cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14330795.v7
title: An Immune Cell Atlas Reveals Dynamic COVID-19 Specific Neutrophil Programming Amendable to Therapy

description: SARS-CoV-2 is a novel coronavirus that causes acute respiratory distress syndrome (ARDS) and death. Innate immune cells are critical for host defense but are also the primary drivers of acute respiratory distress syndrome. The relationships between innate cellular responses in ARDS resulting from COVID-19 compared to other causes of ARDS, such as bacterial sepsis is unclear. Moreover, the beneficial cellular effects of dexamethasone therapy during severe COVID-19 remains speculative but understanding their mechanistic effects could improve rationally targeted drug design. We discovered that compared to bacterial septic ARDS, COVID-19 induced distinct neutrophil polarization characterized by either interferon (IFN) or prostaglandin (PG) active states. IFN polarization required the transcriptional regulators PRDM1, STAT1 and IRF1 while prostaglandin polarization was induced by E2F4. Bacterial ARDS neutrophils upregulated antibacterial molecules such as PLAC8 via STAT5b and demonstrated conventional transcription factors CEBPA and CEBPB. Steroid therapy rapidly altered IFN polarization, downregulated interferon responsive genes, and induced immunoretrained neutrophils withelevations of the decoy IL-1R2 regulatory receptor. Steroids induced the emergence of immature neutrophils expressing immunosuppressive molecules ARG1 and ANXA1. Moreover, steroids remodeled global cellular communication hierarchies by changing neutrophils from information receivers into information providers. Importantly, male patients had higher proportions of IFN-active neutrophils and a greater degree of steroid induced attenuation of cellular polarization. Indeed, the highest proportion of IFN-active neutrophils was associated with mortality. These results define neutrophil states unique to COVID-19 when contextualized to other life-threatening infections, thereby enhancing the relevance of our findings at the bedside. Furthermore, the clinical benefits of dexamethasone therapy are molecularly defined, and this information highlights essential molecular pathways to which improved therapeutic targeting can now be conceived.<br>
DOI: 10.6084/m9.figshare.15101280
title: README

description: Pointer to subsequent analyses<br>
DOI: 10.5281/zenodo.5156251
title: Stockholm sequence-structure alignments for 9 Bacteroides sRNAs

description: Sequence alignment supporting the manuscript "Comparative genomics provides structural and functional insights into Bacteroides RNA biology".
DOI: 10.5281/zenodo.5156250
title: Stockholm sequence-structure alignments for 9 Bacteroides sRNAs

description: Sequence alignment supporting the manuscript "Comparative genomics provides structural and functional insights into Bacteroides RNA biology".
DOI: 10.6084/m9.figshare.13577909
title: Oxylipin Responses to Fasting and Insulin Infusion in a Large Mammalian Model of Fasting-Induced Insulin Resistance, the Northern Elephant Seal

description: This study complements the previous study by examining the effects of fasting duration and insulin infusion on circulating levels of oxylipins, bioactive metabolites derived from the oxygenation of polyunsaturated fatty acids. Northern elephant seal pups were studied at two post-weaning periods (n = 5/period): early fasting (1–2 weeks post-weaning; 127 ± 1 kg) and late fasting (6–7 weeks post-weaning; 93 ± 4 kg). Different cohorts of pups were weighed, sedated, and infused with 65 mU/kg of insulin. Plasma was collected prior to infusion (T0), and at 10, 30, 60, and 120 min post-infusion. A profile of ~80 oxylipins were analyzed by UPLC-ESI-MS/MS.
DOI: 10.6084/m9.figshare.13577909.v1
title: Oxylipin Responses to Fasting and Insulin Infusion in a Large Mammalian Model of Fasting-Induced Insulin Resistance, the Northern Elephant Seal

description: This study complements the previous study by examining the effects of fasting duration and insulin infusion on circulating levels of oxylipins, bioactive metabolites derived from the oxygenation of polyunsaturated fatty acids. Northern elephant seal pups were studied at two post-weaning periods (n = 5/period): early fasting (1–2 weeks post-weaning; 127 ± 1 kg) and late fasting (6–7 weeks post-weaning; 93 ± 4 kg). Different cohorts of pups were weighed, sedated, and infused with 65 mU/kg of insulin. Plasma was collected prior to infusion (T0), and at 10, 30, 60, and 120 min post-infusion. A profile of ~80 oxylipins were analyzed by UPLC-ESI-MS/MS.
DOI: 10.6084/m9.figshare.12831005
title: Cornejo et al., 2021

description: Supplemental materialS1) Raw and corrected dataS2) Normalized dataS3) Johnson transformed dataS4) T-test p and q values comparisonsS5) Pearson correlation r, p and q valuesS6) Scripts for PCA after PLSDA (VIP &gt; 1 metabolites only)
DOI: 10.6084/m9.figshare.12831005.v7
title: Cornejo et al., 2021

description: Supplemental material1) Raw and corrected data2) Normalized data3) Johnson transformed data4) T-test p and q values comparisons5) Pearson correlation r, p and q values6) Scripts for PCA after PLSDA
DOI: 10.3886/e130462v1-93246
title: Data and Code for: Common Ownership and Entrepreneurship

description: This is data and code to accompany the article "Common Ownership and Entrepreneurship." In the article, we complement the literature on common ownership by presenting two new observations from entrepreneurial startups. First, given the increase in common ownership of startups by VC investors, inclusion of high-value startups in standard common ownership measures may actually increase aggregate measures of common ownership. Second, we suggest that even if public-firm common ownership leads to collusive inefficiency and higher prices in the short-term, it may also create opportunities for entry of innovative, high-growth startups. Consistent with this, we document that entrepreneurial activity and common ownership of startups tends to be higher in industries with higher common ownership among public firms.
description: For those with access to Preqin, we provide a crosswalk between Preqin's definition of industry and the Standard Industrial Classification (SIC).
DOI: 10.5281/zenodo.5156116
title: TheyBuyForYou Knowledge Graph data dump

description: Data dump of the Knowledge Graph (KG) for the TheyBuyForYou project in RDF format containing procurement data and company data (for reconciled suppliers) for the period January 2019 to July 2021. In addition to the KG data dump in RDF, we have also made available the source data input for the KG, i.e., procurement data from OpenOpps and company data (for reconciled suppliers) from OpenCorporates in JSON format.
DOI: 10.6073/pasta/df4a9edbd5ddd27e3bb491eed316f4ac
title: Synthesis of Sarracenia Research in North America 1982-2018

description: This archive includes the raw data and code (R scripts) required to reproduce all of the analyses and figures in the book Scaling Sarracenia: Ecology of a Model System by Aaron M. Ellison and Nicholas J. Gotelli. The book is a synthesis of our 25 years of research on the northern (a.k.a. purple) pitcher plant Sarracenia purpurea viewed through the conceptual lens of “scale”: scaling ecological phenomena through levels of biological organization with a model organism, across time and space, and using macroecological relationships.
DOI: 10.6073/pasta/ea16faa93aed4757a73bf5750af5f3fe
title: Foundation Species in Forest Dynamics Plots of China 2004-2014

description: Foundation species structure forest communities and ecosystems but are difficult to identify without long-term observations or experiments. We used statistical criteria---outliers from size-frequency distributions and scale-dependent negative effects on alpha diversity and positive effects on beta diversity---to identify candidate foundation woody plant species in 12 large forest-dynamics plots spanning 26 degrees of latitude in China. We used these data to: [1] identify candidate foundation species in Chinese forests; [2] test the hypothesis---based on observations of a mid-latitude peak in functional trait diversity and high local species richness but few numerically dominant species in tropical forests---that foundation woody plant species are more frequent in temperate than tropical or boreal forests; and [3] compare these results with data from the Americas to suggest candidate foundation genera in Northern Hemisphere forests. Using the most stringent criteria, only two species of Acer, the canopy tree Acer ukurunduense and the shrubby treelet Acer barbinerve, were identified in temperate plots as candidate foundation species. Using more relaxed criteria, we identified four times more candidate foundation species in temperate plots (including species of Acer, Pinus, Juglans, Padus, Tilia, Fraxinus, Prunus, Taxus, Ulmus, and Corlyus) than in (sub)tropical plots (the shrubs or treelets Aporosa yunnanensis, Ficus hispida, Brassaiopsis glomerulata, and Orophea laui). Species diversity of co-occurring woody species was negatively associated with basal area of candidate foundation species more frequently at 5- and 10-m spatial grains (scale) than at a 20-m grain. Conversely, Bray-Curtis dissimilarity was positively associated with basal area of candidate foundation species more frequently at 5-m than at 10- or 20-m grains. Using either stringent or relaxed criteria supported the hypothesis that foundation species are more common in mid-latitude temperate forests. Comparisons of candidate foundation species in Chinese and North American forests suggest that Acer be investigated further as a foundation tree genus.
DOI: 10.6073/pasta/19da2e541f37c859e3ea702436cf6b50
title: Ants in an Induced Drought Experiment at the Caxiuana National Forest in Brazil 2011-2012

description: Environmental change scenarios caused by low precipitation forecast species loss in tropical regions. We used one year of data from a rainwater exclusion experiment in primary Amazonian rainforest to test whether induced water stress, and covarying changes in humidity, soil respiration, and tree species richness, size, and total biomass and its diversity affected species richness and composition (relative abundance) of ground-dwelling ants. Induced drought reduced ant richness, whereas increased humidity and variability in biomass increased it. Species composition differed between control and rainfall-excluded plots. Occurrence of many ant species was strongly reduced, but some generalist groups of ants were favored by induced drought. The expected loss of ant species and changes in ant species composition in tropical forests likely will lead to cascading effects on ecosystem processes and services they mediate.
DOI: 10.6084/m9.figshare.15101415
title: Supplemental Table 1 210803

description: <b>Supplemental Table 1. Targets of miRNA contained in mCBSC-dEXO. </b>Table of miRNA gene targets as predicted by miRDB for miRNA identified as enriched in the mCBSC-dEXO dataset. @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:-536870145 1107305727 0 0 415 0;}p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-unhide:no; mso-style-qformat:yes; mso-style-parent:""; margin:0in; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman";}.MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:Calibri; mso-fareast-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}div.WordSection1 {page:WordSection1;}
DOI: 10.6084/m9.figshare.15101415.v1
title: Supplemental Table 1 210803

description: <b>Supplemental Table 1. Targets of miRNA contained in mCBSC-dEXO. </b>Table of miRNA gene targets as predicted by miRDB for miRNA identified as enriched in the mCBSC-dEXO dataset. @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:-536870145 1107305727 0 0 415 0;}p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-unhide:no; mso-style-qformat:yes; mso-style-parent:""; margin:0in; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman";}.MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:Calibri; mso-fareast-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}div.WordSection1 {page:WordSection1;}
DOI: 10.6084/m9.figshare.15101427
title: Supplemental Table 2 210803

description: <b>Supplemental Table 2. Targets of miRNA contained in hCBSC-dEXO. </b>Table of miRNA gene targets as predicted by miRDB for miRNA identified as enriched in the hCBSC-dEXO dataset. @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:-536870145 1107305727 0 0 415 0;}p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-unhide:no; mso-style-qformat:yes; mso-style-parent:""; margin:0in; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman";}.MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:Calibri; mso-fareast-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}div.WordSection1 {page:WordSection1;}
DOI: 10.6084/m9.figshare.15101427.v1
title: Supplemental Table 2 210803

description: <b>Supplemental Table 2. Targets of miRNA contained in hCBSC-dEXO. </b>Table of miRNA gene targets as predicted by miRDB for miRNA identified as enriched in the hCBSC-dEXO dataset. @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:-536870145 1107305727 0 0 415 0;}p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-unhide:no; mso-style-qformat:yes; mso-style-parent:""; margin:0in; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman";}.MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:Calibri; mso-fareast-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}div.WordSection1 {page:WordSection1;}
DOI: 10.6073/pasta/2dafdef3877256f3e7e755fdb03b63a0
title: Density Anomalies in White Pine at Harvard Forest 2019

description: The density of wood is a primary determinant of the amount of carbon sequestered in forests. For boreal and Mediterranean ecosystems, anomalies from the typical intra-annual density increase in radial growth of conifers are predominantly related to drought. We took 41 wood samples at breast height, ten additional samples near branches, and seven samples from the top of 41 white pines to determine the spatial distribution of density anomalies throughout the stem. We measured the ring width, density anomaly presence, position within a ring, and arc of density anomalies at multiple heights. Even in a mesic forest density anomalies in white pine are predominantly occurring during drier growing seasons. Moreover, we examined the spatial extent of density anomalies within the stems of white pines and discovered density anomalies are more likely to occur near branches, at the top of the tree, and in wider rings. Furthermore, the position of the density anomalies within the rings was remarkably consistent with the anomalies occurring roughly 80% into the fully formed ring at all heights for high-frequency years only as well as all years Density anomalies seem to be triggered by exogenous factors but their distribution within the stem varies along endogenous gradients, thus better understanding these systematic anomalies can help us to understand how wood formation has reacted and will respond to the environment and changes therein.
DOI: 10.6073/pasta/2722f653b309aa1983ae2871070418d5
title: White Pine Girdling and Compression Experiment at Harvard Forest 2017-2019

description: Wood formation is a crucial process for carbon sequestration on land, yet how variations in phloem-transported carbon affect wood formation, respiration and nonstructural carbon pools remains poorly understood. To better understand the role of carbon supply on allocation to wood formation, we constrained phloem transport using girdling and compression around the stem of 40 mature white pines to monitor the effects of contrasting carbon supply (enriched above and reduced below the manipulations) on local wood formation and respiration, as well as on nonstructural carbon pools in needles, stems, and roots. This data set contains all data measured during the experiment. This includes wood anatomy, xylogenesis, stem respiration, nonstructural carbon measurements in coarse roots, stems and needles, as well as pre-dawn water potential measurements and pressure measurements from underneath the phloem compression collars. Furthermore, we provide allometric measurements for all trees. The code to process these data and reproduce our results is available in hf348-14-density-anomaly-analysis-code.zip. For more details pertaining to the methods see Rademacher et al. (in review).
DOI: 10.6084/m9.figshare.15040692
title: GRL Repository 2021

description: Datasets associated with 2021 GRL paper "Ongoing landslide deformation in thawing permafrost" by Patton, Rathburn, Capps, McGrath, and Brown.
DOI: 10.6084/m9.figshare.14668275
title: Sawyer Mill Dam Removal Z Error Standard Deviations and Minimum Level of Detection Thresholds Calculations for the Reservoir Response Manuscript DoDs (2019 & 2020)

description: These are the calculations for determining the minimum level of detection thresholds used to mask areas of uncertain topographic change in the Evans et al. Sawyer Mill dam removal reservoir response manuscript. These thresholds were applied to the DoDs representing the various study areas throughout the Bellamy River Reservoir (Dover, NH, USA) to evaluate topographic changes associated with dam removal. The method used for calculating the minimum level of detection threshold (minLoD) was adapted from Marteau et al. (2017). Please see the manuscript and the spreadsheet for additional information. <br>These materials were made using resources from an NSF EPSCoR funded project “RII Track-2 FEC: Strengthening the scientific basis for decision-making about dams: Multi-scale, coupled-systems research on ecological, social, and economic trade-offs” (a.k.a. "Future of Dams"). Support for this project is provided by the National Science Foundation’s Research Infrastructure Improvement NSF #IIA-1539071. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.<br><br>
DOI: 10.6084/m9.figshare.14668275.v1
title: Sawyer Mill Dam Removal Z Error Standard Deviations and Minimum Level of Detection Thresholds Calculations for the Reservoir Response Manuscript DoDs (2019 & 2020)

description: These are the calculations for determining the minimum level of detection thresholds used to mask areas of uncertain topographic change in the Evans et al. Sawyer Mill dam removal reservoir response manuscript. These thresholds were applied to the DoDs representing the various study areas throughout the Bellamy River Reservoir (Dover, NH, USA) to evaluate topographic changes associated with dam removal. The method used for calculating the minimum level of detection threshold (minLoD) was adapted from Marteau et al. (2017). Please see the manuscript and the spreadsheet for additional information. <br>These materials were made using resources from an NSF EPSCoR funded project “RII Track-2 FEC: Strengthening the scientific basis for decision-making about dams: Multi-scale, coupled-systems research on ecological, social, and economic trade-offs” (a.k.a. "Future of Dams"). Support for this project is provided by the National Science Foundation’s Research Infrastructure Improvement NSF #IIA-1539071. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.<br><br>
DOI: 10.15468/2zrkzj
title: Eubria mesoamericana Barr and Shepard (Coleoptera: Psephenidae: Eubriinae), a New Psephenid Species from Central America with an Enigmatic Generic Distribution

description: This dataset contains the digitized treatments in Plazi based on the original journal article Barr, Cheryl B., Shepard, William D. (2017): Eubria mesoamericana Barr and Shepard (Coleoptera: Psephenidae: Eubriinae), a New Psephenid Species from Central America with an Enigmatic Generic Distribution. The Coleopterists Bulletin 71 (3): 437-444, DOI: 10.1649/0010-065X-71.3.437, URL: http://dx.doi.org/10.1649/0010-065x-71.3.437
DOI: 10.25318/3310033101-eng
title: Average expenditures on innovation activities attributable to each type of innovation, by industry and enterprise size

description: Percentage of expenditures on innovation activities attributable to product (good or service), or process innovation, by North American Industry Classification System (NAICS) code and enterprise size.
DOI: 10.25318/3310033101-fra
title: Dépenses moyennes en activités d’innovation attribuables à chaque type d’innovation, selon l'industrie et la taille de l’entreprise

description: Pourcentage de dépenses attribuables à l’innovation de produits (biens ou services) ou de procédés, selon le code du Système de classification des industries de l’Amérique du Nord (SCIAN) et la taille de l’entreprise.