cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3708324
title: Reconciliation of regulatory data: the regulatory networks of Escherichia coli and Bacillus subtilis

description: The dataset hereby uploaded, presents state-of-art, reconciled transcriptional regulatory networks of <em>Escherichia coli </em>K12 MG1655<em> </em>and <em>Bacillus subtilis </em>str 168<em>. </em>The networks were reconciled through the retrieval and integration of relevant regulatory data from multiple resources, including databases, such as <em>RegulonDB </em>and <em>DBTBS</em> as well as available literature.
DOI: 10.6073/pasta/fda88d1c6d754c328191236f93f5d6a3
title: Precipitation from the Shark River Slough, Everglades National Park (FCE LTER), South Florida from November 2000 to Present

description: Rain level is recorded at least every thirty minutes at the sites SRS 1d, SRS 2 & SRS 3. Not active sites are: SRS 1a and SRS 1c. Rain level data is collected using a tipping bucket rain gauge (SUTRON 5600-0425) attached to ISCO autosamplers, which also act as dataloggers. We condense these data into daily cumulative rainfall, although hourly rain level data are also available.
DOI: 10.5281/zenodo.3708386
title: Dataset related to article "Poly(I:C) stimulation is superior than Imiquimod to induce the antitumoral functional profile of tumor-conditioned macrophages."

description: Macrophage plasticity is the ability of mononuclear phagocytes to change phenotype, function, and genetic reprogramming upon encounter of specific local stimuli. In the tumor microenvironment, Tumor-Associated Macrophages (TAMs) acquire an immune-suppressive and tumor-promoting phenotype. With the aim to re-educate TAMs to antitumor effectors, in this study, we used two immunestimulatory compounds: the TLR7 agonist Imiquimod (IMQ) and the TLR3 agonist Poly(I:C). To better mimic in vitro the response of TAMs, we used Tumor-Conditioned Macrophages (TC-Mϕ) differentiated in the presence of tumor cell supernatants. Our results show that TC-Mϕ respond differently from conventional M2-polarized macrophages. Upon stimulation with IMQ, TC-Mϕ did not upregulate major histocompatibility complex (MHC II) molecules and unexpectedly expressed increased CD206. With both compounds, TC-Mϕ produced higher levels of inflammatory cytokines than M2 macrophages. IMQ and Poly(I:C) differed in the types of regulated genes and secreted mediators. Reflecting their signaling pathways, only IMQ significantly induced IL-1β and IL-6, while only Poly(I:C) stimulated CXCL10, and both upregulated CCL5. Of note, using a novel cytotoxicity assay, Poly(I:C), but not IMQ, was effective in triggering the cytotoxic activity of TC-Mϕ against cancer cells. Overall, the results demonstrate that Poly(I:C) stimulation of TC-Mϕ is superior than IMQ in terms of macrophage re-education toward antitumor effectors.
DOI: 10.5281/zenodo.3708387
title: Dataset related to article "Poly(I:C) stimulation is superior than Imiquimod to induce the antitumoral functional profile of tumor-conditioned macrophages."

description: Macrophage plasticity is the ability of mononuclear phagocytes to change phenotype, function, and genetic reprogramming upon encounter of specific local stimuli. In the tumor microenvironment, Tumor-Associated Macrophages (TAMs) acquire an immune-suppressive and tumor-promoting phenotype. With the aim to re-educate TAMs to antitumor effectors, in this study, we used two immunestimulatory compounds: the TLR7 agonist Imiquimod (IMQ) and the TLR3 agonist Poly(I:C). To better mimic in vitro the response of TAMs, we used Tumor-Conditioned Macrophages (TC-Mϕ) differentiated in the presence of tumor cell supernatants. Our results show that TC-Mϕ respond differently from conventional M2-polarized macrophages. Upon stimulation with IMQ, TC-Mϕ did not upregulate major histocompatibility complex (MHC II) molecules and unexpectedly expressed increased CD206. With both compounds, TC-Mϕ produced higher levels of inflammatory cytokines than M2 macrophages. IMQ and Poly(I:C) differed in the types of regulated genes and secreted mediators. Reflecting their signaling pathways, only IMQ significantly induced IL-1β and IL-6, while only Poly(I:C) stimulated CXCL10, and both upregulated CCL5. Of note, using a novel cytotoxicity assay, Poly(I:C), but not IMQ, was effective in triggering the cytotoxic activity of TC-Mϕ against cancer cells. Overall, the results demonstrate that Poly(I:C) stimulation of TC-Mϕ is superior than IMQ in terms of macrophage re-education toward antitumor effectors.
DOI: 10.6073/pasta/b232c27a13cb02cb3664cc693efecb90
title: NWFSC fish and invertebrate diversity derived from west coast groundfish trawl program

description: This dataset presents the community structure of groundfish and invertebrate in the West Coast since 1977. The community structure indices include the richness and Simpson’s evenness. The raw count data is from West Coast Groundfish Bottom Trawl survey conducted by the Northwest Fisheries Science Center. The spatial coverage of this dataset is between Pt Conception, California and north of U.S.-Mexico border.
DOI: 10.6073/pasta/0d8e8c7870dd8197c5f00da135b49444
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: 10.24431/rw1k443
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: 10.5281/zenodo.3708442
title: Dataset related to article "Lymphatic endothelium contributes to colorectal cancer growth via the soluble matrisome component GDF11."

description: Colorectal cancer (CRC) is one of the most malignant tumors worldwide. Stromal cells residing in the tumor microenvironment strongly contribute to cancer progression through their crosstalk with cancer cells and extracellular matrix. Here we provide the first evidence that CRC-associated lymphatic endothelium displays a distinct matrisome-associated transcriptomic signature, which distinguishes them from healthy intestinal lymphatics. We also demonstrate that CRC-associated human intestinal lymphatic endothelial cells regulate tumor cell growth via growth differentiation factor 11, a soluble matrisome component which in CRC patients was found to be associated with tumor progression. Our data provide new insights into lymphatic contribution to CRC growth, aside from their conventional role as conduits of metastasis. The extension of the set is in Prism form, we attach a pdf information to this format and a link where download a version of it
DOI: 10.5281/zenodo.3708443
title: Dataset related to article "Lymphatic endothelium contributes to colorectal cancer growth via the soluble matrisome component GDF11."

description: Colorectal cancer (CRC) is one of the most malignant tumors worldwide. Stromal cells residing in the tumor microenvironment strongly contribute to cancer progression through their crosstalk with cancer cells and extracellular matrix. Here we provide the first evidence that CRC-associated lymphatic endothelium displays a distinct matrisome-associated transcriptomic signature, which distinguishes them from healthy intestinal lymphatics. We also demonstrate that CRC-associated human intestinal lymphatic endothelial cells regulate tumor cell growth via growth differentiation factor 11, a soluble matrisome component which in CRC patients was found to be associated with tumor progression. Our data provide new insights into lymphatic contribution to CRC growth, aside from their conventional role as conduits of metastasis. The extension of the set is in Prism form, we attach a pdf information to this format and a link where download a version of it
DOI: 10.5281/zenodo.3707210
title: WWV Centennial Festival of Frequency Measurement 5 MHz Collected Data

description: Manually consolidated 5MHz data from the Festival of Frequency Measurement. Instructions posted here: https://hamsci.org/wwv-centennial-festival-frequency-measurements Callsigns of participants who posted data to Zenodo: VK3ZAZ, WX4US, N7IVV, K7KMQ, AG7PQ, KM4YMI, N1IRO, AC6SL, W1KU, N1NAZ, W6OQI, VE3OAT, NA0B, VE3YX, KE0ARE, XE3I, WB4HIR, W6BM, AA6LK, W6MSU, K0ANS, W3FAY, KA6WKE, WV5L, VE7CNF, N7XZ, K2LYV, VE6IXD, K7JKM, K4BSE, N2MD, VE6GRT, WA5FRF, VA3ROM, KG4ARN, N8OBJ, NU0C, W8UM, AA8K Callsigns of participants whose data was not uploaded to Zenodo: AJ4YA, N9MVO, W8EDU, N7QNM, W9INE, WA7BNM
DOI: 10.5281/zenodo.3708448
title: SELENE_COU

description: Glissements sémantiques de COU dans les langues sénégambiennes
DOI: 10.5281/zenodo.3708422
title: Dataset related to article "Combined low densities of FoxP3+ and CD3+ tumor-infiltrating lymphocytes identify stage II colorectal cancer at high risk of progression"

description: The densities of CD3<sup>+</sup> and CD8<sup>+</sup> tumor-infiltrating lymphocytes (TILs), combined with tumor-node-metastasis (TNM) staging, have prognostic value for patients with nonmetastatic colorectal cancer. We compared the prognostic value of CD3<sup>+</sup> and FoxP3<sup>+</sup> TILs at the invasive front, TNM classifiers, and microsatellite (MS) status in a trial set of patients with stage II and III colorectal cancer (<em>n</em> = 413), by recursive partitioning with a classification and regression tree (CART). Significant prognostic factors and interactions were reassessed by logistic regression and Cox proportional-hazards modeling in the trial and a validation set (<em>n</em> = 215) of patients with stage II colorectal cancer. In the trial set, CART indicated that TIL numbers were of value only in predicting recurrence risk for stage II cancers, where low densities of FoxP3<sup>+</sup> TILs ranked first and low densities of CD3<sup>+</sup> TILs further stratifying risk. Multivariate analysis showed that TILs interacted with tumor stage (FoxP3<sup>+</sup>, <em>P</em> = 0.06; CD3<sup>+</sup>, <em>P</em> = 0.02) and MS instability (MSI; FoxP3<sup>+</sup>; <em>P</em> = 0.02). In stage II MS-stable cancers, concomitant low densities of both FoxP3<sup>+</sup> and CD3<sup>+</sup> TILs identified patients with the highest progression risk in the trial [HR 7.24; 95% confidence interval (CI), 3.41-15.4; <em>P</em> &lt; 0.001] and the validation (HR 15.16; 95% CI, 3.43-66.9; <em>P</em> &lt; 0.001) sets. FoxP3<sup>+</sup> and CD3<sup>+</sup> TIL load in colorectal cancer was more informative than other prognostic factors before the cancer progressed to lymph nodes. This prognostic information about TILs, including FoxP3<sup>+</sup> cells, suggests that randomized controlled trials might be refined to include interactions between TNM status, molecular classifiers, and postsurgical treatments.
DOI: 10.5281/zenodo.3708423
title: Dataset related to article "Combined low densities of FoxP3+ and CD3+ tumor-infiltrating lymphocytes identify stage II colorectal cancer at high risk of progression"

description: The densities of CD3<sup>+</sup> and CD8<sup>+</sup> tumor-infiltrating lymphocytes (TILs), combined with tumor-node-metastasis (TNM) staging, have prognostic value for patients with nonmetastatic colorectal cancer. We compared the prognostic value of CD3<sup>+</sup> and FoxP3<sup>+</sup> TILs at the invasive front, TNM classifiers, and microsatellite (MS) status in a trial set of patients with stage II and III colorectal cancer (<em>n</em> = 413), by recursive partitioning with a classification and regression tree (CART). Significant prognostic factors and interactions were reassessed by logistic regression and Cox proportional-hazards modeling in the trial and a validation set (<em>n</em> = 215) of patients with stage II colorectal cancer. In the trial set, CART indicated that TIL numbers were of value only in predicting recurrence risk for stage II cancers, where low densities of FoxP3<sup>+</sup> TILs ranked first and low densities of CD3<sup>+</sup> TILs further stratifying risk. Multivariate analysis showed that TILs interacted with tumor stage (FoxP3<sup>+</sup>, <em>P</em> = 0.06; CD3<sup>+</sup>, <em>P</em> = 0.02) and MS instability (MSI; FoxP3<sup>+</sup>; <em>P</em> = 0.02). In stage II MS-stable cancers, concomitant low densities of both FoxP3<sup>+</sup> and CD3<sup>+</sup> TILs identified patients with the highest progression risk in the trial [HR 7.24; 95% confidence interval (CI), 3.41-15.4; <em>P</em> &lt; 0.001] and the validation (HR 15.16; 95% CI, 3.43-66.9; <em>P</em> &lt; 0.001) sets. FoxP3<sup>+</sup> and CD3<sup>+</sup> TIL load in colorectal cancer was more informative than other prognostic factors before the cancer progressed to lymph nodes. This prognostic information about TILs, including FoxP3<sup>+</sup> cells, suggests that randomized controlled trials might be refined to include interactions between TNM status, molecular classifiers, and postsurgical treatments.
DOI: 10.3886/e118206
title: SSSI Develepment Data

description: Dataset accompanying the working paper "Understanding the Scientific Enterprise: Development and Validation of an Instrument to Measure Grasp of the Social Structure of Science" - Validation study for development of the SSSI<br>
DOI: 10.5281/zenodo.3700745
title: Microwave single scattering properties of non-spheroidal rain drops

description: The database contains single scattering properties (SSP) of non-spheroidal droplets. They were modeled using the parameterization by Chuang and Beard (1990) which make use of Chebyshev polynomials. Spherical and spheroidal drop are also included for reference. The spheroidal drops are set to have the same aspect ratio as the Chebyshev drops. The frequency and temperature grid is identical to the one used for the SSP database presented in Eriksson et al. (2018). Frequencies range from 1 to 886.4 GHz and 5 temperatures from 230 to 310 K are included. Sizes range from 10 μm to 5.75 mm, with logarithmic spacing up to 1 mm and linear spacing above 1 mm in steps of 0.25 mm. Note that below 788 μm the Chebyshev drops are essentially spherical, and are therefore not included. At sizes below 788 μm the spheroidal drop SSP can be used instead. The database is currently in alpha version. Some adjustments to the format will be made before the data is released open access. A manuscript has been submitted to Atmospheric Measurement Techniques, which will serve as the main documentation of the data. Database Specifications: Format:<br> NetCDF4 Version:<br> 1.0.0-alpha Shapes:<br> Chebyshev (non-spheroidal), spheroidal, sphere. Diameter grid (um):<br> 1.00, 1.27, 1.61, 2.04, 2.59, 3.29, 4.18, 5.30, 6.72, 8.53, 10.83, 13.74, 17.43, 22.12, 28.07, 35.62, 45.20, 57.36, 72.79, 92.37, 117.21, 148.74, 188.74, 239.50, 303.92, 385.66, 489.39, 621.02, 788.05, 1000.00, 1250.00, 1500.00, 1750.00, 2000.00, 2250.00, 2500.00, 2750.00, 3000.00, 3250.00, 3500.00, 3750.00, 4000.00, 4250.00, 4500.00, 4750.00, 5000.00, 5250.00, 5500.00, 5750.00. Frequency grid (GHz):<br> 1.00, 1.40, 3.00, 5.00, 7.00, 9.00, 10.00, 13.40, 15.00, 18.60, 24.00, 31.30, 31.50, 35.60, 50.10, 57.60, 88.80, 94.10, 115.30, 122.20, 164.10, 166.90, 175.30, 191.30, 228.00, 247.20, 314.20, 336.10, 439.30, 456.70, 657.30, 670.70, 862.40, 886.40. Temperature grid (K):<br> 230, 250, 270, 290, 310.<br>
description: {"references": ["Chuang, C. C. and Beard, K. V.: A Numerical Model for the Equilibrium Shape of Electrified Raindrops, J. Atmos. Sci., 47, 1374\u20131389, https://doi.org/10.1175/1520-0469(1990)047&lt;1374:ANMFTE&gt;2.0.CO;2, 1990.", "Eriksson, P., Ekelund, R., Mendrok, J., Brath, M., Lemke, O., and Buehler, S. A.: A general database of hydrometeor single scattering properties at microwave and sub-millimetre wavelengths, Earth Syst. Sci. Data, 10, 1301\u20131326, https://doi.org/10.5194/essd-10-1301- 2018, 2018."]}
DOI: 10.5281/zenodo.3708372
title: Automated Evolution of Logging Statement Levels Using Git Histories and Degree of Interest

description: This data is double-blind.
DOI: 10.15468/nbhz5d
title: Mammuthus meridionalis (Nesti, 1825) from Apollonia- 1 (Mygdonia Basin, Northern Greece) and its importance within the Early Pleistocene mammoth evolution in Europe

description: This dataset contains the digitized treatments in Plazi based on the original journal article Konidaris, George E., Kostopoulos, Dimitris S., Koufos, George D. (2020): Mammuthus meridionalis (Nesti, 1825) from Apollonia- 1 (Mygdonia Basin, Northern Greece) and its importance within the Early Pleistocene mammoth evolution in Europe. Geodiversitas 42 (6): 69-91, DOI: 10.5252/geodiversitas2020v42a6
DOI: 10.5281/zenodo.3708379
title: Automated Evolution of Logging Statement Levels Using Git Histories and Degree of Interest

description: This data is double-blind.
DOI: 10.5281/zenodo.3708028
title: Code and data for "Contrasting upper and deep ocean oxygen response to protracted global warming," by Frölicher et al., GBC under review

description: This file contains the data and python/NCL scripts that have been used for the analysis in this paper. See the README.md file for more information.
DOI: 10.5281/zenodo.3708434
title: Dataset related to article "Reirradiation of Locally Recurrent Prostate Cancer With Volumetric Modulated Arc Therapy."

description: PURPOSE: This study explores the efficacy and safety of reirradiation with modern radiation therapy techniques in patients previously irradiated for prostate cancer and affected by local relapse of disease. METHODS AND MATERIALS: Patients affected by previously irradiated prostate cancer were enrolled in this reirradiation study if they had a biochemical relapse and a <sup>11</sup>C-choline positron emission tomography scan revealing the presence of a local recurrence of disease. Reirradiation consisted of a stereotactic treatment delivered by image guided radiation therapy-volumetric modulated arc therapy with flattening filter-free technology in 5 daily fractions. RESULTS: Twenty-three patients underwent reirradiation to the prostate, prostatic bed, or prostate and local recurrence. Re-treatment consisted of a median total dose of 25 Gy in 5 fractions. A biochemical response was observed in all cases. Acute toxicity was mainly genitourinary (GU) grade 1 to 2 (n = 13; 56.5%). One patient (4.3%) had grade 3 hematuria. A grade 1 GU late toxicity was registered in 4 patients (17.4%) and grade 3 in 1 patient (4.3%, urethral obstruction). Gastrointestinal toxicity was negligible. Regression analysis showed that only a short elapsed time in months from primary radiation therapy was significantly correlated with acute GU toxicity. After a median follow-up of 33 months (range, 5-58 months), the median biochemical recurrence-free survival was 19 months, and the 2-year biochemical recurrence-free survival (BRFS) was 41.7%. Median local control was 30 months; the 2-year local control rate was 58.1%. CONCLUSIONS: Reirradiation of patients with prostate cancer who underwent previous radiation therapy is a valuable option that can be safely considered to delay the beginning of hormonal treatment.
DOI: 10.5281/zenodo.3708433
title: Dataset related to article "Reirradiation of Locally Recurrent Prostate Cancer With Volumetric Modulated Arc Therapy."

description: PURPOSE: This study explores the efficacy and safety of reirradiation with modern radiation therapy techniques in patients previously irradiated for prostate cancer and affected by local relapse of disease. METHODS AND MATERIALS: Patients affected by previously irradiated prostate cancer were enrolled in this reirradiation study if they had a biochemical relapse and a <sup>11</sup>C-choline positron emission tomography scan revealing the presence of a local recurrence of disease. Reirradiation consisted of a stereotactic treatment delivered by image guided radiation therapy-volumetric modulated arc therapy with flattening filter-free technology in 5 daily fractions. RESULTS: Twenty-three patients underwent reirradiation to the prostate, prostatic bed, or prostate and local recurrence. Re-treatment consisted of a median total dose of 25 Gy in 5 fractions. A biochemical response was observed in all cases. Acute toxicity was mainly genitourinary (GU) grade 1 to 2 (n = 13; 56.5%). One patient (4.3%) had grade 3 hematuria. A grade 1 GU late toxicity was registered in 4 patients (17.4%) and grade 3 in 1 patient (4.3%, urethral obstruction). Gastrointestinal toxicity was negligible. Regression analysis showed that only a short elapsed time in months from primary radiation therapy was significantly correlated with acute GU toxicity. After a median follow-up of 33 months (range, 5-58 months), the median biochemical recurrence-free survival was 19 months, and the 2-year biochemical recurrence-free survival (BRFS) was 41.7%. Median local control was 30 months; the 2-year local control rate was 58.1%. CONCLUSIONS: Reirradiation of patients with prostate cancer who underwent previous radiation therapy is a valuable option that can be safely considered to delay the beginning of hormonal treatment.