cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19401206
title: Non-compensatory mutations in Spike protein positively selected on RNA structures might be signatures to trace cross-species barrier jumps of Betacoronavirus

description: Similar to other RNA viruses, the evolution and emergence of <i>Betacoronavirus</i> the cross-species transmission is involved. In general, the standard health surveillance system is based on protein-coding information, but since the COVID-19 pandemic it has been extended to wide-genome analysis. The evolutionary jump from natural reservoirs to human hotspot mutations is mainly traced-back to its effect on coding sequence. However, the impact on the structured RNA genome of <i>Betacoronavirus</i> is mainly unexplored. To develop a new landscape of changes in the RNA viral genome were analyzed 1,252,952 viral genomes of circulating SARS-CoV, MERS-CoV, and SARS-CoV-2 viruses distributed worldwide in bats, intermediate animals, and humans. The protein-coding and viral genome architecture were studied for trace back novel insights from cross-species horizontal transmission events. Phylogenetic analyses confirm that bats are natural harbors of <i>Betacoronavirus</i>, with high variation rates in viral proteins, mainly in the S protein S1 subunit. The substitutions (G &gt; T; A577S) in SARS-CoV, (C &gt; T; S746R and C &gt; T; N762A) in MERS-CoV, and (A &gt; G; D614G) in SARS-CoV-2 overlap with mutations that modify secondary RNA structures in the RNA genome complement. These findings provide pivotal factors that might be underlying the eventual jumping the species barrier from bats to the intermediate host which could contribute to their evolutionary diversification. At here also it was found that <i>Betacoronavirus</i> from intermediates and humans are evolutionary related and share a significant proportion of RNA structures than those in bats which could be used as signatures of cross-species barrier jumps.
DOI: 10.6084/m9.figshare.19401206.v2
title: Non-compensatory mutations in Spike protein positively selected on RNA structures might be signatures to trace cross-species barrier jumps of Betacoronavirus

description: Similar to other RNA viruses, the evolution and emergence of <i>Betacoronavirus</i> the cross-species transmission is involved. In general, the standard health surveillance system is based on protein-coding information, but since the COVID-19 pandemic it has been extended to wide-genome analysis. The evolutionary jump from natural reservoirs to human hotspot mutations is mainly traced-back to its effect on coding sequence. However, the impact on the structured RNA genome of <i>Betacoronavirus</i> is mainly unexplored. To develop a new landscape of changes in the RNA viral genome were analyzed 1,252,952 viral genomes of circulating SARS-CoV, MERS-CoV, and SARS-CoV-2 viruses distributed worldwide in bats, intermediate animals, and humans. The protein-coding and viral genome architecture were studied for trace back novel insights from cross-species horizontal transmission events. Phylogenetic analyses confirm that bats are natural harbors of <i>Betacoronavirus</i>, with high variation rates in viral proteins, mainly in the S protein S1 subunit. The substitutions (G &gt; T; A577S) in SARS-CoV, (C &gt; T; S746R and C &gt; T; N762A) in MERS-CoV, and (A &gt; G; D614G) in SARS-CoV-2 overlap with mutations that modify secondary RNA structures in the RNA genome complement. These findings provide pivotal factors that might be underlying the eventual jumping the species barrier from bats to the intermediate host which could contribute to their evolutionary diversification. At here also it was found that <i>Betacoronavirus</i> from intermediates and humans are evolutionary related and share a significant proportion of RNA structures than those in bats which could be used as signatures of cross-species barrier jumps.
DOI: 10.6084/m9.figshare.19401206.v1
title: Non-compensatory mutations in Spike protein positively selected on RNA structures might be signatures to trace cross-species barrier jumps of Betacoronavirus

description: Similar to other RNA viruses, the evolution and emergence of <i>Betacoronavirus</i> the cross-species transmission is involved. In general, the standard health surveillance system is based on protein-coding information, but since the COVID-19 pandemic it has been extended to wide-genome analysis. The evolutionary jump from natural reservoirs to human hotspot mutations is mainly traced-back to its effect on coding sequence. However, the impact on the structured RNA genome of <i>Betacoronavirus</i> is mainly unexplored. To develop a new landscape of changes in the RNA viral genome were analyzed 1,252,952 viral genomes of circulating SARS-CoV, MERS-CoV, and SARS-CoV-2 viruses distributed worldwide in bats, intermediate animals, and humans. The protein-coding and viral genome architecture were studied for trace back novel insights from cross-species horizontal transmission events. Phylogenetic analyses confirm that bats are natural harbors of <i>Betacoronavirus</i>, with high variation rates in viral proteins, mainly in the S protein S1 subunit. The substitutions (G &gt; T; A577S) in SARS-CoV, (C &gt; T; S746R and C &gt; T; N762A) in MERS-CoV, and (A &gt; G; D614G) in SARS-CoV-2 overlap with mutations that modify secondary RNA structures in the RNA genome complement. These findings provide pivotal factors that might be underlying the eventual jumping the species barrier from bats to the intermediate host which could contribute to their evolutionary diversification. At here also it was found that <i>Betacoronavirus</i> from intermediates and humans are evolutionary related and share a significant proportion of RNA structures than those in bats which could be used as signatures of cross-species barrier jumps.
DOI: 10.5281/zenodo.6378067
title: GPT-J Code Clone Detection

description: This is the dataset of GPT-J code clone detection. 'data/' folder contains the data to replicate our study. 'code/' folder contains the code to replicate our study. Each folder has its own README, please check the details there.
DOI: 10.25345/c5707ws3v
title: MassIVE MSV000089104 - Multi-omic profiling of the leukemic microenvironment shows bone marrow interstitial fluid is distinct from peripheral blood
title: Multi-omic profiling of the fluid portion of the leukemic-microenvironment.
DOI: 10.6084/m9.figshare.17252489
title: Benthic habitat map of the marine ecosystems in the Mexican Caribbean: Cabo Catoche - Xcalak

description: The map represents the spatial distribution of benthic habitats in shallow waters of the Mexican Mesoamerican Barrier Reef System, from Cabo Catoche to Xcalak, in an area of 1001 km<sup>2</sup>, with an average maximum depth of 18 m. The resulting map defined 50 classes generated from the union of benthic cover and submarine relief maps, estimated from the processing of 23 WorldView-2 satellite images (2009-2015), and with information from in-situ bathymetric soundings. The information is presented in shapefile format. This product is the result of the ArrecifeSAM project, coordinated by CONABIO as part of the Marine-Coastal Information and Analysis System (SIMAR) (https://simar.conabio.gob.mx).<br><br><b>Acknowledgement:</b>The authors acknowledge the logistical and technical support provided by National Financial Trust Fund for Biodiversity and the National Commission for the Knowledge and Use of Biodiversity (CONABIO).
DOI: 10.5517/ccdc.csd.cc26tbn1
title: CCDC 2050143: Experimental Crystal Structure Determination

description: Related Article: Lidong Shan, Yunxiang Weng, Hongchen Li, Lin Min, Xinyan Wang, Yuefei Hu|2022|J.Org.Chem.|87|4124|doi:10.1021/acs.joc.1c02918
DOI: 10.5517/ccdc.csd.cc26tbp2
title: CCDC 2050144: Experimental Crystal Structure Determination

description: Related Article: Lidong Shan, Yunxiang Weng, Hongchen Li, Lin Min, Xinyan Wang, Yuefei Hu|2022|J.Org.Chem.|87|4124|doi:10.1021/acs.joc.1c02918
DOI: 10.5517/ccdc.csd.cc26ypvq
title: CCDC 2054334: Experimental Crystal Structure Determination

description: Related Article: Lidong Shan, Yunxiang Weng, Hongchen Li, Lin Min, Xinyan Wang, Yuefei Hu|2022|J.Org.Chem.|87|4124|doi:10.1021/acs.joc.1c02918
DOI: 10.5517/ccdc.csd.cc27gjt2
title: CCDC 2069554: Experimental Crystal Structure Determination

description: Related Article: Zhou-Hao Zhu, Yi-Xuan Ding, Yong-Gui Zhou|2022|Chem.Commun.|58|3973|doi:10.1039/D1CC06896B
DOI: 10.5517/ccdc.csd.cc2808xh
title: CCDC 2085646: Experimental Crystal Structure Determination

description: Related Article: Lidong Shan, Yunxiang Weng, Hongchen Li, Lin Min, Xinyan Wang, Yuefei Hu|2022|J.Org.Chem.|87|4124|doi:10.1021/acs.joc.1c02918
DOI: 10.5517/ccdc.csd.cc285d62
title: CCDC 2090553: Experimental Crystal Structure Determination

description: Related Article: Ran Yang, Dong Yi, Kunrong Shen, Qiang Fu, Jun Wei, Ji Lu, Lin Yang, Li Wang, Siping Wei, Zhijie Zhang|2022|Org.Lett.|24|2014|doi:10.1021/acs.orglett.2c00472
DOI: 10.5517/ccdc.csd.cc28f4xs
title: CCDC 2098015: Experimental Crystal Structure Determination

description: Related Article: Hyungdo Cho, Hidehiro Suematsu, Paul H. Oyala, Jonas C. Peters, Gregory C. Fu|2022|J.Am.Chem.Soc.|144|4550|doi:10.1021/jacs.1c12749
DOI: 10.5517/ccdc.csd.cc28f51y
title: CCDC 2098019: Experimental Crystal Structure Determination

description: Related Article: Hyungdo Cho, Hidehiro Suematsu, Paul H. Oyala, Jonas C. Peters, Gregory C. Fu|2022|J.Am.Chem.Soc.|144|4550|doi:10.1021/jacs.1c12749
DOI: 10.5517/ccdc.csd.cc28f541
title: CCDC 2098022: Experimental Crystal Structure Determination

description: Related Article: Hyungdo Cho, Hidehiro Suematsu, Paul H. Oyala, Jonas C. Peters, Gregory C. Fu|2022|J.Am.Chem.Soc.|144|4550|doi:10.1021/jacs.1c12749
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040315.50.3
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-03-15. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040315.50.4
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-03-15. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040315.50.6
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-03-15. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040421.40.1
title: (:unkn)
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040421.40.2
title: (:unkn)
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040421.50.1
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-04-21. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040421.50.3
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-04-21. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040421.50.5
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-04-21. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040801.40.1
title: (:unkn)
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040801.40.2
title: (:unkn)
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040801.50.1
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-08-01. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040801.50.2
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-08-01. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040801.50.3
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-08-01. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040801.50.4
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-08-01. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20040801.50.5
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2004-08-01. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20041111.40.2
title: (:unkn)
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20050510.40.1
title: (:unkn)
DOI: 10.6085/aa/shlx00_xxxitbdxlsr03_20050510.50.6
title: PISCO: Intertidal: site temperature data: Strawberry Hill, Oregon, USA (SHLX00)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Strawberry Hill, Oregon, USA, by PISCO. Measurements were collected using StowAway TidbiT Temperature Loggers (Onset Computer Corp. TBI32-05+37) beginning 2005-05-10. Site temperature loggers are bolted down in a wire cage at three locations within each site near MLLW. Temperature is recorded at 1 hour intervals.
DOI: 10.5063/aa/brooke.36.1
title: PISCO: Intertidal Community Survey Data: Cannonball Site

description: Abstract to be filled in
DOI: 10.5063/aa/chadden.48.2
title: Scots Pine NPP Dataset (Siberia)- data from 14 boreal forest stands in eastern Russia

description: Data from 14 stands of Scots Pine (Pinus sylvestris) at two locations in Siberia have been compiled by Dr. Olga Krankina of Oregon State University, U.S.A. These plots represent one of the main dominant tree species in Siberian forests, growing in stands of relatively high density and productivity. The data reported previously in Gabeev (1990) were gathered from stands studied under the former U.S.S.R. International Biological Programme in Tomsk Region, Western Siberia (approximately 58 N 83 E; 54-year mean precipitation = 501.2 mm). Above-ground measurements were obtained using standard allometric forestry methods, and below-ground data were originally reported in considerable detail by size class and depth. Data reported previously by Buzykin (1978) are from a study of carbon and nutrient cycling in the forests of the Angara River basin, Irkutsk Region, near Lake Baikal (approximately 53 N 103 E). Here Scots Pine (Pinus sylvestris) is the dominant tree species on about 26 percent of the forested area. The three study sites represent the three most common site conditions found in this area. Trees were measured by standard allometric methods on 0.3-0.4 hectare plots, and understory was determined from 20 x 0.25 hectare plots at each site for three successive years. Data on litterfall are mean values, 1968-1974, and were originally reported separately for needles, bark, branches, cones, and other litter. Below-ground biomass was determined by excavation of entire root systems, and root turnover was estimated for different size classes. Both authors have published extensively in the Russian literature. Components of net primary productivity (NPP) and standing biomass, above- and below-ground, are available for each stand of Pinus sylvestris. The range of above-ground biomass was 5000-32700 g/m2 (25-163 tC/ha, assuming mean carbon content of 50 percent for wood and 45 percent for foliage); below-ground coarse roots ranged between 974 and 6430 g/m2 (5-32 tC/ha at 50 percent carbon content). Above-ground NPP averaged 905 g (438 gC)/m2/year and 765 g (374 gC)/m2/year for the Tomsk and Irkutsk studies, respectively; the corresponding mean figures for total NPP were 1018 g (489 gC)/m2/year and 1695 g (792 gC)/m2/year. Abstract from http://www-eosdis.ornl.gov/NPP/other_files/ssp_des.html.
DOI: 10.5063/aa/chadden.60.8
title: Net Primary Production in tropical forests: an evaluation and synthesis of existing field data

description: Information on net primary production (NPP) in tropical forests is needed for the development of realistic global carbon budgets, for projecting how these ecosystems will be affected by climatic and atmospheric changes, and for evaluating eddy covariance measurements of tropical forest carbon flux. However, a review of the database commonly used to address these issues shows that it has serious flaws. In this paper we synthesize the data in the primary literature on NPP in old-growth tropical forests to produce a consistent data set on NPP for these forests. Studies in this biome have addressed only a few NPP components, all aboveground. Given the limited scope of the direct field measurements, we sought relationships in the existing data that allow estimation of unmeasured aspects of production from those that are more easily assessed. We found a predictive relationship between annual litterfall and aboveground biomass increment. For 39 diverse tropical forest sites, we then developed consistent, documented estimates of the upper and lower bounds around total NPP to serve as benchmarks for calibrating and validating biogeochemical models with respect to this biome. We developed these estimates based on existing field measurements, current understanding of aboveground consumption and biogenic volatile organic carbon emissions, and our judgment that belowground production is bounded by the range 0.2-1.2 x ANPP (aboveground NPP). Across this broad spectrum of tropical forests (dry to wet, lowland to montane, nutrient-rich to nutrient-poor soils), our estimates of lower and upper bounds on total NPP range from 1.7 to 11.8 Mg C/ha-yr (lower bounds) and from 3.1 to 21.7 Mg C/ha-yr (upper bounds). We also showed that two relationships that have been used for estimating NPP (the Bray-Gorham relationship based on leaf litterfall and the Miami model based on temperature or precipitation) are not valid for the tropical forest biome.
DOI: 10.5063/aa/chadden.61.1
title: A compilation of literature estimates of tropical forest total NPP or aboveground NPP, with notes on how those estimates were derived

description: This is the appendix of the Ecol Apps tropical forest NPP paper"NPP in tropical forests: an evaluation and synthesis of existing field data", and it is available online in the data journal Ecological Archives: Clark, D.A., S. Brown, D. Kicklighter, J. Chambers, J.R. Thomlinson, Jian Ni, and E.A. Holland. 2001. Appendix 1. Estimates from the literature of net primary productivity in tropical forests. Ecological Archives A011-006. Because of the difficulties of measuring NPP* components in tropical forests (see text), several approaches have been used to estimate NPP in these ecosystems. Although these approaches have attempted to make the best use of limited data on NPP* components, they often relied on relationships extrapolated from temperate forests, information from secondary forests, or dubious assumptions about the constancy of environmental conditions in tropical forests to develop estimates of annual NPP. Below we list estimates of total NPP, aboveground NPP (ANPP) and belowground NPP (BNPP) reported in the literature. Our objective is to highlight the problems associated with developing a consistent database of NPP in tropical forests. Most sites listed below do not meet the criteria established in this study due to problematic or undocumented methods. However, many of these NPP estimates have been used in past compilations of tropical forest NPP (e.g., Lieth 1975, Murphy 1975, DeAngelis et al. 1981, Vogt et al. 1996, Esser et al. 1997). Unfortunately, conflicting NPP estimates for a particular site among reviews of tropicalforest NPP has also added to confusion about NPP in these biomes. To clarify such cases, where possible we provide brief descriptions of how NPP was estimated in these studies. If necessary, we converted the units of the following NPP estimates from dry weight of biomass to carbon by multiplying dry biomass by 0.5 (Note: Raich et al. [1991] and McGuire et al. [1992] reported NPP in units of g C m-2 yr-1; however, both of these authors used a factor of 0.475 g C (g OM)-1 to convert dry weight of organic matter into grams of carbon).