Related Article: Akshay Nair|2022|CSD Communication|||
description: Related Article: Shreemoyee Kumar, Akshay M. Nair, Jatin Patra, Chandra M. R. Volla|2023|Org.Lett.|25|1114|doi:10.1021/acs.orglett.3c00033
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dr9vb
title: CCDC 2226942: Experimental Crystal Structure Determination

description: Related Article: Arnaud Osi, Aurélien Chardon, Nikolay Tumanov, Johan Wouters, Guillaume Berionni|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dx48r
title: CCDC 2231574: Experimental Crystal Structure Determination

description: Related Article: Milan Gembicky|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dx94s
title: CCDC 2231725: Experimental Crystal Structure Determination

description: Related Article: Dinesh Kumar Gopalakrishnan|2022|CSD Communication|||
description: Related Article: Dinesh Kumar Gopalakrishnan, Sourav Panigrahi, Raju Sen, Janakiram Vaitla|2023|Org.Lett.|25|1519|doi:10.1021/acs.orglett.3c00303
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dxbnb
title: CCDC 2231772: Experimental Crystal Structure Determination

description: Related Article: Markus Hoelscher, Gregor Kemper, Walter Leitner|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dxbxl
title: CCDC 2231780: Experimental Crystal Structure Determination

description: Related Article: ZhouLunan zhoulunan|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.21227/s3xd-2s66
title: LaSBiRD

description: The dataset consists of a large collection of images of 10,916 different species of birds, with a total of 5 million images. This dataset represents a valuable resource for researchers, conservationists, and bird enthusiasts alike, allowing for a more comprehensive understanding of the diversity and distribution of avian species around the world. The data could be used for a wide range of applications, including species identification, biodiversity monitoring, and ecological research. The sheer size of the dataset makes it a powerful tool for machine learning and computer vision algorithms, enabling the development of accurate and efficient automated bird identification systems. Overall, this dataset represents an unprecedented opportunity to advance our knowledge of birds and their role in the natural world.
DOI: 10.35078/kupehg
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Caratinga| Município: Bom Jesus do Amparo

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es
DOI: 10.15784/601679
title: Remotely-sensed iceberg geometries and meltwater fluxes

description: This dataset includes manually-extracted iceberg geometries and meltwater fluxes from 2011-2022 WorldView digital elevation model time series for 15 study sites around Antarctica. Each file contains the coordinates, median surface elevation, density, volume, surface area, draft, and submerged area estimated for an iceberg on two different observation dates (specified in the file name). The submarine meltwater flux for each iceberg, calculated as the volume change over time corrected for surface mass balance processes and creep thinning between observation dates, is provided for each iceberg. Dates listed in file names are in YYYYMMDDhhmmss format. Site abbreviations in file names are as follows: BG = Blanchard Glacier, CG = Cadman Glacier, FG = Ferrigno Glacier, FI = Filchner Ice Shelf, HG = Heim Glacier, LA = Edgeworth Glacier (Larsen A tributary), LB = Cadman Glacier (Larsen B tributary), LG = Leonardo Glacier, MI = Mertz Ice Tongue, PT = Polar Times, RI = Ronne Ice Shelf, SG = Seller Glacier, TG = Thwaites Glacier, TI = Totten Ice Shelf, and WG = Widdowson Glacier.
DOI: 10.35078/mxo7f9
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Varginha| Município: São Sebastião do Oeste

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.6084/m9.figshare.22567984
title: Frequency of A. nasoniae in calliphorid fly pupae collected from European bird's nests

description: <em>Nasonia vitripennis </em>commonly oviposits in calliphorid ‘filth fly’ pupae found in birds’ nests. Nests of blue tit (<em>Cyanistes caeruleus</em>), great tit (<em>Parus major</em>) and other passerine birds were collected shortly following fledging from the nest and placed in bags. Collections were made in June/July 2012 from the area surrounding Harjavalta Town, Finland; from Lausanne, Switzerland; from Kraslava, Latvia; and from Marbury, Cheshire in the UK. Each nest was given an ID number, was manually inspected for calliphorid/protocalliphorid pupae, and these pupae removed individually to a tube for any parasitising wasps to emerge. Where more than one pupa was collected from the same nest this was noted, as pupae from the same nest may be parasitised by the same individual wasp. The pupae, which were monitored daily, were placed at 25 °C for 14 days to allow for <em>N. vitripennis</em> wasps to emerge. <br> Arsenophonus nasoniae presence in <em>N. vitripennis</em> was then assayed. DNA was prepared using the Chelex method. Template quality was assessed based on COI amplification using primers HCO/LCO (Folmer et al, (1994), with 30 PCR cycles of 93°C for 15s, 47°C for 1m, 72°C for 1m and an expected amplicon size of. c. 710bp. Templates passing this quality control were then tested for <em>A. nasoniae</em> using primers amplifying the metalloprotease gene (M1f GGGTCACATACCTATTTT, M1r GTAGTCGCCTGGGTGGG), with 30 cycles of 93°C for 15s, 55°C for 45s, 72°C for 30s and an expected amplicon size of 594bp . <br> Sheet 1: Pupa ID: Unique identifier for fly pupa collected from birds nest. Note, the initial number represents the nest ID (column B) and a suffix letter indicates independent pupae from that nest. Nest ID: Unique identified for the birds nest the pupa was collected from. Arse +/-: Presence of Arsenophonus (+) in Nasonia emerging from that wasp as ascertained through PCR assay. Null value means Arsenophonus not detected. Location: Place the nest/pupa was located. <br> Sheet 2: Summary data. <br>
DOI: 10.6084/m9.figshare.22568065
title: Presence of Nasonia wasps and the bacterium Arsenophonus nasoniae in calliphorid fly pupae collected from great tit nests in Coimbra, Portugal.

description: During the breeding season of 2021, we sampled pupae from great tit nests at Mata Nacional do Choupal (40º13’N, 8º27’W), a mixed woodland on the periphery of the city of Coimbra, Portugal (more details of the study area in (Norte et al., 2009). Old nest material from all nest boxes had been previously removed at the end of the previous breeding season to avoid the accumulation of overwintering <em>Protocalliphora</em> spp. adults (Gold and Dahlsten, 1983). Once all fledglings had left their nests in May/June, the nests were collected in plastic bags and transported to the laboratory. Blowfly puparia were sorted manually from the nest material and were stored in 1.5 mL tubes with absolute ethanol for further genetic analysis. <br> To determine the presence of <em>N. vitripennis </em>and its endosymbiont <em>A. nasoniae</em>, up to five pupae collected from each nest were surface sterilised with 70% ethanol, added to a 2 ml Eppendorf tube, crushed and homogenised using a sterile pestle. Fly pupal shells were removed with the aid of a sterile forceps and DNA was extracted from the homogenised sample using a Zymoresearch Quick DNA TM Miniprep plus kit (Zymoresearch, USA). These were then subject to diagnostic QC PCR of the COI gene with HCO/LCO primers described above (this amplifies fly DNA in the absence of other parties, and establishes template quality). Then, PCR assays for wasp and microbe were performed. Amplicons for the <em>A. nasoniae</em> PCR assay were sequenced using the Sanger method to confirm identity. <br> Column A: Nest ID Column B: Collection date for fly pupae Column C: Number of fly pupae combined for testing. Column D: Presence of Nasonia (- = not present += present) Column E: Presence of A. nasoniae (- = not present += present)
DOI: 10.6084/m9.figshare.22568479
title: Efficient Multimodal Sampling via Tempered Distribution Flow

description: Sampling from high-dimensional distributions is a fundamental problem in statistical research and practice. However, great challenges emerge when the target density function is unnormalized and contains isolated modes. We tackle this difficulty by fitting an invertible transformation mapping, called a transport map, between a reference probability measure and the target distribution, so that sampling from the target distribution can be achieved by pushing forward a reference sample through the transport map. We theoretically analyze the limitations of existing transport-based sampling methods using the Wasserstein gradient flow theory, and propose a new method called TemperFlow that addresses the multimodality issue. TemperFlow adaptively learns a sequence of tempered distributions to progressively approach the target distribution, and we prove that it overcomes the limitations of existing methods. Various experiments demonstrate the superior performance of this novel sampler compared to traditional methods, and we show its applications in modern deep learning tasks such as image generation. The programming code for the numerical experiments is available in the supplementary material.
DOI: 10.6084/m9.figshare.22568479.v1
title: Efficient Multimodal Sampling via Tempered Distribution Flow

description: Sampling from high-dimensional distributions is a fundamental problem in statistical research and practice. However, great challenges emerge when the target density function is unnormalized and contains isolated modes. We tackle this difficulty by fitting an invertible transformation mapping, called a transport map, between a reference probability measure and the target distribution, so that sampling from the target distribution can be achieved by pushing forward a reference sample through the transport map. We theoretically analyze the limitations of existing transport-based sampling methods using the Wasserstein gradient flow theory, and propose a new method called TemperFlow that addresses the multimodality issue. TemperFlow adaptively learns a sequence of tempered distributions to progressively approach the target distribution, and we prove that it overcomes the limitations of existing methods. Various experiments demonstrate the superior performance of this novel sampler compared to traditional methods, and we show its applications in modern deep learning tasks such as image generation. The programming code for the numerical experiments is available in the supplementary material.
DOI: 10.35078/lgl0ki
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Caratinga| Município: Bom Jesus do Galho

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es
DOI: 10.15129/d1c8b4eb-6dec-4237-8cd4-384717ce0c9f
title: Data for: "Porous Metal-Organic Cages Based on Rigid Bicyclo[2.2.2]oct-7-ene Type Ligands: Synthesis, Structure, and Gas Uptake Properties"

description: Raw data used to plot the results presented in the published paper. The folder contains 5 separate folders corresponding to each of the experimental techniques used in the paper. 1. Gas sorption analysis 2. Infra-red spectra 3. NMR spectra 4. Powder X-ray diffraction data 5. Thermogravimetric analysis data (TGA). Each folder contains the raw data and a .txt file explaining the sample names and the relation to the data in the paper. Full information on methodology and equipment used is provided in the paper itself.
DOI: 10.6084/m9.figshare.22568461.v1
title: Site_data

description: Dataset on sites used in study
DOI: 10.6084/m9.figshare.22568461
title: Site_data

description: Dataset on sites used in study
DOI: 10.5281/zenodo.7780589
title: Systematic Literature Review - Selected Articles Data Extraction

description: The files included are the following: - CSV with the raw data extracted from abstract + full-text review from the selected articles. - CSV with normalized data according to the article.
DOI: 10.5281/zenodo.7780590
title: Systematic Literature Review - Selected Articles Data Extraction

description: The files included are the following: - CSV with the raw data extracted from abstract + full-text review from the selected articles. - CSV with normalized data according to the article.
DOI: 10.5281/zenodo.7515205
title: GRAND-SLAM analysis of simulated and real SLAM-seq datasets for grandRescue

description: These are several processed datasets for the purpose of investigating 4sU-induced toxicity, mapping impairment and the potential of grandRescue to alleviate these effects. Published dataset: Narain dataset (Narain, et al.): https://doi.org/10.1016/j.molcel.2021.06.016 The zip files contain the full output from the processing pipeline (including the mapped reads, the scripts to run the pipeline and the output). The json file is required if you want to start from scratch. The *.tsv.gz files are the GRAND-SLAM output tables. <br> To generate the GRAND-SLAM output yourself, first prepare the mouse & human genomes. Then run the following command with the respective cit-files, prefixes (*.cit) and genomes (e.g. h.ens90 or m.ens102): gedi -e Slam -trim5p 15 -reads *.cit -genomic m.ens102 -prefix grandslam_t15/* -plot -D -modelall To generate the cit file you have to modify the first lines in start.bash to match the paths on your file system, and then run it. You can also start from scratch (i.e., the json file): Prepare the human/mouse genome and their rRNA sequence<br> Run: gedi -e Pipeline -r parallel -j *.json rnaseq_mapping.sh report.sh grandslam.sh Software versions: gedi toolkit 1.0.5<br> GRAND-SLAM 2.0.7<br> STAR version 2.7.10b