cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26208/b01x-aq20
title: On bridging paired-end RNA-seq data

description: The widely-used high-throughput RNA-sequencing technologies (RNA-seq) usually produce paired-end reads. We explore if full fragments can be computationally reconstructed from the sequenced two ends—a problem here we refer to as bridging. Solving this problem provides longer, more informative RNA-seq reads, and hence benefits downstream RNA-seq analysis such as transcriptome assembly and expression quantification. However, bridging is a challenging and complicated task owing to alternative splicing, transcript noises, and sequencing errors. It remains unclear if the data itself provides sufficient information for accurate bridging, let alone proper models and efficient algorithms that characterize and determine the true bridges. Algorithmic Results: We studied this problem in two settings: reference-based bridging, which assumes reads alignments are available and reconstructs the alignments of full fragments, and de novo bridging, which reconstructs sequences of entire fragments from sequences of the two ends. We proposed a novel mathematical formulation that works for both settings—to seek a path in an underlying graph data structure (i.e., splice graph for reference-based bridging, and compacted de Bruijn graph for de novo bridging) such that its bottleneck weight is maximized. This formulation characterizes true bridges and is efficient in filtering out false bridges. This formulation admits optimal substructure property, and hence efficient dynamic programming algorithms can be designed. For reference-based bridging, we designed such an algorithm to calculate the top N bridging paths, followed by a voting approach to select one using the distribution of fragment length. For de novo bridging, we designed a new truncated Dijkstra’s algorithm. To further speed up, we proposed a novel algorithm that reuses the shortest path tree to avoid running the truncated Dijkstra’s algorithm from scratch for all vertices. These innovative techniques result in scalable algorithms that can bridge all paired-end reads in a compacted de Bruijn graph with millions of vertices. Experimental Results: We showed that paired-end RNA-seq reads can be accurately bridged to a large extend. Our reference-based bridging tool could correctly bridge more than 79.6% of reads. For de novo bridging, high precision was observed with varied sensitivity. We also showed that bridging can improve reference-based transcript assembly: the improvement was significant (up to 14.4% measured with adjusted precision), and universal in all combinations with different aligners and assemblers. Availability: The implementation of the algorithms for reference-based and de novo bridging are available at https://github.com/Shao-Group/rnabridge-align and https://github.com/Shao-Group/rnabridge-denovo, respectively. Scripts, datasets, and documentations that can reproduce the experimental results in this manuscript are available at https://github.com/Shao-Group/rnabridge-test.
DOI: 10.6084/m9.figshare.13103414
title: Dataset associated with the article "Affordable mobile microfluidic diagnostics: minimum requirements for smartphones and digital imaging for colorimetric and fluorometric viral antibody detection"

description: The dataset consists in a list of images taken with various imaging systems and in various conditions. The first aim was to compare the analytical performance of a range of imaging systems (digital cameras, smartphones, laboratory imaging systems) to detect colorimetric and fluorescent signals. The second aim was to determine whether they were capable of measuring simulated antibody responses and whether smartphones could be used in serologic diagnostic tests using microfluidics.<br>
DOI: 10.6084/m9.figshare.13103414.v1
title: Dataset associated with the article "Affordable mobile microfluidic diagnostics: minimum requirements for smartphones and digital imaging for colorimetric and fluorometric viral antibody detection"

description: The dataset consists in a list of images taken with various imaging systems and in various conditions. The first aim was to compare the analytical performance of a range of imaging systems (digital cameras, smartphones, laboratory imaging systems) to detect colorimetric and fluorescent signals. The second aim was to determine whether they were capable of measuring simulated antibody responses and whether smartphones could be used in serologic diagnostic tests using microfluidics.<br>
DOI: 10.6084/m9.figshare.12912080
title: chemblDB3.sqlitdb

description: Matched molecular pair transformations from ChEMBL database
DOI: 10.34740/kaggle/dsv/1925791
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.5281/zenodo.4499184
title: Mechanisms driving MJO teleconnection changes with warming in CMIP6: Data for figures

description: This dataset contains files that can be used to reproduce the figures in<br> Jenney et al., (2021) " Mechanisms driving MJO teleconnection changes with <br> warming in CMIP6". Most of the files are MATLAB structures as described below I. Output from linear baroclinic model (LBM): meridional wind at 850 hPa<br> description: LBM output for experiments with control MJO and varied <br> mean states<br> name: "v850_&lt;model_name&gt;.mat"<br> format: matlab structure "out" with <br> fields: <br> ThVh (historical dry static energy & historical winds)<br> ThVs (historical dry static energy & future winds)<br> TsVh (future dry static energy & historical winds)<br> TsVs (future dry static energy & future winds)<br> dimensions:<br> [30 x 128 x 64 x 59] = <br> [ensemble member x lon x lat x simulation day] II. Output from linear baroclinic model (LBM) for MJO perturbed experiments<br> name: "&lt;EXPERIMENT&gt;_v850_&lt;model&gt;.mat"<br> experiments: <br> EAST20: 20-degree eastward shifted thermal forcing<br> MEDIUM: lower bound of increased prop. speed experiment<br> FAST: upper bound of increased prop. speed experiment<br> STRONG: 20% stronger thermal forcing<br> format, fields, & dimensions: files with format identical to I III. Linearized Rossby wave source<br> name: "rws.mat"<br> format: matlab structure "rws"<br> fields & dimensions: these are described and listed in the structure IV. Stationary Rossby wave number<br> description: K_s computed for individual CMIP6 model mean states and for<br> the multi-model mean wind<br> name: "Ks.mat"<br> format: matlab structure "Ks_struct"<br> fields & dimensions: described and listed in the structure V. Model global mean surface temperature<br> description: global mean surface temperature for individual CMIP6 models<br> for the historical and future periods<br> name: "mmGlobalSfcTemp.nc"<br> format: netcdf file
DOI: 10.5281/zenodo.4473008
title: Evaluation and optimisation of the I/O scalability for the next generation of Earth system models: IFS CY43R3 and XIOS 2.0 integration as a case study

description: Two different output datasets based on the AMIP configuration are used to check the correctness of the IFS CY43R3 and XIOS 2.0 integration. They are GRIB and NetCDF files corresponding to the sequential output scheme and XIOS respectively. It is a 10-day forecast with an output frequency of 3 and 6 hours using a Tco255L91 configuration.
DOI: 10.5281/zenodo.4473007
title: Evaluation and optimisation of the I/O scalability for the next generation of Earth system models: IFS CY43R3 and XIOS 2.0 integration as a case study

description: Two different output datasets based on the AMIP configuration are used to check the correctness of the IFS CY43R3 and XIOS 2.0 integration. They are GRIB and NetCDF files corresponding to the sequential output scheme and XIOS respectively. It is a 10-day forecast with an output frequency of 3 and 6 hours using a Tco255L91 configuration.
DOI: 10.5517/ccdc.csd.cc210g7s
title: CCDC 1877274: Experimental Crystal Structure Determination

description: Related Article: Fuli Zhang, Pengchao Zhou, Shulin Zhang, Yuanyang Li, Quanfeng Zhang, Wenlong Guo, Jing Huang, Wenyu Wang, Zhen Dong, Bin Wei, Donghui Wei, Guangxiu Cao, Bin Zhai|2021|J.Lumin.|233|117880|doi:10.1016/j.jlumin.2020.117880
DOI: 10.5517/ccdc.csd.cc23f5vl
title: CCDC 1949089: Experimental Crystal Structure Determination

description: Related Article: Hai-Yan Zhang, Lei Liu, Hai-Jun Wang, Jing-Wen Sun|2021|J.Solid State Chem.|296|121986|doi:10.1016/j.jssc.2021.121986
DOI: 10.5281/zenodo.4526127
title: Stream radar data and locations

description: This is a supplement to the journal article titled Uncertainty in Remote Sensing of Streams using Noncontact Radars by Khan et al., submitted to the Journal of Hydrology. Dataset includes time series of variables collected by 8 stream radars. A kmz file is included for the stream radar locations.
DOI: 10.5281/zenodo.4526126
title: Stream radar data and locations

description: This is a supplement to the journal article titled Uncertainty in Remote Sensing of Streams using Noncontact Radars by Khan et al., submitted to the Journal of Hydrology. Dataset includes time series of variables collected by 8 stream radars. A kmz file is included for the stream radar locations.
DOI: 10.15468/86uah6
title: Two new species of Eumeninae from Iran (Hymenoptera: Vespidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Gusenleitner, J., Fallahzadeh, M., Haghighi, A., Dousti, A. F. (2013): Two new species of Eumeninae from Iran (Hymenoptera: Vespidae). Linzer biologische Beiträge 45 (1): 109-116, DOI: http://doi.org/10.5281/zenodo.4526089
DOI: 10.15468/fjugx9
title: Aceria species associated with Solanaceae worldwide with description of a new species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Tajaddod, Sadegh, Lotfollahi, Parisa, Lillo, Enrico de (2020): Aceria species associated with Solanaceae worldwide with description of a new species. Acarologia 60 (2): 243-253, DOI: 10.24349/acarologia/20204365, URL: http://dx.doi.org/10.24349/acarologia/20204365
DOI: 10.5281/zenodo.4526224
title: XQuAD-ca

description: Professional translation of XQuAD into Catalan XQuAD (Cross-lingual Question Answering Dataset) is a benchmark dataset for evaluating cross-lingual question answering performance. The dataset consists of a subset of 240 paragraphs and 1190 question-answer pairs from the development set of SQuAD v1.1 (Rajpurkar et al., 2016) together with their professional translations into ten languages: Spanish, German, Greek, Russian, Turkish, Arabic, Vietnamese, Thai, Chinese, and Hindi. Rumanian was added later. We added the 13th language to the corpus using also native, professional catalan translators. For more information on how XQuAD was created, refer to the paper, On the Cross-lingual Transferability of Monolingual Representations (https://arxiv.org/abs/1910.11856), or visit the webpage https://github.com/deepmind/xquad Translation into Catalan was commissioned by BSC TeMU (https://temu.bsc.es/) within the AINA project.
DOI: 10.25345/c57b85
title: MassIVE MSV000086827 - EDC X-linking of recombinant RdRp/Nsp12
title: EDC cross-linking of the recombinant SARS-CoV-2/hCoV-19 RdRp Nsp12
DOI: 10.6084/m9.figshare.13807955
title: Database.xlsx

description: This database contains demographical and clinical data on vision of children aged 0-18 years who consulted in the Department of Ophthalmology of Baguio General Hospital and Medical Center in Baguio City, Northern Luzon, Philippines in 2018.
DOI: 10.6084/m9.figshare.13807955.v1
title: Database.xlsx

description: This database contains demographical and clinical data on vision of children aged 0-18 years who consulted in the Department of Ophthalmology of Baguio General Hospital and Medical Center in Baguio City, Northern Luzon, Philippines in 2018.
DOI: 10.15468/fh5jcf
title: Survey of phytoseiid mites (Acari: Mesostigmata, Phytoseiidae) in citrus orchards and a key for Amblyseiinae in Vietnam

description: This dataset contains the digitized treatments in Plazi based on the original journal article Fang, Xiao-Duan, Nguyen, Van-Liem, Ouyang, Ge-Cheng, Wu, Wei-Nan (2020): Survey of phytoseiid mites (Acari: Mesostigmata, Phytoseiidae) in citrus orchards and a key for Amblyseiinae in Vietnam. Acarologia 60 (2): 254-267, DOI: 10.24349/acarologia/20204366, URL: http://dx.doi.org/10.24349/acarologia/20204366
DOI: 10.5281/zenodo.4526286
title: McCarthy 2021 EJWR Archive

description: Data and code archive for McCarthy et al. 2021. Bird and small mammal community composition and abundance in upland open habitats and early conifer forests. European Journal of Wildlife Research.
DOI: 10.5281/zenodo.4526285
title: McCarthy 2021 EJWR Archive

description: Data and code archive for McCarthy et al. 2021. Bird and small mammal community composition and abundance in upland open habitats and early conifer forests. European Journal of Wildlife Research.
DOI: 10.5281/zenodo.1493407
title: Landsat-based Gypsy Moth Defoliation Assessment (Southern New England)

description: The re-analysis dataset hosted here extends the work presented in the the manuscript, "Extensive gypsy moth defoliation in Southern New England characterized using Landsat satellite observations" to a larger study area that includes Landsat WRS-2 Path/Rows 12/30, 13/30, 1/131, 12/31 and 13/31 and covers all of Southern New England (RI, CT, and MA) and the southern portions of NH and VT. This re-analysis dataset utilizes Landsat Collection 1 data and the stable base period has been adjusted to 2000-2010. Therefore, the products hosted here may differ slightly from our previously published datasets. ** Dataset updated on 11-21-2018 Mapped values represent condition scores (NRT) or condition score averages (annual), with "condition" estimated as the difference between observed and predicted Tasseled Cap Greenness divided by the baseline harmonic model RMSE Large negative changes in Greenness values are assumed to indicate more severe defoliation. Condition assessments provide a continuous measure of change; however, to aid in interpretation, we often use four severity categories to visualize condition scores: slight change (deviations 1-2 times the model RMSE), moderate change (deviations 2-3 times the model RMSE), large change (deviations 3-4 times the model RMSE), and very large change (deviations greater than 4 times the model RMSE). Categorical versions of annual products are provided as part of this dataset. The current version of this dataset includes results for 2015, 2016, 2017, and 2018. Results are available as both single-date Near-Real_time (NRT) products, as well as season-averaged annual (final) products. A summary archive that includes stacked results for all years is also available. All GeoTIFFs are georeferenced and provided in NAD/Conus Albers (EPSG: 5070). Final products are available with and without an NLCD forest mask applied. NRT products have been cloud masked using Fmask results.. Please cite as: Pasquarella, Valerie J. (2018). Landsat-based Gypsy Moth Defoliation Assessment (Southern New England) (Version 3.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.1493407 For more on the methods used to generate these datasets, see Pasquarella, V.J., Bradley, B.A, & Woodcock, C.E. Near-real-time monitoring of insect defoliation using Landsat time series. Forests 8(8), 275; doi:10.3390/f8080275, available online: http://www.mdpi.com/1999-4907/8/8/275.
DOI: 10.15468/4tc674
title: Biodiversitätsforschung in Vorarlberg, Austria occ. Zur Schmetterlingsfauna des Verwalls - 1. Teil Tagfalter, Spinner und Schwärmer (Insecta, Lepidoptera, Diurna, Bombyces et Sphinges sensu

description: This dataset contains the digitized treatments in Plazi based on the original journal article Aistleitner, E. (2014): Biodiversitätsforschung in Vorarlberg, Austria occ. Zur Schmetterlingsfauna des Verwalls - 1. Teil Tagfalter, Spinner und Schwärmer (Insecta, Lepidoptera, Diurna, Bombyces et Sphinges sensu. Linzer biologische Beiträge 46 (1): 221-290, DOI: http://doi.org/10.5281/zenodo.4526236
DOI: 10.15468/d37jq7
title: On the Staphylinidae of Sardinia, Italy (Insecta: Coleoptera)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Assing, V. (2014): On the Staphylinidae of Sardinia, Italy (Insecta: Coleoptera). Linzer biologische Beiträge 46 (1): 415-428, DOI: http://doi.org/10.5281/zenodo.4526290
DOI: 10.15468/zynqa4
title: New records of the genusBryobia (Acari: Tetranychidae) from Syria with description of a new species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Barbar, Ziad, Auger, Philippe (2020): New records of the genusBryobia (Acari: Tetranychidae) from Syria with description of a new species. Acarologia 60 (2): 268-288, DOI: 10.24349/acarologia/20204367, URL: http://dx.doi.org/10.24349/acarologia/20204367
DOI: 10.15468/aa8avf
title: A revision of Palaearctic and Oriental Rugilus. V. Two new species from China and additional records (Coleoptera: Staphylinidae: Paederinae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Assing, Volker (2015): A revision of Palaearctic and Oriental Rugilus. V. Two new species from China and additional records (Coleoptera: Staphylinidae: Paederinae). Linzer biologische Beiträge 47 (1): 73-82, DOI: http://doi.org/10.5281/zenodo.4526339
DOI: 10.15468/grhug4
title: A new species of Phloeocharis MANNERHEIM from Spain, with a note on P. brachyptera SHARP (Coleoptera: Staphylinidae: Phloeocharinae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Assing, Volker (2015): A new species of Phloeocharis MANNERHEIM from Spain, with a note on P. brachyptera SHARP (Coleoptera: Staphylinidae: Phloeocharinae). Linzer biologische Beiträge 47 (1): 57-62, DOI: http://doi.org/10.5281/zenodo.4526324
DOI: 10.5281/zenodo.4428937
title: Supporting Data for: Information Retrieval Interfaces in Virtual Reality - A Scoping Review Focused on Current Generation Technology

description: This is the full data set of all reviewed research items obtained from Google Scholar, Web of Science and Scopus for the Scoping Literature Review <em>Information Retrieval Interfaces in Virtual Reality - A Scoping Review Focused on Current Generation VR technology.</em>
DOI: 10.5281/zenodo.3985948
title: Supporting Data for: Information Retrieval Interfaces in Virtual Reality - A Scoping Review Focused on Current Generation Technology

description: This is the full data set of all reviewed research items obtained from Google Scholar, Web of Science and Scopus for the Scoping Literature Review <em>Information Retrieval Interfaces in Virtual Reality - A Scoping Review Focused on Current Generation VR technology.</em>
DOI: 10.5281/zenodo.4526306
title: Retrospective analysis of the use of osteoporosis medication at the presentation of non-vertebral fragility fractures in a predominantly Hispanic population.

description: This is a de identified data set including 719 patients older than 50 years of age. The patients has a fragility fracture of the hip, shoulder, wrist and ankle. Comorbidities and medications taken at the time of presentation are documented.
DOI: 10.5281/zenodo.4526305
title: Retrospective analysis of the use of osteoporosis medication at the presentation of non-vertebral fragility fractures in a predominantly Hispanic population.

description: This is a de identified data set including 719 patients older than 50 years of age. The patients has a fragility fracture of the hip, shoulder, wrist and ankle. Comorbidities and medications taken at the time of presentation are documented.
DOI: 10.5281/zenodo.4526322
title: Design of sand-based, 3D-printed analogue faults with controlled frictional properties

description: Experimental Raw Data for the paper "Design of sand-based, 3D-printed analogue faults with controlled frictional properties" submitted to JGR: Solid Earth.
DOI: 10.5281/zenodo.4526321
title: Design of sand-based, 3D-printed analogue faults with controlled frictional properties

description: Experimental Raw Data for the paper "Design of sand-based, 3D-printed analogue faults with controlled frictional properties" submitted to JGR: Solid Earth.
DOI: 10.5281/zenodo.3957432
title: Datasets from the study Peer learning as a key component of an Integrated Teaching Method in large size classes

description: The theory and research on learning in higher education are pointing out that active methods are able to improve learners’ performance more than passive ones and to trigger situated and deep learning. However, some factors prevent their spread and trust amongst university instructors, like their complex logistics in large size lectures. Indeed, in academic crowded classes these interactive-engagement methodologies are sporadically employed and seem to be rarely successful. In this context, in the academic years 2017-2018 and 2018-2019 we carried out a quasi-experiment at Politecnico di Milano aimed at investigating the effectiveness of the integration of peer learning activities, strengthened by the use of technology, into traditional Physics lectures as a teaching method in large size classes. Data related to both an experimental and a control group were gathered and analysed through descriptive and inferential statistics; Shapiro-Wilk, Levene, Mann-Whitney U, Wilcoxon signed-rank and Kruskal-Wallis tests were employed. Our combined strategy appears to be effective with relation to learning Physics and more successful than traditional courses centred on academic lectures, regardless of the difficulty of the issues investigated. Furthermore, a threshold for the exposure to peer learning in order for it to be effective has been highlighed. In this page it is shared: 1) Dataset with reference to both 2017-2018 and 2018-2019 2) R Script with reference to both 2017-2018 and 2018-2019
DOI: 10.25386/genetics.13724035
title: Supplemental Material for Holmes et al., 2021

description: Supplemental Material for Holmes et al., 2021
DOI: 10.25403/upresearchdata.13312547.v1
title: Business plan accommodation swap

description: This is excel data collected through a survey. The respondents are individuals aged 50 years. Quantitative study was conducted, wherein questionnaires where used to collect data. The instrument was a google forms questionnaire. My data set is a excel sheet which was an extract from the Google forms responses.
DOI: 10.25403/upresearchdata.13312547
title: Business plan accommodation swap

description: This is excel data collected through a survey. The respondents are individuals aged 50 years. Quantitative study was conducted, wherein questionnaires where used to collect data. The instrument was a google forms questionnaire. My data set is a excel sheet which was an extract from the Google forms responses.
DOI: 10.25403/upresearchdata.13312760
title: Dealing with social activism in the South African Mining Industry

description: Datasets underpins the research study. Methodology: Semi-structured interviews. Inductive, exploratory, purposive & snowball sampling and thematic analysis. <br>
DOI: 10.25403/upresearchdata.13312760.v1
title: Dealing with social activism in the South African Mining Industry

description: Datasets underpins the research study. Methodology: Semi-structured interviews. Inductive, exploratory, purposive & snowball sampling and thematic analysis. <br>
DOI: 10.15468/t2z7nz
title: Beschreibung neuer Clytini und Anaglyptini vorwiegend aus dem indonesischen Teil von Borneo (Kalimantan) (Coleoptera, Cerambycidae, Cerambycinae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Dauber, Diethard (2016): Beschreibung neuer Clytini und Anaglyptini vorwiegend aus dem indonesischen Teil von Borneo (Kalimantan) (Coleoptera, Cerambycidae, Cerambycinae). Linzer biologische Beiträge 48 (1): 21-54, DOI: http://doi.org/10.5281/zenodo.4526379