cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3712258
title: Dataset related to article "Tumor-Infiltrating Lymphocytes and Macrophages in Intrahepatic Cholangiocellular Carcinoma. Impact on Prognosis after Complete Surgery."

description: BACKGROUND: Immune infiltrate impacts prognosis of several tumors. To assess the prognostic impact of tumor-infiltrating lymphocytes and macrophages in patients undergoing resection for intrahepatic cholangiocellular carcinoma (ICC). METHODS: All consecutive patients undergoing surgery for ICC between 2008 and 2016 were considered. Inclusion criteria were complete resection and follow-up &gt; 12 months. Tissue sections were immunostained for CD3+, CD4+, CD8+, Foxp3+, and CD68+. The number of positive cells was quantified using a computer-aided image analysis system. Different cut-off values were tested as predictors of overall survival (OS). RESULTS: Fifty-three patients were analyzed. ICC were T1 in 28 patients, multifocal in 11, and N+ in 13. After a median follow-up of 42 months, 5-year OS was 52.1%. The following immune infiltrate values were associated with better OS: CD3+ &gt; 0.10% (5-year OS 63.3% vs. 13.6% if ≤ 0.10%, p = 0.001); CD8+ &gt; 0.10% (56.2% vs. 28.6% if ≤ 0.10%, p = 0.051); Foxp3+ absent (59.4% vs. 16.0% if present, p = 0.049). CD4+ and CD68+ infiltrates were not associated with OS. Three-year OS rates in patients with 0, 1, and ≥ 2 negative prognostic factors were 73.6%, 47.3%, and 14.3%, respectively (p &lt; 0.001). CD3+ infiltrate stratified prognosis in T1 tumors (3-year OS 71.7% if CD3+ &gt; 0.10% vs. 14.3% if ≤ 0.10%, p &lt; 0.001). CONCLUSIONS: Tumor-infiltrating lymphocytes are associated with prognosis of ICC patients after complete surgery. CD3+ and CD8+ infiltrate is associated with higher survival and lower recurrence risk, while Foxp3+ infiltrate is associated with worse prognosis. CD3+ infiltrate allows refining prediction of prognosis in early tumors.
DOI: 10.25934/00003328
title: Mapping of components of the complete blood count and comprehensive metabolic profile to disease-specific clinical and endoscopy endpoints in phase 2 and 3 clinical trials of ulcerative colitis and Crohn’s disease

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25345/c5kh5v
title: MassIVE MSV000085105 - GNPS_T_ISH_SEVEN STRAIN_MODELLING
title: Mining Microbial Peptides and other Compounds of Novelty.
DOI: 10.5281/zenodo.3698238
title: Wi-Fi RSSI fingerprint dataset from two malls with validation routes in a shop-level for indoor positioning

description: <strong>Th</strong>e dataset is composed of the RSSI fingerprinting calibration of two malls employing four different smartphones with the random walking survey method. Moreover, the dataset includes validation routes performed with ten smartphones from various brands and labeled with the code of the shops where they were registered. For evaluation purposes, together with the samples, information related to the shopping center like the Euclidean distance between shops is provided. The files are described as follows: building.csv’: two rows with the id of mall 1 and mall 2. ‘floor.csv’: there is a row for each of the floors of the two malls. Three floors for mall 1 and two floors for mall 2 ‘zones.csv’: for each zone is indicated the id of the mall and the id floor. There are 69 zones from mall 1 and 124 for mall 2 ‘training.csv’: in this file are registered the ids and the description of the five different calibrations performed (one per smartphone) in each of the malls. ‘training_sample.csv’: each row of the file has the RSSI in dBm recorded during the off-line calibration phase together with the timestamp, channel, and MAC of the AP. ‘route.csv’: the id’s and the description of each of the validation routes are recorded in this file. ‘route_sample.csv’: with a similar structure than the training_sample.csv, the RSSI, timestamp, channel, and MAC acquired during the validation routes are stored in this file. ‘euclidea_distance.csv”: to evaluate the error of the different algorithms, this file recorded the euclidean distance from the center of a shop to each other in meters. The dataset is to be cited as follows:<br> J. A. López-Pastor, A.J. Ruiz-Ruiz, A.J. García-Sánchez, J.L. Gómez-Tornero. Wi-Fi RSSI fingerprint dataset from two malls with validation routes in a shop-level for indoor positioning. Zenodo repository. DOI: 10.5281/zenodo.3698238
DOI: 10.5281/zenodo.3698237
title: Wi-Fi RSSI fingerprint dataset from two malls with validation routes in a shop-level for indoor positioning

description: <strong>Th</strong>e dataset is composed of the RSSI fingerprinting calibration of two malls employing four different smartphones with the random walking survey method. Moreover, the dataset includes validation routes performed with ten smartphones from various brands and labeled with the code of the shops where they were registered. For evaluation purposes, together with the samples, information related to the shopping center like the Euclidean distance between shops is provided. The files are described as follows: building.csv’: two rows with the id of mall 1 and mall 2. ‘floor.csv’: there is a row for each of the floors of the two malls. Three floors for mall 1 and two floors for mall 2 ‘zones.csv’: for each zone is indicated the id of the mall and the id floor. There are 69 zones from mall 1 and 124 for mall 2 ‘training.csv’: in this file are registered the ids and the description of the five different calibrations performed (one per smartphone) in each of the malls. ‘training_sample.csv’: each row of the file has the RSSI in dBm recorded during the off-line calibration phase together with the timestamp, channel, and MAC of the AP. ‘route.csv’: the id’s and the description of each of the validation routes are recorded in this file. ‘route_sample.csv’: with a similar structure than the training_sample.csv, the RSSI, timestamp, channel, and MAC acquired during the validation routes are stored in this file. ‘euclidea_distance.csv”: to evaluate the error of the different algorithms, this file recorded the euclidean distance from the center of a shop to each other in meters. The dataset is to be cited as follows:<br> J. A. López-Pastor, A.J. Ruiz-Ruiz, A.J. García-Sánchez, J.L. Gómez-Tornero. Wi-Fi RSSI fingerprint dataset from two malls with validation routes in a shop-level for indoor positioning. Zenodo repository. DOI: 10.5281/zenodo.3698238
DOI: 10.25345/c5ft4b
title: MassIVE MSV000085106 - New actinomycin produced by Streptomyces sp. MBT27
title: In the current study Streptomyces sp. MBT27, strain isolated from remote area of Qinling mountains, was fermented with different carbon sources and metabolomic analysis of secondary metabolites was carried out by MS and multivariate data analysis. The statistical analysis suggested that extracts with stronger antimicrobial activity against B. subtilis contained higher concentrations of actinomycins. Further analyses of the metabolic profiles by oPLS-DA and GNPS molecular networking resulted in the isolation of a novel actinomycin analog, actinomycin L1 and L2 and three known actinomycins D, X0beta and X2.
DOI: 10.5281/zenodo.3710994
title: PatCit: A Comprehensive Dataset of Patent Citations

description: <em><strong>PATCIT: A Comprehensive Dataset of Patent Citations</strong></em> [Website, Newsletter, GitHub] Patents are at the crossroads of many innovation nodes: science, industry, products, competition, etc. Such interactions can be identified through citations <em>in a broad sense</em>. It is now common to use front-page patent citations to study some aspects of the innovation system. However, <strong>there is much more buried in the Non Patent Literature (NPL) citations and in the patent text itself</strong>. Good news: Natural Language Processing (NLP) tools now enable social scientists to excavate and structure this long hidden information. <strong>That's the purpose of this project</strong> <strong><em>IN PRACTICE</em></strong> A detailed presentation of the current state of the project is available in our March 2020 presentation. So far, we have: <strong>classified</strong> the 40 million NPL citations reported in the <strong>DOCDB</strong> database in 9 distinct research oriented classes with a 90% accuracy rate. <strong>parsed</strong> and <strong>consolidated</strong> the 27 million <strong>NPL</strong> citations classified as bibliographical references. <strong>extracted</strong>, <strong>parsed</strong> and <strong>consolidated</strong> in-text bibliographical references and patent citations from the body of all time USPTO patents. The latest version of the dataset is the <strong>v0.15</strong>. It is made of the v0.1 of the US contextual citations dataset and v0.2 of the front-page NPL citations dataset. <strong>Give it a try!</strong> The dataset is publicly available on Google Cloud BigQuery, just click here. <strong><em>FEATURES</em></strong> <strong>Open</strong> The code is licensed under MIT-2 and the dataset is licensed under CC4. Two highly permissive licenses. The project is thought to be <em>dynamically improved by and for the community</em>. Anyone should feel free to open discussions, raise issues, request features and contribute to the project. <strong>Comprehensive</strong> We address <em>worldwide patents</em>, as long as the data is available. We address <em>all classes of citations</em>, not only bibliographical references. We address front-page and in-text citations. <strong>Highest standards</strong> We use and implement state-of-the art machine learning solutions. We take great care to implement only the most efficient solutions. We believe that computational resources should be used sparsely, for both environmental sustainability and long term financial sustainability of the project.
DOI: 10.5281/zenodo.3712121
title: Dataset related to article "NK cell recruitment in salivary glands provides early viral control but is dispensable for tertiary lymphoid structure formation."

description: Salivary glands (SGs) represent a permissive site for several sialotropic viruses whose persistence is linked to the development of autoimmunity. Natural Killer (NK) cells play a key role in viral clearance but their involvement in viral infection control and in tertiary lymphoid structures (TLS) development within SGs is unknown. By using an inducible model of TLS in the SGs of wild-type C57BL/6 mice, induced by the local delivery of a replication-defective adenovirus (AdV), we demonstrated that circulating NK cells are rapidly recruited to SGs and highly enrich the early inflammatory infiltrate prior to TLS development. NK cells migrating to SGs in response to AdV infection up-regulate NKp46, undergo proliferation, acquire cytotoxic potential, produce Granzyme-B and IFN-γ, and reduce viral load in the acute phase of the infection. Nonetheless, the selective depletion of both circulating and infiltrating NK cells in AdV-infected mice neither affect the development and frequency of TLS nor the onset of autoimmunity. These data demonstrate that, upon local viral delivery of AdV, peripheral NK cells homing to SGs can exert an early control of the viral infection but are dispensable for the formation of TLS and breach of immunologic tolerance.
DOI: 10.5281/zenodo.3712247
title: ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets (drug matrix dataset)

description: This data was generated by Ganter B, Snyder RD, Halbert DN, Lee MD. Toxicogenomics in drug discovery and development: mechanistic analysis of compound/class-dependent effects using the DrugMatrix database. Pharmacogenomics [Internet]. 2006 Oct;7(7):1025–1044. Available from: http://dx.doi.org/10.2217/14622416.7.7.1025 PMID: 17054413. The data have been curated and analyzed using our open-source R package, <em>ToxicoGx</em> (cran.r-project.org/web/packages/ToxicoGx) and are available publicly in the <em>ToxicoDB </em>web application (www.toxicodb.ca).
DOI: 10.5281/zenodo.3712120
title: Dataset related to article "NK cell recruitment in salivary glands provides early viral control but is dispensable for tertiary lymphoid structure formation."

description: Salivary glands (SGs) represent a permissive site for several sialotropic viruses whose persistence is linked to the development of autoimmunity. Natural Killer (NK) cells play a key role in viral clearance but their involvement in viral infection control and in tertiary lymphoid structures (TLS) development within SGs is unknown. By using an inducible model of TLS in the SGs of wild-type C57BL/6 mice, induced by the local delivery of a replication-defective adenovirus (AdV), we demonstrated that circulating NK cells are rapidly recruited to SGs and highly enrich the early inflammatory infiltrate prior to TLS development. NK cells migrating to SGs in response to AdV infection up-regulate NKp46, undergo proliferation, acquire cytotoxic potential, produce Granzyme-B and IFN-γ, and reduce viral load in the acute phase of the infection. Nonetheless, the selective depletion of both circulating and infiltrating NK cells in AdV-infected mice neither affect the development and frequency of TLS nor the onset of autoimmunity. These data demonstrate that, upon local viral delivery of AdV, peripheral NK cells homing to SGs can exert an early control of the viral infection but are dispensable for the formation of TLS and breach of immunologic tolerance. This research used pzf and ets file form extensions, we attach pdfs information about
DOI: 10.25934/00004184.0
title: Available IPD datapackage for study 'An International Observational Study Among Severe Sepsis Patients Treated in the Intensive Care Unit'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00004184.1
title: IPD datapackage for study 'An International Observational Study Among Severe Sepsis Patients Treated in the Intensive Care Unit' and research request: 'Severe sepsis in the cardiac intensive care unit: management strategies and outcomes'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.7910/dvn/vuye2m/hicjkg
title: HH_JT_survey_public.tab

description: :unav
DOI: 10.7910/dvn/vuye2m/ngaf1b
title: HH_JT_desc_public.do

description: :unav
DOI: 10.5281/zenodo.3712401
title: Time-series measurements of size fractionated primary production (&gt;3 micron) in the subtropical North Pacific Ocean

description: Filter size-fractionated (&gt;3 μm) particulate 14C-based rates of primary production were measured at six discrete depths (5, 25, 45, 75, 100, and 125 m) throughout the euphotic zone. Seawater samples from each depth were subsampled into triplicate 30-mL polycarbonate centrifuge tubes from a pre-dawn cast, inoculated with 70 µL of NaH14CO3-, then incubated over the full photoperiod (~12-14 hours) on a floating in situ array at the corresponding depths where the water was collected. At the end of the incubation period (after sundown), 25 mL of each sample was vacuum-filtered first onto a 25-mm diameter 3-μm pore size polycarbonate membrane.
description: {"references": ["YM Rii, DM Karl and MJ Church, Temporal and vertical variability in picophytoplankton primary productivity in the North Pacific Subtropical Gyre, Marine Ecology Progress Series, 10.3354/meps11954, 562, (1-18), (2016)."]}
DOI: 10.5281/zenodo.3712402
title: Time-series measurements of size fractionated primary production (&gt;3 micron) in the subtropical North Pacific Ocean

description: Filter size-fractionated (&gt;3 μm) particulate 14C-based rates of primary production were measured at six discrete depths (5, 25, 45, 75, 100, and 125 m) throughout the euphotic zone. Seawater samples from each depth were subsampled into triplicate 30-mL polycarbonate centrifuge tubes from a pre-dawn cast, inoculated with 70 µL of NaH14CO3-, then incubated over the full photoperiod (~12-14 hours) on a floating in situ array at the corresponding depths where the water was collected. At the end of the incubation period (after sundown), 25 mL of each sample was vacuum-filtered first onto a 25-mm diameter 3-μm pore size polycarbonate membrane.
description: {"references": ["YM Rii, DM Karl and MJ Church, Temporal and vertical variability in picophytoplankton primary productivity in the North Pacific Subtropical Gyre, Marine Ecology Progress Series, 10.3354/meps11954, 562, (1-18), (2016)."]}
DOI: 10.5281/zenodo.3711592
title: Dataset: Number of diagnoses with coronavirus disease (COVID-19) in The Netherlands

description: Datasets in this publication report the number of diagnoses with coronavirus disease (COVID-19) based on RIVM reports in The Netherlands. Since 3 March, RIVM reports the number of diagnoses with the coronavirus and their municipality of residence on a daily base. The data contains the total number of positively tested patients. It is not a dataset with the current number of sick people in the Netherlands. The RIVM does not currently provide data on people who have been cured. RIVM provides daily updates of the data. The data is not stored in a persistent way and is updated on the fly. RIVM removes data from previous days from their website. Therefore, it is not possible to monitor the spread of the coronavirus disease in the Netherlands on this data standalone. The data in this publication is composed of hourly downloads of the data of the website of RIVM. All code to compose the data was found on https://github.com/J535D165/CoronaWatchNL as well as graphs based on the data.
DOI: 10.25919/5e6fdbe7ac53a
title: Parkes pulsar observations with undefined project IDs for 2020_02

description: Parkes pulsar observations with undefined project IDs for 2020. This collections contains observations from Parkes projects PX052 and PX737.
DOI: 10.5281/zenodo.3712265
title: Dataset related to article "Survival outcomes of robotic radical hysterectomy for early stage cervical cancer: A 9-year study."

description: BACKGROUND: Recently, the results of a RCT have raised concerns on the management of cervical cancer through a minimally invasive approach. This study reports on the outcomes of patients with early stage cervical cancer submitted to robotics. METHODS: Retrospective review of a consecutive series of patients with an early cervical cancer treated with robotics at a single Institution over a 9-year period. RESULTS: A total of 91 women were managed; 39 (41.1%) had cervical adenocarcinoma. One (1.1%) conversion to laparotomy and one (1.1%) intraoperative complication occurred. Five (5.5%) patients experienced postoperative (&gt;G2) complications; 24 (26.4%) patients required further adjuvant therapies. After a median follow-up of 40.7 (3.8-96.6) months, the DFS and OS were 90.4 (95%CI 85.3-95.6)% and 94.5 (95%CI 91.8-97.2)%, respectively. CONCLUSIONS: According to the available literature, the survival outcomes of this series of RRH for ECC are not inferior to what recorded in the past by an open approach.
DOI: 10.5281/zenodo.3712266
title: Dataset related to article "Survival outcomes of robotic radical hysterectomy for early stage cervical cancer: A 9-year study."

description: BACKGROUND: Recently, the results of a RCT have raised concerns on the management of cervical cancer through a minimally invasive approach. This study reports on the outcomes of patients with early stage cervical cancer submitted to robotics. METHODS: Retrospective review of a consecutive series of patients with an early cervical cancer treated with robotics at a single Institution over a 9-year period. RESULTS: A total of 91 women were managed; 39 (41.1%) had cervical adenocarcinoma. One (1.1%) conversion to laparotomy and one (1.1%) intraoperative complication occurred. Five (5.5%) patients experienced postoperative (&gt;G2) complications; 24 (26.4%) patients required further adjuvant therapies. After a median follow-up of 40.7 (3.8-96.6) months, the DFS and OS were 90.4 (95%CI 85.3-95.6)% and 94.5 (95%CI 91.8-97.2)%, respectively. CONCLUSIONS: According to the available literature, the survival outcomes of this series of RRH for ECC are not inferior to what recorded in the past by an open approach.
DOI: 10.18739/a21z41t0t
title: Model simulations from Modèle Atmosphérique Regionale (MAR) over Greenland, 1948-2016

description: Here we provide an archive of Modèle Atmosphérique Regionale v. 3.5.2 simulations over Greenland. This archive contains daily data at 20-kilometer resolution with lateral boundary forcings from the National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis model. Data are provided in netCDF format, where information of all variables and their units are provided within the netCDF files. See method section for more detailed description of the data. Citation: If this dataset is used in any publication, this data repository and Fettweis et al. 2017 should be cited. Contact Xavier Fettweis for obtaining more recent MAR based simulations (see contact information in metadata). References: Fettweis X, Box JE, Agosta C, Amory C, Kittel C, Lang C, van As D, Machguth H and Gallée H (2017) Reconstructions of the 1900–2015 Greenland ice sheet surface mass balance using the regional climate MAR (Modèle Atmosphérique Régional) model. The Cryosphere 11(2), 1015–1033 (doi:10.5194/tc-11-1015-2017)
DOI: 10.5281/zenodo.3712406
title: Time series measurements of group-specific picophytoplankton primary production

description: 14C-based primary production by flow cytometrically determined pico plankton (Prochlorococcus, Synechococcus, and photosynthetic picoeukaryotes) were measured at six discrete depths (5, 25, 45, 75, 100, and 125 m) at Station ALOHA. Seawater samples from each depth were subsampled into triplicate 30-mL polycarbonate centrifuge tubes from a pre-dawn cast, inoculated under subdued light with 70 µL of NaH14CO3-, then incubated over the full photoperiod (~12-14 hours). At the end of the incubation period (after sundown), 5 mL of each radiolabeled sample was preserved in cryotubes containing 30 µL of 16% (final concentration 0.24% w/v) microscopy-grade paraformaldehyde, flash-frozen in liquid nitrogen, and stored at -80°C for subsequent flow cytometric sorting. Group-specific rates of 14C-assimilation by Prochlorococcus, Synechococcus, and PPE were determined by measuring the amount of 14C assimilated into populations sorted using a BD Influx sorting flow cytometer.
description: {"references": ["YM Rii, DM Karl and MJ Church, Temporal and vertical variability in picophytoplankton primary productivity in the North Pacific Subtropical Gyre, Marine Ecology Progress Series, 10.3354/meps11954, 562, (1-18), (2016)."]}