cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3573994
title: MS data set: Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data

description: Data set consisting of raw LC-MS2 data, LC-MS1 peak data and a description For unreviewed publication preprint: <strong>Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS<sup>1</sup>) and <em>in silico </em>Peptide Mass Data</strong> ABSTRACT Over the past decade, modern methods of mass spectrometry (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms. While MALDI-TOF MS has already revolutionized the way microorganisms are identified, recent years have witnessed also substantial progress in the development of liquid chromatography (LC)-MS based proteomics for microbiological applications. For example, LC-tandem mass spectrometry (LC-MS<sup>2</sup>) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at the strain level. However, such investigations can be very time-consuming, especially if the experimental LC-MS<sup>2</sup> data are tested against sequence databases covering a broad panel of different microbiological taxa. In this proof of concept study, we present an alternative bottom-up proteomics method for microbial identification. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC-MS measurements. MS<sup>1</sup> data are then extracted and systematically tested against an in silico library of peptide mass data compiled in house. The library has been computed from the UniProt Knowledgebase Swiss-Prot and TrEMBL databases and comprises more than 12,000 strain-specific in silico profiles, each containing tens of thousands of peptide mass entries. Identification analysis involves computation of score values derived from spectral distances between experimental and in silico peptide mass data and compilation of score ranking lists. The taxonomic positions of the microbial samples are then determined by using the best-matching database entries. The suggested method is computationally efficient – less than two minutes per sample - and has been successfully tested by a set of 19 different microbial pathogens. The approach is rapid, accurate and automatable and holds great potential for future microbiological applications. <em>For details see the following preprint: Lasch, P. Schneider, A. Blumenscheit, C. and Doellinger, J. “Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data”. bioRxiv preprint, http://dx.doi.org/10.1101/870089</em>
description: License type for data base files (spectra): Creative Commons Attribution Non Commercial 4.0 International (CC-BY-NC): Licensees must credit the original authors by stating their names & the original work's title. Licensees may copy, distribute, display, and perform the work and make derivative works and remixes based on it only for non-commercial purposes.
DOI: 10.15468/jefd6o
title: Nueva especie de Aleuropleurocelus Drews y Sampson (Hemiptera: Aleyrodidae) y clave para especies del grupo de forma oval

description: This dataset contains the digitized treatments in Plazi based on the original journal article Sánchez-Flores, Oscar Ángel, Carapia-Ruiz, Vicente Emilio (2018): Nueva especie de Aleuropleurocelus Drews y Sampson (Hemiptera: Aleyrodidae) y clave para especies del grupo de forma oval. Insecta Mundi 651: 1-12, DOI: http://doi.org/10.5281/zenodo.3709653
DOI: 10.5281/zenodo.3703075
title: Alpiner Ortsnamen Gazeteer/Mountaineering Place Name Gazeteer

description: The unified gazetteer for this project was derived from 6 sources named here as local gazetteers. Entries from these gazeteers were automatically matched to the Alpenwort Corpus, its Table of Content and to the OeAV Photo Index. All matches where integrated in the file "mount_place_name_gaz.txt". For these 6 gazetteers a matching of the place types present in these gazetteers to broader categories was performed and the matching is in the file "gaz_union_thes.txt". details on semanticmountain.at
description: Research fund: Austrian Academy of Sciences, Semantics for Mountaineering History, Projector.: GD 2016/45
DOI: 10.5281/zenodo.3703076
title: Alpiner Ortsnamen Gazeteer/Mountaineering Place Name Gazeteer

description: The unified gazetteer for this project was derived from 6 sources named here as local gazetteers. Entries from these gazeteers were automatically matched to the Alpenwort Corpus, its Table of Content and to the OeAV Photo Index. All matches where integrated in the file "mount_place_name_gaz.txt". For these 6 gazetteers a matching of the place types present in these gazetteers to broader categories was performed and the matching is in the file "gaz_union_thes.txt". details on semanticmountain.at
description: Research fund: Austrian Academy of Sciences, Semantics for Mountaineering History, Projector.: GD 2016/45
DOI: 10.15468/tktaif
title: A new species of Copionodon lacking a free orbital rim (Siluriformes: Trichomycteridae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Pinna, Mario de, Burger, Rafael, Zanata, Angela Maria (2018): A new species of Copionodon lacking a free orbital rim (Siluriformes: Trichomycteridae). Neotropical Ichthyology 16 (2): 1-9, DOI: 10.1590/1982-0224-20170146
DOI: 10.15468/vnpnm2
title: Redescription of Hyphessobrycon itaparicensis, a senior synonym of H. sergipanus (Characiformes: Characidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Zanata, Angela M., Camelier, Priscila, Carvalho, Fernando R., Lima, Sergio M. Q. (2018): Redescription of Hyphessobrycon itaparicensis, a senior synonym of H. sergipanus (Characiformes: Characidae). Neotropical Ichthyology 16 (1): 1-12, DOI: 10.1590/1982-0224-20170141
DOI: 10.5281/zenodo.3709717
title: Chameleon CHI@UC cloud trace (2019-11-01)

description: This cloud trace contains instance events and machine events for the bare-metal cloud on the Chameleon testbed since it was built in 2015. Several text fields have been anonymized to hide user information. This trace contains data from 2015-06-17T17:54:29.000Z until 2019-11-01T00:41:54.000Z. The epoch time for timestamps is 2015-06-08T00:00:00. It follows <strong>version 0.3</strong> of the cloud trace format. You can find more information and trace datasets at Science Clouds.
description: Please contact the data owner for using this data for any research purpose prior to release and acknowledge the source of the data in any published material based on it.
description: {"references": ["Keahey, Kate, et al. \"Chameleon: a scalable production testbed for computer science research.\" Contemporary High Performance Computing. CRC Press, 2019. 123-148."]}
DOI: 10.15468/udujnc
title: Contributions to the systematic of Pimelodidae (Osteichthyes, Siluriformes): basic and molecular cytogenetics on seven species of Pimelodus from three Brazilian hydrographic systems

description: This dataset contains the digitized treatments in Plazi based on the original journal article Girardi, Simone C., Pavanelli, Carla S., Margarido, Vladimir P. (2018): Contributions to the systematic of Pimelodidae (Osteichthyes, Siluriformes): basic and molecular cytogenetics on seven species of Pimelodus from three Brazilian hydrographic systems. Neotropical Ichthyology 16 (2): 1-16, DOI: 10.1590/1982-0224-20170148
DOI: 10.15468/yyvmte
title: Contribution to the knowledge of Chilean Phycitinae (Lepidoptera: Pyralidae): new species of Passadena Hulst, 1900, and Ragonotia Grote, 1888, from northern Chile

description: This dataset contains the digitized treatments in Plazi based on the original journal article Cepeda, Danilo E. (2018): Contribution to the knowledge of Chilean Phycitinae (Lepidoptera: Pyralidae): new species of Passadena Hulst, 1900, and Ragonotia Grote, 1888, from northern Chile. Insecta Mundi 654: 1-12, DOI: http://doi.org/10.5281/zenodo.3709729
DOI: 10.15468/b0aghf
title: Descripción de cuatro especies nuevas de Aleurovitreus Martin (Hemiptera: Aleyrodidae) y clave para especies del género

description: This dataset contains the digitized treatments in Plazi based on the original journal article Sánchez-Flores, Oscar Ángel, Carapia-Ruiz, Vicente Emilio, García-Martínez, Oswaldo, Castillo-Gutiérrez, Antonio, Garcia-Ochaeta, José Francisco (2018): Descripción de cuatro especies nuevas de Aleurovitreus Martin (Hemiptera: Aleyrodidae) y clave para especies del género. Insecta Mundi 655: 1-15, DOI: http://doi.org/10.5281/zenodo.3709759
DOI: 10.15468/n9kzld
title: A new species of Tetragonopterus (Characiformes: Characidae) from Central Amazon lowlands, Brazil

description: This dataset contains the digitized treatments in Plazi based on the original journal article Urbanski, Bruna Q., Melo, Bruno F., Silva, Gabriel S. C., Benine, Ricardo C. (2018): A new species of Tetragonopterus (Characiformes: Characidae) from Central Amazon lowlands, Brazil. Neotropical Ichthyology 16 (2): 1-7, DOI: 10.1590/1982-0224-20170158
DOI: 10.15468/gkqcjs
title: External morphology, postcranial and appendicular osteology of three southwestern Atlantic flatfishes (Paralichthys, Paralichthyidae), and comparisons with other congeneric species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Díaz de Astarloa, Juan M., Munroe, Thomas A., Béarez, Philippe, Gonzalez-Castro, Mariano, Castellini, Damián L. (2018): External morphology, postcranial and appendicular osteology of three southwestern Atlantic flatfishes (Paralichthys, Paralichthyidae), and comparisons with other congeneric species. Neotropical Ichthyology 16 (2): 1-21, DOI: 10.1590/1982-0224-20170164
DOI: 10.7910/dvn/x1nxjy/9ixqv3
title: paper.tex

description: :unav
DOI: 10.15468/1xpw08
title: Miscellaneous notes on the fireflies (Coleoptera: Lampyridae) in McDermott’s 1966 catalogue of Lampyridae

description: This dataset contains the digitized treatments in Plazi based on the original journal article Keller, Oliver, Branham, Marc A. (2018): Miscellaneous notes on the fireflies (Coleoptera: Lampyridae) in McDermott’s 1966 catalogue of Lampyridae. Insecta Mundi 656: 1-10, DOI: http://doi.org/10.5281/zenodo.3709818
DOI: 10.5281/zenodo.3710424
title: Data for Investigating the Technical Debt in Procedural Model Transformation Languages

description: The content presents the data for Investigating the Technical Debt in Procedural Model Transformation Languages
DOI: 10.5281/zenodo.3710425
title: Data for Investigating the Technical Debt in Procedural Model Transformation Languages

description: The content presents the data for Investigating the Technical Debt in Procedural Model Transformation Languages
DOI: 10.7910/dvn/x1nxjy/df3dhr
title: paper.pdf

description: :unav
DOI: 10.7910/dvn/x1nxjy/i1dpug
title: S1 Appendix.Rmd

description: :unav
DOI: 10.7910/dvn/x1nxjy/mczw1w
title: S1-Appendix.tex

description: :unav
DOI: 10.15468/8v5tlj
title: New species of Elaphidiini from Central America (Coleoptera: Cerambycidae: Cerambycinae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Wappes, James E., Botero, Juan Pablo, Santos-Silva, Antonio (2018): New species of Elaphidiini from Central America (Coleoptera: Cerambycidae: Cerambycinae). Insecta Mundi 657: 1-12, DOI: http://doi.org/10.5281/zenodo.3709833
DOI: 10.7910/dvn/x1nxjy/zqtyga
title: paper.Rmd

description: :unav
DOI: 10.15468/c8uyxv
title: Review of the family Rivulidae (Cyprinodontiformes, Aplocheiloidei) and a molecular and morphological phylogeny of the annual fish genus Austrolebias Costa 1998

description: This dataset contains the digitized treatments in Plazi based on the original journal article Loureiro, Marcelo, Sá, Rafael de, Serra, Sebastián W., Alonso, Felipe, Lanés, Luis Esteban Krause, Volcan, Matheus Vieira, Calviño, Pablo, Nielsen, Dalton, Duarte, Alejandro, Garcia, Graciela (2018): Review of the family Rivulidae (Cyprinodontiformes, Aplocheiloidei) and a molecular and morphological phylogeny of the annual fish genus Austrolebias Costa 1998. Neotropical Ichthyology 16 (3): 1-20, DOI: 10.1590/1982-0224-20180007
DOI: 10.5281/zenodo.3709650
title: Dataset related to article "Intracerebral Injection of Extracellular Vesicles from Mesenchymal Stem Cells Exerts Reduced Aβ Plaque Burden in Early Stages of a Preclinical Model of Alzheimer's Disease."

description: Bone marrow Mesenchymal Stem Cells (BM-MSCs), due to their strong protective and anti-inflammatory abilities, have been widely investigated in the context of several diseases for their possible therapeutic role, based on the release of a highly proactive secretome composed of soluble factors and Extracellular Vesicles (EVs). BM-MSC-EVs, in particular, convey many of the beneficial features of parental cells, including direct and indirect β-amyloid degrading-activities, immunoregulatory and neurotrophic abilities. Therefore, EVs represent an extremely attractive tool for therapeutic purposes in neurodegenerative diseases, including Alzheimer's disease (AD). We examined the therapeutic potential of BM-MSC-EVs injected intracerebrally into the neocortex of APPswe/PS1dE9 AD mice at 3 and 5 months of age, a time window in which the cognitive behavioral phenotype is not yet detectable or has just started to appear. We demonstrate that BM-MSC-EVs are effective at reducing the Aβ plaque burden and the amount of dystrophic neurites in both the cortex and hippocampus. The presence of Neprilysin on BM-MSC-EVs, opens the possibility of a direct β-amyloid degrading action. Our results indicate a potential role for BM-MSC-EVs already in the early stages of AD, suggesting the possibility of intervening before overt clinical manifestations.
DOI: 10.5281/zenodo.3709651
title: Dataset related to article "Intracerebral Injection of Extracellular Vesicles from Mesenchymal Stem Cells Exerts Reduced Aβ Plaque Burden in Early Stages of a Preclinical Model of Alzheimer's Disease."

description: Bone marrow Mesenchymal Stem Cells (BM-MSCs), due to their strong protective and anti-inflammatory abilities, have been widely investigated in the context of several diseases for their possible therapeutic role, based on the release of a highly proactive secretome composed of soluble factors and Extracellular Vesicles (EVs). BM-MSC-EVs, in particular, convey many of the beneficial features of parental cells, including direct and indirect β-amyloid degrading-activities, immunoregulatory and neurotrophic abilities. Therefore, EVs represent an extremely attractive tool for therapeutic purposes in neurodegenerative diseases, including Alzheimer's disease (AD). We examined the therapeutic potential of BM-MSC-EVs injected intracerebrally into the neocortex of APPswe/PS1dE9 AD mice at 3 and 5 months of age, a time window in which the cognitive behavioral phenotype is not yet detectable or has just started to appear. We demonstrate that BM-MSC-EVs are effective at reducing the Aβ plaque burden and the amount of dystrophic neurites in both the cortex and hippocampus. The presence of Neprilysin on BM-MSC-EVs, opens the possibility of a direct β-amyloid degrading action. Our results indicate a potential role for BM-MSC-EVs already in the early stages of AD, suggesting the possibility of intervening before overt clinical manifestations.
DOI: 10.7910/dvn/x1nxjy/v8e7py
title: S1-Appendix.pdf

description: :unav
DOI: 10.15468/wyxs1t
title: New records and combinations in Neotropical Premnobius Eichhoff (Coleoptera: Curculionidae: Scolytinae: Ipini) with an illustrated key to New World species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Atkinson, Thomas H., Petrov, Alexander V., Flechtmann, Carlos A. H. (2018): New records and combinations in Neotropical Premnobius Eichhoff (Coleoptera: Curculionidae: Scolytinae: Ipini) with an illustrated key to New World species. Insecta Mundi 658: 1-11, DOI: http://doi.org/10.5281/zenodo.3709871
DOI: 10.5281/zenodo.3710370
title: Dataset related to article "Role of stereotactic body radiation therapy in the treatment of liver metastases: clinical results and prognostic factors."

description: PURPOSE: To evaluate feasibility and efficacy of Stereotactic Body Radiation Therapy (SBRT) for unresectable liver metastasis in oligometastatic patients. METHODS: Oligometastatic patients with up to three liver metastases of a maximum diameter of 6 cm were treated with SBRT. Total dose was 75 Gy in three consecutive fractions. Study endpoints were efficacy of this fractionation in terms of local control (LC), overall survival (OS), toxicity, and prognostic factors affecting OS and LC. RESULTS: Between February 2010 and December 2016, we enrolled 202 patients, with a total of 268 unresectable liver metastases. Median follow-up time from SBRT was 33 months (5-87 months). One-, 3‑, and 5‑year LC rates were 92%, 84%, and 84%, respectively. In univariate analysis, the primary histology and previous local ablative therapies were significant. Median OS was 21 months and the survival rates were 79%, 27%, and 15% at 1, 3, and 5 years after SBRT, respectively. At univariate analysis, sex, primary disease histology, intra-, and extra-hepatic progression were significant prognostic factors. This analysis confirmed the absence of late toxicity &gt;G3. CONCLUSION: This study confirms the efficacy and safety of SBRT for unresectable liver metastases. Selection of cases may improve survival and LC.
DOI: 10.5281/zenodo.3710371
title: Dataset related to article "Role of stereotactic body radiation therapy in the treatment of liver metastases: clinical results and prognostic factors."

description: PURPOSE: To evaluate feasibility and efficacy of Stereotactic Body Radiation Therapy (SBRT) for unresectable liver metastasis in oligometastatic patients. METHODS: Oligometastatic patients with up to three liver metastases of a maximum diameter of 6 cm were treated with SBRT. Total dose was 75 Gy in three consecutive fractions. Study endpoints were efficacy of this fractionation in terms of local control (LC), overall survival (OS), toxicity, and prognostic factors affecting OS and LC. RESULTS: Between February 2010 and December 2016, we enrolled 202 patients, with a total of 268 unresectable liver metastases. Median follow-up time from SBRT was 33 months (5-87 months). One-, 3‑, and 5‑year LC rates were 92%, 84%, and 84%, respectively. In univariate analysis, the primary histology and previous local ablative therapies were significant. Median OS was 21 months and the survival rates were 79%, 27%, and 15% at 1, 3, and 5 years after SBRT, respectively. At univariate analysis, sex, primary disease histology, intra-, and extra-hepatic progression were significant prognostic factors. This analysis confirmed the absence of late toxicity &gt;G3. CONCLUSION: This study confirms the efficacy and safety of SBRT for unresectable liver metastases. Selection of cases may improve survival and LC.
DOI: 10.15468/cvgoek
title: A review of the systematic biology of fossil and living bony-tongue fishes, Osteoglossomorpha (Actinopterygii: Teleostei)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Hilton, Eric J., Lavoué, Sébastien (2018): A review of the systematic biology of fossil and living bony-tongue fishes, Osteoglossomorpha (Actinopterygii: Teleostei). Neotropical Ichthyology 16 (3): 1-35, DOI: 10.1590/1982-0224-20180031
DOI: 10.15468/tgaqup
title: A new Anomiopus Westwood (Coleoptera: Scarabaeidae: Scarabaeinae) from the Mayan Biosphere Reserve, Petén, Guatemala

description: This dataset contains the digitized treatments in Plazi based on the original journal article Cano, Enio B. (2018): A new Anomiopus Westwood (Coleoptera: Scarabaeidae: Scarabaeinae) from the Mayan Biosphere Reserve, Petén, Guatemala. Insecta Mundi 659: 1-9, DOI: http://doi.org/10.5281/zenodo.3709947
DOI: 10.24431/rw1k444
title: Estimation of Abundance and Demographic Rates of Pacific Walruses in the Bering and Chukchi Seas, 2015

description: This study estimated abundance and demographic rates, including survival and recruitment, of Pacific walruses in the Beaufort Sea in 2015. The data collected was used to determine the feasibility of conducting a large scale and long-term capture-mark-recapture effort to determine the size of the Pacific walrus population as well as age and sex specific survival and recruitment of the population. The decline in sea ice habitat and the associated stressors are causing a population decline of Pacific walrus. This study provided a baseline for monitoring Pacific walrus populations. The data was collected from visual observations of Pacific walruses in which skin biopsy samples were collected and used for individual identification. The field data was collected on an electronic field entry system, a Juniper Mesa and converted to a csv file.
DOI: 10.15468/i2gowi
title: Expanded concept and revised taxonomy of the milliped family Xystodesmidae Cook, 1895 (Polydesmida: Leptodesmidea: Xystodesmoidea): incorporations of Euryuridae Pocock, 1909 and Eurymerodesmidae Causey, 1951, taxon revivals / proposals / transferrals, and a distributional update

description: This dataset contains the digitized treatments in Plazi based on the original journal article Shelley, Rowland M., Smith, Jamie M. (2018): Expanded concept and revised taxonomy of the milliped family Xystodesmidae Cook, 1895 (Polydesmida: Leptodesmidea: Xystodesmoidea): incorporations of Euryuridae Pocock, 1909 and Eurymerodesmidae Causey, 1951, taxon revivals / proposals / transferrals, and a distributional update. Insecta Mundi 660: 1-41, DOI: http://doi.org/10.5281/zenodo.3709976
DOI: 10.5281/zenodo.3710201
title: Dataset related to article "Volumetric Modulated Arc Therapy After Lung Sparing Surgery for Malignant Pleural Mesothelioma: A Single Institution Experience."

description: INTRODUCTION: We investigated the possible role of volumetric modulated arc therapy (VMAT) in the setting of adjuvant treatment of malignant pleural mesothelioma (MPM) after lung-sparing surgery with pleurectomy and decortication. MATERIALS AND METHODS: Patients affected by MPM who had undergone pleurectomy and decortication and adjuvant radiotherapy with VMAT were included. The endpoints of the present analysis were local control, progression-free survival, and overall survival. Assessment of the variables affecting survival was performed using univariate and multivariate Cox proportional hazard models. RESULTS: A total of 49 patients were included in the present study. Of the 49 patients, 96% had been treated with a trimodality approach. Radiotherapy was delivered to a median dose of 44 Gy in 22 fractions (range, 22-59.4 Gy). The treatment was well tolerated, with just 2 grade 3 acute toxicities, 1 grade 5, and 2 grade 4 toxicities recorded during the follow-up period. The median follow-up period was 27.4 months. The local control rate at 12, 24, and 36 months was 75.2%, 67.4%, and 56.5%, respectively. The median progression-free survival was 14.9 months (95% confidence interval [CI], 7.5-25.2). The median overall survival was 21.5 months (95% CI, 15.3-37.1). On multivariate analysis, the administration of carboplatin- instead of cisplatin-based chemotherapy (hazard ratio, 2.97; 95% CI, 1.22-7.26; P = .017) and R2 resection (hazard ratio, 1.95; 95% CI, 1.27-2.99; P = .002) showed a negative correlation with overall survival. On univariate analysis, the percentage of the heart receiving &gt;20 Gy and &gt;30 was associated with the occurrence of late pneumonitis (P = .018 and P = .077). CONCLUSION: VMAT is feasible in the setting of MPM after lung-sparing surgery. The toxicity rates were reduced with this technique compared with historical data of older techniques. Local and distant failure remain a major issue to be addressed in future trials.