cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13250198
title: Chemogenomic profiling of nitrosamines in yeast

description: We used the yeast chemogenomic assay to screen N-nitrosamines (N-nitrosodimethylamine, N-nitrosodiethylamine and N-methyl-N-aminobutyric acid), their metabolic intermediates (methylamine, ethylamine, formamide and formaldehyde) and related compounds (N,N-dimethylformamide, ammonium sulfate and 4-Nitroquinoline-1-oxide). This work was inspired by the global recalls of sartan class of medications after N-nitrosamine contaminants were detected. In our experiment, a pool containing equal amounts of each of 4,800 homozygous yeast deletion strains were challenged with each compound at 10-20% inhibitory dose and grown competitively for five generations. We used barcode next generation sequencing to quantitatively determine relative strain abundance, and thus estimated the sensitivity or resistance of each strain against the compounds. We found several genes and pathways are required for nitrosamines toxicity, including the arginine biosynthetic pathway. To confirm the involvement of arginine biosynthesis in nitrosamine toxicity, we selected nineteen deletion strains that are of arginine and ammonium metabolism and tested them against these compounds. The attached files contain the count matrices from the barcode sequencing data, as well as the optical density versus time readings during the confirmation screens.
DOI: 10.6084/m9.figshare.13250198.v1
title: Chemogenomic profiling of nitrosamines in yeast

description: We used the yeast chemogenomic assay to screen N-nitrosamines (N-nitrosodimethylamine, N-nitrosodiethylamine and N-methyl-N-aminobutyric acid), their metabolic intermediates (methylamine, ethylamine, formamide and formaldehyde) and related compounds (N,N-dimethylformamide, ammonium sulfate and 4-Nitroquinoline-1-oxide). This work was inspired by the global recalls of sartan class of medications after N-nitrosamine contaminants were detected. In our experiment, a pool containing equal amounts of each of 4,800 homozygous yeast deletion strains were challenged with each compound at 10-20% inhibitory dose and grown competitively for five generations. We used barcode next generation sequencing to quantitatively determine relative strain abundance, and thus estimated the sensitivity or resistance of each strain against the compounds. We found several genes and pathways are required for nitrosamines toxicity, including the arginine biosynthetic pathway. To confirm the involvement of arginine biosynthesis in nitrosamine toxicity, we selected nineteen deletion strains that are of arginine and ammonium metabolism and tested them against these compounds. The attached files contain the count matrices from the barcode sequencing data, as well as the optical density versus time readings during the confirmation screens.
DOI: 10.17632/kbyd3hzwbj.1
title: Data for: Microfiber abundance associated with coral tissue varies geographically on the Belize Mesoamerican Barrier Reef System

description: Data files and R code to support Oldenburg et al. (2020).
DOI: 10.5517/ccdc.csd.cc24sx2y
title: CCDC 1990140: Experimental Crystal Structure Determination

description: Related Article: Martin Hejda, Robert Jirásko, Aleš Růžička, Roman Jambor, Libor Dostál|2020|Organometallics|39|4320|doi:10.1021/acs.organomet.0c00418
DOI: 10.5517/ccdc.csd.cc24sx3z
title: CCDC 1990141: Experimental Crystal Structure Determination

description: Related Article: Martin Hejda, Robert Jirásko, Aleš Růžička, Roman Jambor, Libor Dostál|2020|Organometallics|39|4320|doi:10.1021/acs.organomet.0c00418
DOI: 10.5517/ccdc.csd.cc24sx40
title: CCDC 1990142: Experimental Crystal Structure Determination

description: Related Article: Martin Hejda, Robert Jirásko, Aleš Růžička, Roman Jambor, Libor Dostál|2020|Organometallics|39|4320|doi:10.1021/acs.organomet.0c00418
DOI: 10.5517/ccdc.csd.cc24sx62
title: CCDC 1990144: Experimental Crystal Structure Determination

description: Related Article: Martin Hejda, Robert Jirásko, Aleš Růžička, Roman Jambor, Libor Dostál|2020|Organometallics|39|4320|doi:10.1021/acs.organomet.0c00418
DOI: 10.5517/ccdc.csd.cc24sx73
title: CCDC 1990145: Experimental Crystal Structure Determination

description: Related Article: Martin Hejda, Robert Jirásko, Aleš Růžička, Roman Jambor, Libor Dostál|2020|Organometallics|39|4320|doi:10.1021/acs.organomet.0c00418
DOI: 10.5517/ccdc.csd.cc24sx84
title: CCDC 1990146: Experimental Crystal Structure Determination

description: Related Article: Martin Hejda, Robert Jirásko, Aleš Růžička, Roman Jambor, Libor Dostál|2020|Organometallics|39|4320|doi:10.1021/acs.organomet.0c00418
DOI: 10.5517/ccdc.csd.cc24sx95
title: CCDC 1990147: Experimental Crystal Structure Determination

description: Related Article: Martin Hejda, Robert Jirásko, Aleš Růžička, Roman Jambor, Libor Dostál|2020|Organometallics|39|4320|doi:10.1021/acs.organomet.0c00418
DOI: 10.5517/ccdc.csd.cc24sxb6
title: CCDC 1990148: Experimental Crystal Structure Determination

description: Related Article: Martin Hejda, Robert Jirásko, Aleš Růžička, Roman Jambor, Libor Dostál|2020|Organometallics|39|4320|doi:10.1021/acs.organomet.0c00418
DOI: 10.6084/m9.figshare.13426103
title: Dataset_3_Mallory_Hardcastle_et_al

description: This dataset contains the raw data (cell spike times, behavioral data) that was used for Figures 4-8 from Mallory and Hardcastle et al., Mouse entorhinal cortex encodes a diverse repertoire of self-motion signals. Cells were recorded via Neuropixels probes inserted in the medial entorhinal cortex of head-fixed mice navigating in VR. Animals' virtual body position and right eye position/velocity were tracked simultaneously. Each file contains data from one session and contains information pertaining to all unique cells included in analysis including: session recording times (s), spike times (s), body position (x position in cm), virtual body speed (cm/s), horizontal eye position, vertical eye position, horizontal eye velocity and vertical eye velocity.
DOI: 10.6084/m9.figshare.13425392
title: Dataset_1_Mallory_Hardcastle_et_al

description: This dataset contains the raw data (cell spike times, behavioral data) that was used for Figures 1-3 from Mallory and Hardcastle et al., Mouse entorhinal cortex encodes a diverse repertoire of self-motion signals. Cells were recorded in the medial entohrinal cortex of freely moving mice. Animals' body and 3D head position were tracked simultaneously. The dataset is a matfile (structure) containing information pertaining to all unique cells included in analysis including: session recording times (s), spike times (s), arena size (cm), body position (x and y position in cm), body speed (cm/s), azimuthal head direction (degrees), azimuthal head velocity (degrees/s), pitch (radians), and roll (radians).
DOI: 10.6084/m9.figshare.13425017
title: Dataset_2_Mallory_Hardcastle_et_al

description: This dataset contains the raw data (cell spike times, behavioral data) that was used for Figures 1-3 from Mallory and Hardcastle et al., Mouse entorhinal cortex encodes a diverse repertoire of self-motion signals. Cells were recorded in the medial entorhinal cortex of freely moving mice. Animals' body position and azimuthal head direction and velocity were tracked simultaneously. The dataset is a matfile (structure) containing information pertaining to all unique cells included in analysis including: session recording times (s), spike times (s), arena size (cm), body position (x and y position in cm), body speed (cm/s), azimuthal head direction (degrees), and azimuthal head velocity (degrees/s).
DOI: 10.5281/zenodo.4361685
title: VC-SLAM Versatile Corpus for Semantic Labeling And Modeling

description: Benchmark Corpus for semantic labeling and modeling. This corpus contains 101 data sets from different open data portals.<br> Each data set consists of the following data: Raw csv data [rawdata_csv] Large json data sample [json_sample_large] Small json data sample [json_sample_small] Textual description / Metadata [descriptions] Semantic model as rdf/xml [semantic_models] Mappings describing mapping between raw data attributes and concepts from the ontology [mappings] List of attributes that have been ignored during modeling [ignored_attributes] Additionally the corpus contains a target ontology and an additional ontology for mappings to the PLASMA platform, both as rdf/xml [ontology]. The individual data sets are licensed by the licenses specified in the attached Excel sheet (DataSetOverview.xlsx) These data are provided "as is", without any warranties of any kind. The data are provided under the Creative Commons Attribution 4.0 International license.
DOI: 10.5063/319t8n
title: Ecosystem-Atmosphere fluxes of water, carbon and energy from a basin mangrove in Puerto Morelos, Quintana Roo, Mexico (2017-2018)

description: Data uploaded corresponds to data collected from a flux tower installed at the basin mangrove located in Puerto Morelos (Jardín Botánico Dr. Alfredo Barrera Marín), Quintana Roo, Mexico. The collection pediod was from 13 June 2017 to 30 Nov 2018. Conventional procedures of the eddy covariance method (Burba, 2013) were followed to process raw flux data and produce half-hourly averaged data of net ecosystem-atmosphere CO2 flux (µmol s-1 m-2), latent heat flux (W m-2), and sensible heat flux (W m-2), using the software EddyPro 6.2.1 (LI-COR). Surface energy balance components are included (net radiation and its components, and soil heat flux). Ancillary data includes meteorological variables (air temperature and relative humidity, vapor pressure deficit, atmospheric pressure, precipitation, soil temperature, photosynthetically active radiation) as well as inundation water level and water temperature.
DOI: 10.6084/m9.figshare.7090607.v2
title: Tissue-specific gene expression shows a cynipid wasp repurposes oak host gene networks to create a complex and novel parasite-specific organ

description: Every organism on Earth depends on interactions with other organisms to survive. In each of these interactions, an organism must utilize the limited toolbox of genes, proteins, and pathways it possesses to successfully manipulate or cooperate with another species, but it can also coopt the genome machinery of its partner. An insect-induced plant gall is an extreme example of this, wherein the wasp hijacks the plant genome to direct the initiation and development of a gall composed of plant tissue. This unique and complex species interaction has been studied for hundreds of years, and yet the mechanism(s) behind gall development remains elusive. Here we show that cynipid wasps are creating an entirely new and complex organ from its oak host’s tissue, significantly changing the expression of 28% of oak genes. The inner larval capsule shows suppression of large parts of the plant innate immune system and evidence for the wasp utilizing the plant’s RNA interference mechanisms (RNA<i>i</i>), which may be a mechanism of gall induction. We also find significant overlap between cynipid galls and agricultural gall pests, supporting a common underlying mechanisms of gall development even in disparate plants and insect galling guilds.<br>This data set includes: the filtered and unfiltered de novo transcriptome of Quercus rubra, <br><br>
DOI: 10.6084/m9.figshare.7090607.v1
title: Tissue-specific gene expression shows a cynipid wasp repurposes oak host gene networks to create a complex and novel parasite-specific organ

description: Every organism on Earth depends on interactions with other organisms to survive. In each of these interactions, an organism must utilize the limited toolbox of genes, proteins, and pathways it possesses to successfully manipulate or cooperate with another species, but it can also coopt the genome machinery of its partner. An insect-induced plant gall is an extreme example of this, wherein the wasp hijacks the plant genome to direct the initiation and development of a gall composed of plant tissue. This unique and complex species interaction has been studied for hundreds of years, and yet the mechanism(s) behind gall development remains elusive. Here we show that cynipid wasps are creating an entirely new and complex organ from its oak host’s tissue, significantly changing the expression of 28% of oak genes. The inner larval capsule shows suppression of large parts of the plant innate immune system and evidence for the wasp utilizing the plant’s RNA interference mechanisms (RNA<i>i</i>), which may be a mechanism of gall induction. We also find significant overlap between cynipid galls and agricultural gall pests, supporting a common underlying mechanisms of gall development even in disparate plants and insect galling guilds.<br>This data set includes: the filtered and unfiltered de novo transcriptome of Quercus rubra, <br><br>
DOI: 10.5281/zenodo.4323596
title: Metaproteomics analysis of SARS-CoV-2-infected patient samples reveals presence of potential co-infecting microorganisms

description: Supplemental data for SARS-CoV-2 patient sample metaproteomics analysis
DOI: 10.5281/zenodo.4323595
title: Metaproteomics analysis of SARS-CoV-2-infected patient samples reveals presence of potential co-infecting microorganisms

description: Supplemental data for SARS-CoV-2 patient sample metaproteomics analysis
DOI: 10.21227/rq2a-vh38
title: Bed-Based Ballistocardiography Dataset

description: This dataset of heart-driven signals collected from 40 participants, under Kansas State University IRB protocol #9386, includes ballistocardiograms (BCGs) and time-aligned electrocardiograms (ECGs), photoplethysmograms (PPGs), and blood pressure waveforms. The BCGs were collected from a custom, bed-based ballistocardiographic system comprised of four electromechanical films and four load cells. Affiliated cardiopulmonary signals were acquired using a GE Datex CardioCap 5 patient monitor (which collected ECG and PPG data) and a Finapres Medical Systems Finometer PRO (which provided continuous reconstructed brachial artery pressure waveforms and derived cardiovascular parameters). Note: A publication detailing the custom bed system used to collect the data provided in this dataset is awaiting a DOI from Sensors, Carlson, C.; Turpin, V.-R.; Suliman, A.; Ade, C.; Warren, S.; Thompson, D.E.; Bed-Based Ballistocardiography: Dataset and Ability to Track Cardiovascular Parameters. Anyone downloading this dataset should check back for an updated, full citation prior to publication.
DOI: 10.21227/2fad-3a90
title: Bed-Based Ballistocardiography Dataset

description: This dataset of heart-driven signals collected from 40 participants, under Kansas State University IRB protocol #9386, includes ballistocardiograms (BCGs) and time-aligned electrocardiograms (ECGs), photoplethysmograms (PPGs), and blood pressure waveforms. The BCGs were collected from a custom, bed-based ballistocardiographic system comprised of four electromechanical films and four load cells. Affiliated cardiopulmonary signals were acquired using a GE Datex CardioCap 5 patient monitor (which collected ECG and PPG data) and a Finapres Medical Systems Finometer PRO (which provided continuous reconstructed brachial artery pressure waveforms and derived cardiovascular parameters). Note: A publication detailing the custom bed system used to collect the data provided in this dataset is awaiting a DOI from Sensors, Carlson, C.; Turpin, V.-R.; Suliman, A.; Ade, C.; Warren, S.; Thompson, D.E.; Bed-Based Ballistocardiography: Dataset and Ability to Track Cardiovascular Parameters. Anyone downloading this dataset should check back for an updated, full citation prior to publication.
DOI: 10.3886/e118645
title: Data and Code for: Interactions and Coordination between Monetary and Macro-Prudential Policies

description: Abstract: I study monetary and macro-prudential policy intervention in a general equilibrium economy with recurrent boom-bust cycles. Recurrence causes forward-looking variables to also react to policy intervention during phases in which the intervention is inactive. Macro-prudential policies that contain systemic risk in financial markets during booms, therefore, relax market-based funding constraints during busts, which helps mitigate the severity and shorten the duration of economic meltdowns. Contractionary monetary interventions during booms also have (latent) beneficial effects during busts. Coordination between the two policy instruments improves social welfare over standard, non coordinated policy interventions, but improvement is moderate.
DOI: 10.3886/e116218v1-72502
title: Replication data for: Medium-Term Business Cycles

description: Over the postwar period, many industrialized countries have experienced significant medium-frequency oscillations between periods of robust growth versus relative stagnation. Conventional business cycle filters, however, tend to sweep these oscillations into the trend. In this paper we explore whether they may, instead, reflect a persistent response of economic activity to the high-frequency fluctuations normally associated with the cycle. We define as the medium-term cycle the sum of the highand medium-frequency variation in the data, and then show that these kinds of fluctuations are substantially more volatile and persistent than are the conventional measures. These fluctuations, further, feature significant procyclical movements in both embodied and disembodied technological change, and research and development (R&D), as well as the efficiency and intensity of resource utilization. We then develop a model of medium-term business cycles. A virtue of the framework is that, in addition to offering a unified approach to explaining the high- and mediumfrequency variation in the data, it fully endogenizes the movements in productivity that appear central to the persistence of these fluctuations. For comparison, we also explore how well an exogenous productivity model can explain the facts. (JEL E3, O3)
DOI: 10.3886/e115388
title: Data and Code for: Consumption Insurance Against Wage Risk: Family Labor Supply and Optimal Progressive Income Taxation

description: We show that a calibrated life-cycle two-earner household model with endogenous labor supply can rationalize the extent of consumption insurance against shocks to male and female wages, as estimated empirically by Blundell, Pistaferri and Saporta-Eksten (2016) in U.S. data. In the model, 35% of male and 18% of female permanent wage shocks pass through to consumption, compared to the empirical estimates of 32% and 19%. Most of the consumption insurance against permanent male wage shocks is provided through the presence and labor supply response of the female earner. Abstracting from this private intra-household income insurance mechanism strongly biases upward the welfare losses from idiosyncratic wage risk as well as the desired extent of public insurance through progressive income taxation. Relative to the standard one-earner life cycle model, the optimal degree of tax progressivity is significantly lower and the welfare gains from implementing the optimal system are cut roughly in half.<br><br>
DOI: 10.3886/e115388v1
title: Data and Code for: Consumption Insurance Against Wage Risk: Family Labor Supply and Optimal Progressive Income Taxation

description: We show that a calibrated life-cycle two-earner household model with endogenous labor supply can rationalize the extent of consumption insurance against shocks to male and female wages, as estimated empirically by Blundell, Pistaferri and Saporta-Eksten (2016) in U.S. data. In the model, 35% of male and 18% of female permanent wage shocks pass through to consumption, compared to the empirical estimates of 32% and 19%. Most of the consumption insurance against permanent male wage shocks is provided through the presence and labor supply response of the female earner. Abstracting from this private intra-household income insurance mechanism strongly biases upward the welfare losses from idiosyncratic wage risk as well as the desired extent of public insurance through progressive income taxation. Relative to the standard one-earner life cycle model, the optimal degree of tax progressivity is significantly lower and the welfare gains from implementing the optimal system are cut roughly in half.<br><br>
DOI: 10.3886/e116622
title: Data and Code for: Optimal Positive Capital Taxes at Interior Steady States

description: We generalize recent results of Bassetto and Benhabib (2006) and Straub and Werning (2019) in a neo-classical model with endogenous labor-leisure choice where all agents are allowed to save and accumulate capital. We provide a sufficient condition under which optimal redistributive capital taxes remain at their allowed upper bound forever, even if the resulting equilibrium trajectory converges to a unique steady state with positive and finite consumption, capital, and labor. We then provide an interpretation of our sufficient condition. Using recent evidence on wealth distribution in the United States, we argue that our sufficient condition is empirically plausible.
DOI: 10.3886/e116622v1
title: Data and Code for: Optimal Positive Capital Taxes at Interior Steady States

description: We generalize recent results of Bassetto and Benhabib (2006) and Straub and Werning (2019) in a neo-classical model with endogenous labor-leisure choice where all agents are allowed to save and accumulate capital. We provide a sufficient condition under which optimal redistributive capital taxes remain at their allowed upper bound forever, even if the resulting equilibrium trajectory converges to a unique steady state with positive and finite consumption, capital, and labor. We then provide an interpretation of our sufficient condition. Using recent evidence on wealth distribution in the United States, we argue that our sufficient condition is empirically plausible.
DOI: 10.3886/e115791
title: Data and Code for: College Quality and Attendance Patterns: A Long-Run View

description: Abstract: We construct a time series of college attendance patterns for the United States and document a reversal: family background was a better predictor of college attendance before World War II, but academic ability was afterwards. We construct a model of college choice that explains this reversal. The model’s central mechanism is that an exogenous surge of college attendance leads better colleges to be oversubscribed, institute selective admissions, and raise their quality relative to their peers, as in Hoxby (2009). Rising quality at better colleges attracts high-ability students, while falling quality at the remaining colleges dissuades low-ability students, generating the reversal.
DOI: 10.3886/e115791v1
title: Data and Code for: College Quality and Attendance Patterns: A Long-Run View

description: Abstract: We construct a time series of college attendance patterns for the United States and document a reversal: family background was a better predictor of college attendance before World War II, but academic ability was afterwards. We construct a model of college choice that explains this reversal. The model’s central mechanism is that an exogenous surge of college attendance leads better colleges to be oversubscribed, institute selective admissions, and raise their quality relative to their peers, as in Hoxby (2009). Rising quality at better colleges attracts high-ability students, while falling quality at the remaining colleges dissuades low-ability students, generating the reversal.
DOI: 10.3886/e116781
title: Data and Code for: Sectoral Price Facts in a Sticky-Price Model

description: We develop a multisector sticky-price DSGE model that can endogenously deliver differential responses of prices to aggregate and sectoral shocks. Input-output production linkages and a (standard) monetary policy rule contribute to a slow response of prices to aggregate shocks. In turn, labor market segmentation at the sectoral level induces within-sector strategic substitutability in price-setting decisions, which helps the model deliver a fast response of prices to sector-specific shocks. We estimate the model using aggregate and sectoral price and quantity data for the U.S., and find that it accounts well for a range of sectoral price facts.