cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22309213.v9
title: Targeting Cancer Cell Signaling Using Precision Oncology Towards a Holistic Approach to Cancer Therapeutics

description: The mutational changes occurring in the regulatory genes responsible for the maintenance of optimal cell growth and proliferation gradually lead to cancer progression and metastasis. Furthermore, patients with the same cancer types often respond differently to different cancer therapies, indicating the need for a patient-specific treatment regimen for the disease. Precision oncology is the new field of cancer research that relies on genetic profiling of individual tumors to identify targetable alterations for custom-tailored personalized treatment of the disease. It is to rely upon the genomic study of cancer cells to get a clear picture of the prognosis and pathways involved in disease progression and to look for the means to selectively target them for a cure. This article intends to briefly explain the foundations and frontiers of precision oncology in the context of technological advances being made in this direction to assess its scope and importance in the realization of a proper cure for cancer.
DOI: 10.25318/1610001301-eng
title:  Real manufacturing sales, orders, inventory owned and inventory to sales ratio, 2017 dollars, seasonally adjusted

description: Canadian Sales of goods manufactured (shipments), new orders, unfilled orders, inventories, raw materials, goods or work in process, finished goods, and inventory to sales ratios for durable and non-durable goods by North American Industry Classification System (NAICS) for reference periods January 2002 to the current reference month. Not all combinations are available. Values are in constant dollars.
DOI: 10.25318/1610001301-fra
title: Valeur réelle des ventes, des commandes, des stocks possédés et le ratio des stocks aux ventes des industries manufacturières, en dollars de 2017, désaisonnalisées

description: Valeur mensuelle des ventes de biens fabriqués (livraisons), des nouvelles commandes, des commandes en carnet, des stocks, des stocks de matières premières, des stocks de biens en cours de fabrication ou travaux en cours, des stocks de produits finis, et des rapports des stocks aux ventes pour les biens durables et non durables du secteur de la fabrication au Canada, selon le Système de classification des industries de l’Amérique du Nord (SCIAN), pour les périodes de référence allant de janvier 2002 au mois de référence en cours. Les combinaisons ne sont pas toutes disponibles. Valeurs exprimées en dollars constants.
DOI: 10.5519/qd.3gkqy748
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (48 records)
DOI: 10.5066/p900bqzr
title: Water-quality profiles within the Caloosahatchee River and twelve fiberglass tanks, during experimental nutrient addition treatments, 2020

description: The dataset includes water-quality sensor readings collected by the U.S Geological Survey (USGS) from the Caloosahatchee River at the Franklin Lock and Dam and 12 open-air fiberglass tanks filled with Caloosahatchee River water used for mesocosm experiments testing the effects of elevated nutrients on harmful algal bloom (HAB) dynamics. This dataset contains water quality sensor readings from two of eight total independent experiments conducted from June 8-11, 2020 and September 14-17, 2020. Each of the 12 tanks were randomly treated with either ammonium hydroxide, sodium nitrate, sodium phosphate, or left untreated (controls) for a total of three replicates of each treatment. The tanks were treated with incrementally higher dosing solutions every 24 hours for the first three days of the four-day experiment (T0, T24, and T48). Biological and nutrient concentration samples were collected each day before and after the dosing solution was applied and at T72, the final day of the experiment. Water-quality sensor data were collected on all four days (T0, T24, T48, T72) at three depths within each tank and the river using a multi-parameter water-quality sonde before the dosing solutions were applied. Each point reading is provided as an instantaneous measurement. Water-quality parameters measured include chlorophyll fluorescence, dissolved oxygen, fluorescence of dissolved organic matter, pH, phycocyanin fluorescence, specific conductance, turbidity, and water temperature. The data is provided as a table in comma delimited format.
DOI: 10.48324/dandi.000036/0.230515.1917
title: Allen Institute Openscope - Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex

description: Despite significant progress in understanding neural coding, it remains unclear how the coordinated activity of large populations of neurons relates to what an observer actually perceives. Since neurophysiological differences must underlie differences among percepts, differentiation analysis-quantifying distinct patterns of neurophysiological activity-has been proposed as an "inside-out" approach that addresses this question. This methodology contrasts with "outside-in" approaches such as feature tuning and decoding analyses, which are defined in terms of extrinsic experimental variables. Here, we used two-photon calcium imaging in mice of both sexes to systematically survey stimulus-evoked neurophysiological differentiation (ND) in excitatory neuronal populations in layers (L)2/3, L4, and L5 across five visual cortical areas (primary, lateromedial, anterolateral, posteromedial, and anteromedial) in response to naturalistic and phase-scrambled movie stimuli. We find that unscrambled stimuli evoke greater ND than scrambled stimuli specifically in L2/3 of the anterolateral and anteromedial areas, and that this effect is modulated by arousal state and locomotion. By contrast, decoding performance was far above chance and did not vary substantially across areas and layers. Differentiation also differed within the unscrambled stimulus set, suggesting that differentiation analysis may be used to probe the ethological relevance of individual stimuli.

For more details, consult the associated publication : https://doi.org/10.1523/eneuro.0280-21.2021
DOI: 10.25345/c5q81530k
title: MassIVE MSV000091948 - GNPS - fecal and serum sample extraction method test
title: Extraction methods testing for fecal and serum samples. Solvents tested include 5/95, 50/50, 95/5 H2O/MeOH, and 5/95 H2O/EtOH.
DOI: 10.25345/c5kh0f85b
title: MassIVE MSV000091949 - Syncytin1 sequesters viral LF2 to enhance the Epstein-Barr virus lytic phase
title: Previously, we identified Syncytin1 to be expressed in human B cells and enhance EBV ability to undergo lytic replication. To gain mechanistic insight, we performed liquid chromatography tandem mass spectrometry (LC-MS/MS) on tryptic peptides from immunoprecipitated FLAG-tagged Syncytin-1 in latently infected EBV+ Burkitt lymphoma cells. This revealed a number of cellular proteins as potential Syncytin-1 interacting partners during latency and/or during the lytic phase as well as two EBV lytic phase proteins, the viral protein kinase and LF2, a negative regulator of EBV lytic gene transcription. We now find that Syncytin1 reduces the association between LF2 and the EBV replication and transcription activator to promote EBV lytic gene expression.
DOI: 10.5281/zenodo.4013811
title: The Varying Openness of Digital Open Science Tools

description: Dataset accompanying the paper submitted to F1000 entitled <strong>The Varying Openness of Digital Open Science Tools.</strong> Abstract of paper Digital tools that support Open Science practices play a key role in the seamless accumulation, archiving and dissemination of scholarly data, outcomes and conclusions. Despite their integration into Open Science practices, the providence and design of these digital tools are rarely explicitly scrutinized. This means that influential factors, such as the funding models of the parent organizations, their geographic location, and the dependency on digital infrastructures are rarely considered. Suggestions from literature and anecdotal evidence already draw attention to the impact of these factors, and raise the question of whether the Open Science ecosystem can realise the aspiration to become a truly “unlimited digital commons” in its current structure. In an online research approach, we compiled and analysed the geolocation, terms and conditions as well as funding models of 242 digital tools increasingly being used by researchers in various disciplines. Our findings indicate that design decisions and restrictions are biased towards researchers in North American and European scholarly communities. In order to make the future Open Science ecosystem inclusive and operable for researchers in all world regions including Africa, Latin America, Asia and Oceania, those should be actively included in design decision processes. Digital Open Science Tools carry the promise of enabling collaboration across disciplines, world regions and language groups through responsive design. We therefore encourage long term funding mechanisms and ethnically as well as culturally inclusive approaches serving local prerequisites and conditions to tool design and construction allowing a globally connected digital research infrastructure to evolve in a regionally balanced manner.
DOI: 10.5281/zenodo.7554848
title: Open Science resources by research discipline

description: This is the underlying data set to our map of Open Science resources by discipline: https://kumu.io/access2perspectives/open-science#disciplines For context and related resources please refer to https://access2perspectives.pubpub.org/open-science Explore the map by clicking on individual nodes and see descriptions, related websites, and other information about the resources.<br> With the navigation buttons to the right, you can zoom in and out, and select and focus on specific elements. Learn more about our work at access2perspectives.org<br> If you have comments, questions or suggestions for improvements on this map email us at info@access2perspectives.org. LICENSE: <strong>Creative Commons Attribution-ShareAlike 4.0 International</strong>
DOI: 10.5281/zenodo.7554849
title: Open Science resources by research discipline

description: This is the underlying data set to our map of Open Science resources by discipline: https://kumu.io/access2perspectives/open-science#disciplines For context and related resources please refer to https://access2perspectives.pubpub.org/open-science Explore the map by clicking on individual nodes and see descriptions, related websites, and other information about the resources.<br> With the navigation buttons to the right, you can zoom in and out, and select and focus on specific elements. Learn more about our work at access2perspectives.org<br> If you have comments, questions or suggestions for improvements on this map email us at info@access2perspectives.org. LICENSE: <strong>Creative Commons Attribution-ShareAlike 4.0 International</strong>
DOI: 10.5281/zenodo.7878558
title: Open Science resources by research discipline

description: This is the underlying data set to our map of Open Science resources by discipline: https://kumu.io/access2perspectives/open-science#disciplines For context and related resources please refer to https://access2perspectives.pubpub.org/open-science Explore the map by clicking on individual nodes and see descriptions, related websites, and other information about the resources.<br> With the navigation buttons to the right, you can zoom in and out, and select and focus on specific elements. Learn more about our work at access2perspectives.org<br> If you have comments, questions or suggestions for improvements on this map email us at info@access2perspectives.org. LICENSE: <strong>Creative Commons Attribution-ShareAlike 4.0 International</strong>
DOI: 10.5066/p96vpgh7
title: Cyanotoxin concentrations in extracts from cyanobacteria colonies, plankton net tows, and Solid Phase Adsorption Toxin Tracking (SPATT) samplers in western rivers, lakes, and reservoirs, including drinking water sources in the Oregon Cascades: 2016-2020

description: This data release contains cyanotoxin concentrations for microcystins, cylindrospermopsins, anatoxins, and saxitoxins assessed using Enzyme-Linked Immunosorbent Assays (ELISA) on 363 samples collected from 82 surface-water sites located in the Cascade Range in Oregon, and eight sites located outside of the Oregon Cascade Range in Washington and California, during 2016-2020. Three sample types were assessed: 1) benthic colonies and mats of cyanobacteria (n=109), 2) plankton net tows (n=90), and 3) Solid Phase Adsorption Toxin Tracking samplers (SPATTs)(n=164).
DOI: 10.25921/es56-4z08
title: Reson7125 Water Column Sonar Data Collected During NF1408
DOI: 10.25921/8hdx-6m58
title: Reson7125 Water Column Sonar Data Collected During NF1509
DOI: 10.5281/zenodo.7761409
title: Human STING is a proton channel (Live-cell GALT pH Measurement upon STING agonist treatment with or without C53)

description: hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to GALT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM Bafilomycin A1 (Santa Cruz Biotechnology cat. #sc-201550),<strong> </strong>1 µM diABZI (Invivogen, #tlrl-diabzi), 20 µg/mL cGAMP (Invivogen, #tlrl-nacga23-1) with 5 ng/µL digitonin (Promega, #G9441) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection. Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.
DOI: 10.5281/zenodo.7761408
title: Human STING is a proton channel (Live-cell GALT pH Measurement upon STING agonist treatment with or without C53)

description: hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to GALT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM Bafilomycin A1 (Santa Cruz Biotechnology cat. #sc-201550),<strong> </strong>1 µM diABZI (Invivogen, #tlrl-diabzi), 20 µg/mL cGAMP (Invivogen, #tlrl-nacga23-1) with 5 ng/µL digitonin (Promega, #G9441) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection. Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.
DOI: 10.5281/zenodo.7938713
title: Date Fruit classification using a wide range of classifiers

description: Datasets generated by the techniques RUS and SMOTE. These datasets were used in the paper Date Fruit classification using a wide range of classifiers, accepted for publication in the International Conference on Systems, Signals and Image Processing (IWSSIP) 2023.
DOI: 10.5281/zenodo.7938712
title: Date Fruit classification using a wide range of classifiers

description: Datasets generated by the techniques RUS and SMOTE. These datasets were used in the paper Date Fruit classification using a wide range of classifiers, accepted for publication in the International Conference on Systems, Signals and Image Processing (IWSSIP) 2023.
DOI: 10.6084/m9.figshare.22825313
title: Data for forest type classification and tree species habitat models in North America

description: Grid-level input data with tree species importance value index (IVI) for each region (West, East, and Boreal) for each time frame (2000–2019 and 1970–1999) and raster layers (geoTIFF) of forest type and biome. Coordinates in the grid-level input data denote the location of the grid centroid. Raster values are described in RasterAttributes.xlsx.
DOI: 10.34740/kaggle/dsv/5693265
title: 🇺🇦 Ukraine Conflict Twitter Dataset
DOI: 10.5281/zenodo.7783355
title: Human STING is a proton channel (Live-cell MGAT STING WT or S53L pH Measurement upon STING agonist treatment with or without C53)

description: hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to MGAT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. Cells then were transduced with pXPR023 (lentiCRISPRv2) expressing an sgRNA targeting STING and selected with 0.1 µg/mL puromycin for 5 days. Finally, cells were transduced with blasticidin-STING-HA (WT or S53L) and selected using 10 µg/mL blasticidin HCl for 5 days.<strong> </strong> BJ1 SEP-mRuby3 STING-HA (WT or S53L) cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM diABZI (Invivogen, #tlrl-diabzi) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection. Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.
DOI: 10.5281/zenodo.7783354
title: Human STING is a proton channel (Live-cell MGAT STING WT or S53L pH Measurement upon STING agonist treatment with or without C53)

description: hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to MGAT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. Cells then were transduced with pXPR023 (lentiCRISPRv2) expressing an sgRNA targeting STING and selected with 0.1 µg/mL puromycin for 5 days. Finally, cells were transduced with blasticidin-STING-HA (WT or S53L) and selected using 10 µg/mL blasticidin HCl for 5 days.<strong> </strong> BJ1 SEP-mRuby3 STING-HA (WT or S53L) cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM diABZI (Invivogen, #tlrl-diabzi) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection. Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.