cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3710202
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.
DOI: 10.15468/uxhhbz
title: Phorodon cannabis Passerini (Hemiptera: Aphididae), a newly recognized pest in North America found on industrial hemp

description: This dataset contains the digitized treatments in Plazi based on the original journal article Cranshaw, Whitney S., Halbert, Susan E., Favret, Colin, Britt, Kadie E., Miller, Gary L. (2018): Phorodon cannabis Passerini (Hemiptera: Aphididae), a newly recognized pest in North America found on industrial hemp. Insecta Mundi 662: 1-12, DOI: http://doi.org/10.5281/zenodo.3710022
DOI: 10.5066/p9espl41
title: Stand density and climate data in the Taylor Woods study area (Fort Valley Experimental Forest) on the Colorado Plateau in Northern Arizona, 1961-2011

description: These data were compiled for research pertaining to the effects of stand density on growth rates in semi-arid forests. Increasing heat and aridity in coming decades is expected to negatively impact tree growth and threaten forest sustainability in dry areas. Maintaining low stand density has the potential to mitigate the negative effects of increasingly severe droughts by minimizing competitive intensity. By inspecting growth rates and the climate and soil moisture conditions that drive these growth rates we can understand better the positive effects of reducing stand density and the specific dynamics that are beneficial to growth.
DOI: 10.5281/zenodo.3709995
title: Dataset related to article "Hyaluronan Accelerates Intestinal Mucosal Healing through Interaction with TSG-6."

description: Hyaluronan (HA) has proven to be beneficial in the treatment of several diseases. Recently, it has been shown that the local application of HA (IBD98E) improves endoscopic and clinical outcomes in subjects with active distal ulcerative colitis (UC). However, the mechanisms by which this polysaccharide exerts its beneficial effects are unclear. Here, we demonstrated that HA treatment in vitro and in vivo improved mucosal healing by accelerating intestinal epithelial regeneration. Indeed, mice treated with HA showed a faster recovery from colitis and reduced endoscopic signs of mucosal inflammation compared to those receiving saline. Furthermore, histological analysis revealed less ulcerated mucosa in mice treated with HA, characterized by re-epithelialized areas. TSG-6, the secreted product of TNF-stimulated gene-6, is an HA-binding protein shown previously to have tissue-protective properties and promote wound healing. Mucosal levels of TSG-6 increased in UC patients compared to the healthy controls and also after wounding in mice. TSG-6 deletion prevented the beneficial properties of HA in mucosal wound repair, suggesting that the interaction of HA with TSG-6 is crucial for intestinal epithelial regeneration. Overall these results are consistent with HA having a therapeutic effect via the promotion of mucosal healing in patients with ulcerative colitis.
DOI: 10.5281/zenodo.3709996
title: Dataset related to article "Hyaluronan Accelerates Intestinal Mucosal Healing through Interaction with TSG-6."

description: Hyaluronan (HA) has proven to be beneficial in the treatment of several diseases. Recently, it has been shown that the local application of HA (IBD98E) improves endoscopic and clinical outcomes in subjects with active distal ulcerative colitis (UC). However, the mechanisms by which this polysaccharide exerts its beneficial effects are unclear. Here, we demonstrated that HA treatment in vitro and in vivo improved mucosal healing by accelerating intestinal epithelial regeneration. Indeed, mice treated with HA showed a faster recovery from colitis and reduced endoscopic signs of mucosal inflammation compared to those receiving saline. Furthermore, histological analysis revealed less ulcerated mucosa in mice treated with HA, characterized by re-epithelialized areas. TSG-6, the secreted product of TNF-stimulated gene-6, is an HA-binding protein shown previously to have tissue-protective properties and promote wound healing. Mucosal levels of TSG-6 increased in UC patients compared to the healthy controls and also after wounding in mice. TSG-6 deletion prevented the beneficial properties of HA in mucosal wound repair, suggesting that the interaction of HA with TSG-6 is crucial for intestinal epithelial regeneration. Overall these results are consistent with HA having a therapeutic effect via the promotion of mucosal healing in patients with ulcerative colitis.
DOI: 10.15785/sbgrid/691
title: X-Ray Diffraction data from Leptospira biflexa Flagellar-coiling protein A (FcpA), source of 6NQX structure

description: Native data set (monoclinic form of FcpA from L. biflexa)
DOI: 10.15151/esrf-es-189537994
title: High-resolution structure determination of GluK3-kainate receptors
DOI: 10.15785/sbgrid/695
title: X-Ray Diffraction data from Leptospira interrogans Flagellar-coiling protein B (FcpB), source of 6NQZ structure

description: iodide + magic triangle soaking, SAD data set (@1.5418 angstroms wavelength) These data were used to refine the structure (but not for structure solution, for which a separate data set was used, and deposited under #694)
DOI: 10.15785/sbgrid/694
title: X-Ray Diffraction data from Leptospira interrogans Flagellar-coiling protein B (FcpB), source of 6NQZ structure

description: iodide + magic triangle soaking, SAD data set (@1.5418 angstroms wavelength) These data were used to solve the structure by direct methods using the iodine atoms as anomalous scatterers (but not for final refinement, for which a separate data set has been used and deposited)
DOI: 10.15152/qdb.221
title: QDB archive #221

description: This QDB archive contains data and model(s) from the following publication: Bajot, F.; Cronin, M. Polar narcosis QSAR for fathead minnow acute toxicity. Q17-33-0032. Liverpool John Moores University, 2009.
DOI: 10.25345/c5c11n
title: MassIVE MSV000085099 - GNPS - Dark Web Drugs - Positive and Negative Mode ESI - Untargeted Metabolomics
title: analysis of drugs from the dark web. analyzed by positive and negative mode electrospray ionization. UPHLC-MS. reverse-phase chromatography (C18).
DOI: 10.5281/zenodo.3710506
title: Modeling Factual Claims with Semantic Frames

description: We introduce an extension of the Berkeley FrameNet for the structured and semantic modeling of factual claims. Modeling is a robust tool that can be leveraged in many different tasks such as matching claims to existing fact-checks and translating claims to structured queries. Our work introduces 11 new manually crafted frames along with 9 existing FrameNet frames, all of which have been selected with fact-checking in mind. Along with these frames, we are also providing 2,540 fully annotated sentences, which can be used to understand how these frames are intended to work and to train machine learning models.
DOI: 10.5281/zenodo.3710507
title: Modeling Factual Claims with Semantic Frames

description: We introduce an extension of the Berkeley FrameNet for the structured and semantic modeling of factual claims. Modeling is a robust tool that can be leveraged in many different tasks such as matching claims to existing fact-checks and translating claims to structured queries. Our work introduces 11 new manually crafted frames along with 9 existing FrameNet frames, all of which have been selected with fact-checking in mind. Along with these frames, we are also providing 2,540 fully annotated sentences, which can be used to understand how these frames are intended to work and to train machine learning models.
DOI: 10.5281/zenodo.3710384
title: Dataset related to article "PSMA expression level predicts differentiated thyroid cancer aggressiveness and patient outcome"

description: BACKGROUND: Prostate-specific membrane antigen (PSMA) is overexpressed on the endothelial cells of tumor neo-vessels of several solid malignancies, including differentiated thyroid cancer (DTC). We aimed to test the potential role of PSMA as a biomarker for DTC aggressiveness and outcome prediction. We retrospectively screened all patients who underwent thyroidectomy between 1 January 2010 and 31 December 2017 in our institution. Applying the inclusion (histological diagnosis of thyroid cancer and tissue availability) and exclusion criteria (no clinical or follow-up data or diagnosis of medullary thyroid cancer), a cohort of 59 patients was selected. The monoclonal mouse anti-human PSMA antibody was used to stain tissue sections. A 3-point scale was used to score PSMA positivity: 0-5% expression was considered as negative (score 0), 6-50% as moderately positive (score 1), and 51-100% as highly positive (score 2). A cumulative score (0-10%, 11-79%, and 80-100%) was also explored. Univariate and multivariate logistic regression analyses were performed to predict the presence of distant metastases, chosen as endpoint of aggressiveness. The area under the curve (AUC) was calculated. Cox models were built to predict patient outcome in terms of recurrence, iodine refractoriness, and status at last follow-up, which were calculated using the Kaplan-Meier failure function. RESULTS: At immunostaining, 12, 25, and 22 patients had scores of 0, 1, and 2, respectively. According to the cumulative score, PSMA expression was ≤ 10% in 17 cases, 11-79% in 31 cases, and ≥ 80% in 11 cases. At multivariate analysis, age, sex, histotype, vascular invasion, T and N parameters, and PSMA positivity were significant predictors of distant metastases. The AUC was 0.92. Recurrence or progression occurred in 19/59 patients. Twelve patients developed radioiodine (RAI) refractoriness, after a median time of 17 months (range 2-32). One patient died of DTC; 46 of the 58 patients alive at last follow-up were disease free. Median DFS was 23 months (range 3-82). The final multivariate model to predict RAI refractoriness included as covariates the stage, high PSMA expression (≥ 80%), and the interaction between moderate PSMA expression (11-79%) and stage. CONCLUSIONS: PSMA, a marker of neovasculature formation expressed by DTC, contributes in the prediction of tumor aggressiveness and patient outcome.
DOI: 10.5281/zenodo.3710385
title: Dataset related to article "PSMA expression level predicts differentiated thyroid cancer aggressiveness and patient outcome"

description: BACKGROUND: Prostate-specific membrane antigen (PSMA) is overexpressed on the endothelial cells of tumor neo-vessels of several solid malignancies, including differentiated thyroid cancer (DTC). We aimed to test the potential role of PSMA as a biomarker for DTC aggressiveness and outcome prediction. We retrospectively screened all patients who underwent thyroidectomy between 1 January 2010 and 31 December 2017 in our institution. Applying the inclusion (histological diagnosis of thyroid cancer and tissue availability) and exclusion criteria (no clinical or follow-up data or diagnosis of medullary thyroid cancer), a cohort of 59 patients was selected. The monoclonal mouse anti-human PSMA antibody was used to stain tissue sections. A 3-point scale was used to score PSMA positivity: 0-5% expression was considered as negative (score 0), 6-50% as moderately positive (score 1), and 51-100% as highly positive (score 2). A cumulative score (0-10%, 11-79%, and 80-100%) was also explored. Univariate and multivariate logistic regression analyses were performed to predict the presence of distant metastases, chosen as endpoint of aggressiveness. The area under the curve (AUC) was calculated. Cox models were built to predict patient outcome in terms of recurrence, iodine refractoriness, and status at last follow-up, which were calculated using the Kaplan-Meier failure function. RESULTS: At immunostaining, 12, 25, and 22 patients had scores of 0, 1, and 2, respectively. According to the cumulative score, PSMA expression was ≤ 10% in 17 cases, 11-79% in 31 cases, and ≥ 80% in 11 cases. At multivariate analysis, age, sex, histotype, vascular invasion, T and N parameters, and PSMA positivity were significant predictors of distant metastases. The AUC was 0.92. Recurrence or progression occurred in 19/59 patients. Twelve patients developed radioiodine (RAI) refractoriness, after a median time of 17 months (range 2-32). One patient died of DTC; 46 of the 58 patients alive at last follow-up were disease free. Median DFS was 23 months (range 3-82). The final multivariate model to predict RAI refractoriness included as covariates the stage, high PSMA expression (≥ 80%), and the interaction between moderate PSMA expression (11-79%) and stage. CONCLUSIONS: PSMA, a marker of neovasculature formation expressed by DTC, contributes in the prediction of tumor aggressiveness and patient outcome.
DOI: 10.15785/sbgrid/692
title: X-Ray Diffraction data from Leptospira biflexa Flagellar-coiling protein A (FcpA), source of 6NQY structure

description: Iodine quick-soak - SAD data set (monoclinic C2 form of FcpA from L. biflexa)
DOI: 10.15785/sbgrid/693
title: X-Ray Diffraction data from Leptospira biflexa Flagellar-coiling protein A (FcpA), source of 6NQW structure

description: native data set (hexagonal P622 form of FcpA from L. biflexa)
DOI: 10.21227/5aeq-rr34
title: Dataset of article: Synthetic Datasets Generator for Testing Information Visualization and Machine Learning Techniques and Tools

description: Dataset used in the article entitled 'Synthetic Datasets Generator for Testing Information Visualization and Machine Learning Techniques and Tools'. These datasets can be used to test several characteristics in machine learning and data processing algorithms.
DOI: 10.21227/j3yv-5216
title: Dataset of article: Synthetic Datasets Generator for Testing Information Visualization and Machine Learning Techniques and Tools

description: Dataset used in the article entitled 'Synthetic Datasets Generator for Testing Information Visualization and Machine Learning Techniques and Tools'. These datasets can be used to test several characteristics in machine learning and data processing algorithms.
DOI: 10.3886/e112946v1-23003
title: Replication data for: How Do Voters Respond to Information? Evidence from a Randomized Campaign

description: In a large-scale controlled trial in collaboration with the reelection campaign of an Italian incumbent mayor, we administered (randomized) messages about the candidate's valence or ideology. Informational treatments affected both actual votes in the precincts and individual vote declarations. Campaigning on valence brought more votes to the incumbent, but both messages affected voters' beliefs. Cross-learning occurred, as voters who received information about the incumbent also updated their beliefs on the opponent. With a novel protocol of beliefs elicitation and structural estimation, we assess the weights voters place upon politicians' valence and ideology, and simulate counterfactual campaigns. (JEL D12, D72, D83)
DOI: 10.5281/zenodo.3709611
title: University of Nebraska-Lincoln Mobile Mesonet files from LAPSE-RATE

description: This dataset includes files from the University of Nebraska-Lincoln mobile mesonets operated during the LAPSE-RATE field campaign.
DOI: 10.6073/pasta/8a4c368841eda22e0d7ea6636c48d40f
title: SBC LTER: Kelp Removal Experiment: Hourly photon irradiance at the surface and seafloor

description: These data represent mean hourly values of photosynthetically active radiation (PAR) (in units of mol m-2 s-1) at the sea surface and the sea floor at SBC LTER kelp removal experiment sites. Sensors record instantaneous irradiance at one-minute intervals, and data are averaged hourly. Sensors are mounted on the sea floor at five sites (Arroyo Quemado, Carpinteria, Naples Reef, Isla Vista, and Mohawk Reef). A surface sensor is deployed on an unobstructed coastal rooftop at the UC Santa Barbara campus; some historical observations are available from sensors mounted above the sea surface at a subset of the five sites.
DOI: 10.15784/601265
title: Investigating Ultra-low Velocity Zones (ULVZs) using an Antarctic Dataset

description: Dataset includes information on all A- and B-ranked earthquakes (see Hansen et al., 2020) recorded by the Antarctic TAMNNET seismic array that were examined for ULVZ evidence. Information on their attenuation (t*) parameter, signal-to-noise ratio, core-mantle boundary bouncepoint location, and average remainder trace standard deviation are also provided. The provided figure indicates where ULVZ evidence has been found and where possible ULVZ evidence may be indicated.
DOI: 10.25345/c5797f
title: MassIVE MSV000085100 - Enzymatic Site-specific Biotinylation Enables Analysis of RNA-protein Interactions and Enrichment of Cellular RNA
title: The importance of RNA in regulating cellular processes has generated tremendous interest in methods to reliably characterize RNAs and their interactions within cells. Existing methodologies rely on noncovalent interactions to facilitate RNA affinity purification, hindering the purification of less abundant transcripts and limiting the stringency of the purification conditions. Here we demonstrate that enzymatic installation of a single covalent biotin modification directly onto an RNA of interest enables robust affinity purification of RNA-protein complexes via immunoblotting or quantitative mass spectrometry. Using this approach, known binding partners of 7SK snRNA, an important regulatory RNA, were successfully identified. This approach was further applied to the study of the long-noncoding RNA HOTAIR, using a modification of existing hairpin structures to allow for RNA-TAG labeling. A 4-nucleotide internal mutation enabled RNA-TAG mediated identification of putative HOTAIR binding partners in MCF7 breast cancer cells. Lastly, the selective and efficient labeling of an expressed RNA in mammalian cell lysate was demonstrated using a dimerized TGT enzyme through quantitative PCR and RNA-sequencing, enabling 145-fold direct enrichment from mammalian cell lysates. The flexibility and breadth of the RNA-TAG approach suggest that this methodology could be routinely applied to study RNA-protein complexes with minimal perturbation of the RNA sequence and to target less abundant RNA transcripts.
DOI: 10.5281/zenodo.3710428
title: CONUS NG-IDF Dataset

description: This dataset includes: <strong>The 24-hour events with return intervals of 2 years, 5 years, 10 years, 25 years, 50 years, 100 years, and 500 years from distinct hydrometeorological conditions for the conterminous United States at 1/6-degree resolution:</strong> rainfall only on snow-free ground (filename: 24hr_max_rainfall.mat) melt only with no concurrent rain (filename: 24hr_melt_only.mat) rain-on-snow (filename: 24hr_ROS.mat) precipitation (filename: 24hr_max_precip.mat) all events including rain, melt and ROS (filename: 24hr_AWR.mat) <strong>The 72-hour events with return intervals of 2 years, 5 years, 10 years, 25 years, 50 years, 100 years, and 500 years from distinct hydrometeorological conditions for the conterminous United States at 1/6-degree resolution:</strong> rainfall only on snow-free ground (filename: 72hr_max_rainfall.mat) melt only with no concurrent rain (filename: 72hr_melt_only.mat) rain-on-snow (filename: 72hr_ROS.mat) precipitation (filename: 72hr_max_precip.mat) all events including rain, melt and ROS (filename: 72hr_AWR.mat)
DOI: 10.6073/pasta/c0044e5b2112ac2bc1cd6497dadf047d
title: SBC LTER: Reef: Long-term experiment: Taxon-specific seasonal net primary production (NPP) for macroalgae

description: This dataset provides estimates of seasonal net primary production (NPP) for all taxa of macroalgae sampled in fixed plots at SBC LTER's long-term kelp removal experiment sites. NPP of understory taxa are calculated using field measurements of irradiance and biomass (derived from abundance) and laboratory estimates of taxon-specific photosynthetic parameters. NPP for the giant kelp, Macrocystis pyrifera, is calculated using linear relationships between frond density in a given season and average NPP for that season. Importantly, estimates for understory species include production lost as dissolved exudates while estimates of NPP for giant kelp do not.
DOI: 10.5281/zenodo.3627259
title: The potential of sector coupling in future European energy systems soft linking between the Dispa-SET and JRC-EU-TIMES models - Dataset

description: Supporting dataset and Dispa-SET version used within "The potential of sector coupling in future European energy systems soft linking between the Dispa-SET and JRC-EU-TIMES models" paper.
DOI: 10.5281/zenodo.3627258
title: The potential of sector coupling in future European energy systems soft linking between the Dispa-SET and JRC-EU-TIMES models - Dataset

description: Supporting dataset and Dispa-SET version used within "The potential of sector coupling in future European energy systems soft linking between the Dispa-SET and JRC-EU-TIMES models" paper.