cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4066513
title: Monthly CO2 emissions projections from 2015-2025: modified SSP2-4.5 to account for COVID-19 impacts on sector activity

description: Monthly CO2 emissions projections 2015-2025, modified by country-specific impacts of COVID-19 lockdown in 2020-2023, with 4 different projections for the period 2024-2025. This repository holds the netcdf files for CO2 emissions from ground-level and aviation sources from the MESSAGE_GLOBIOM scenario SSP2-4.5, from the Scenario4MIPs database (https://esgf-node.llnl.gov/search/input4mips/), modified by the country and sector activity levels associated with lockdown for 2020. Sector activity level in 2020 is based on data up until June, and a fixed estimate is used thereafter. This is the monthly equivalent of https://zenodo.org/record/3951601#.XxYBsihKhPY for this time period. Funding was provided by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement nos. 820829 (CONSTRAIN) http://constrain-eu.org/ see https://github.com/Priestley-Centre/COVID19_emissions for more details.
description: Note that the data and normalisation process used in the aviation data is subtly updated since the version 4 found in related databases, hence that is referred to as v4.5. It still does not cover the whole month of July, due to publication date. The whole dataset is now considered version 4.5.4 as it features more years and differently cropped timeframes to versions 4.5.0-2 (these now extend to 2050) and fixes a bug associated with 4.5.3. The input data is still consistent with versions 4.5.0 and 4.0.
DOI: 10.5281/zenodo.3957429
title: Monthly CO2 emissions projections from 2015-2025: modified SSP2-4.5 to account for COVID-19 impacts on sector activity

description: Monthly CO2 emissions projections 2015-2025, modified by country-specific impacts of COVID-19 lockdown in 2020-2023, with 4 different projections for the period 2024-2025. This repository holds the netcdf files for CO2 emissions from ground-level and aviation sources from the MESSAGE_GLOBIOM scenario SSP2-4.5, from the Scenario4MIPs database (https://esgf-node.llnl.gov/search/input4mips/), modified by the country and sector activity levels associated with lockdown for 2020. Sector activity level in 2020 is based on data up until June, and a fixed estimate is used thereafter. This is the monthly equivalent of https://zenodo.org/record/3951601#.XxYBsihKhPY for this time period. Funding was provided by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement nos. 820829 (CONSTRAIN) http://constrain-eu.org/ see https://github.com/Priestley-Centre/COVID19_emissions for more details.
description: Note that the data and normalisation process used in the aviation data is subtly updated since the version 4 found in related databases, hence that is referred to as v4.5. It still does not cover the whole month of July, due to publication date. The whole dataset is now considered version 4.5.4 as it features more years and differently cropped timeframes to versions 4.5.0-2 (these now extend to 2050) and fixes a bug associated with 4.5.3. The input data is still consistent with versions 4.5.0 and 4.0.
DOI: 10.6084/m9.figshare.11297591.v2
title: Identification of the phospholipid binding regions of the envelope E protein of flaviviruses by molecular dynamics

description: The <i>Flavivirus</i> genus comprise several important human pathogens, including dengue, West Nile, Yellow fever, Japanese encephalitis, Zika, and tick-borne encephalitis viruses. These enveloped viruses affect more than 2 billion people in the world, mainly in less developed countries. Although some vaccines exist for some flaviviruses, these vaccines are not universally available due to many factors and since their infections are a world-wide public health issue, the development of antiviral molecules is fundamental. Flavivirus membranes, through the help of the envelope E glycoprotein, fuse with endosomal compartments in a pH-dependent way to release their genome into the cytoplasm and require specific lipids, such as bis(monoacylglycero)phosphate (BMP), for efficient fusion. The fundamental role the envelope E protein has on viral entry and membrane fusion suggest that it is an essential antiviral target. In this work, we have used atomistic molecular dynamics simulations to study the binding of the head-group of BMP to the tip of the envelope E proteins of ZIKV, DENV, TBEV and JEV viruses whose three-dimensional structures are known. Our results indicate that, apart from the fusion loop, there are different amino acid residues in different regions of the envelope E proteins of flaviviruses capable of binding the head-group of BMP. These regions should work together to accomplish the binding and fusion of the envelope and endosomal membranes and represent a new target to develop and design potent and effective antiviral agents capable of blocking flavivirus-endosome membrane fusion.
DOI: 10.6084/m9.figshare.11294402
title: Delineating the conformational dynamics of intermediate structures on the unfolding pathway of β-lactoglobulin in aqueous urea and dimethyl sulfoxide

description: The funnel shaped energy landscape model of the protein folding suggests that progression of folding proceeds through multiple pathways, having the multiple intermediates which leads to multidimensional free-energy surface. Herein, we applied all-atom MD simulation to conduct a comparative study on the structure of β-lactoglobulin (β-LgA) in aqueous mixture of 8 M urea and 8 M dimethyl sulfoxide (DMSO), at different temperatures. The cumulative results of multiple simulations suggest a common unfolding pathway of β-LgA, occurred through the stable and meta-stable intermediates (I), in both urea and DMSO. However, the free-energy landscape (FEL) analyses show that the structural transitions of I-states are energetically different. In urea, FEL shows distinct ensemble of intermediates, I1 and I2, separated by the energy barrier of ∼3.0 kcal mol<sup>−1</sup>. Similarly, we find the population of two distinct I1 and I2 states in DMSO, however, the I1 appeared transiently around ∼30–35 ns and is short-lived. But, the I2 ensemble is observed structurally compact and long-lived (∼50–150 ns) as compared to unfolding in urea. Furthermore, the I1 and I2 are separated through a high energy barrier of ∼6.0 kcal mol<sup>−1</sup>. Thus, our results provide the structural insights of intermediates which essentially bear the signature of a different unfolding pathway of β-LgA in urea and DMSO. Abbreviationsβ-LgAβ-lactoglobulinDMSOdimethyl sulfoxideFELfree-energy landscapeGdmClguanidinium chlorideIintermediate stateMGmolten globule statePMEparticle mesh EwaldQfraction of native contactsRMSDroot mean square deviationRMSFroot mean square fluctuation<i>R</i><sub>g</sub>radius of gyrationSASAsolvent Accessible Surface AreascSASAthe side chain SASATrptryptophan β-lactoglobulin dimethyl sulfoxide free-energy landscape guanidinium chloride intermediate state molten globule state particle mesh Ewald fraction of native contacts root mean square deviation root mean square fluctuation radius of gyration solvent Accessible Surface Area the side chain SASA tryptophan Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11294402.v1
title: Delineating the conformational dynamics of intermediate structures on the unfolding pathway of β-lactoglobulin in aqueous urea and dimethyl sulfoxide

description: The funnel shaped energy landscape model of the protein folding suggests that progression of folding proceeds through multiple pathways, having the multiple intermediates which leads to multidimensional free-energy surface. Herein, we applied all-atom MD simulation to conduct a comparative study on the structure of β-lactoglobulin (β-LgA) in aqueous mixture of 8 M urea and 8 M dimethyl sulfoxide (DMSO), at different temperatures. The cumulative results of multiple simulations suggest a common unfolding pathway of β-LgA, occurred through the stable and meta-stable intermediates (I), in both urea and DMSO. However, the free-energy landscape (FEL) analyses show that the structural transitions of I-states are energetically different. In urea, FEL shows distinct ensemble of intermediates, I1 and I2, separated by the energy barrier of ∼3.0 kcal mol<sup>−1</sup>. Similarly, we find the population of two distinct I1 and I2 states in DMSO, however, the I1 appeared transiently around ∼30–35 ns and is short-lived. But, the I2 ensemble is observed structurally compact and long-lived (∼50–150 ns) as compared to unfolding in urea. Furthermore, the I1 and I2 are separated through a high energy barrier of ∼6.0 kcal mol<sup>−1</sup>. Thus, our results provide the structural insights of intermediates which essentially bear the signature of a different unfolding pathway of β-LgA in urea and DMSO. Abbreviationsβ-LgAβ-lactoglobulinDMSOdimethyl sulfoxideFELfree-energy landscapeGdmClguanidinium chlorideIintermediate stateMGmolten globule statePMEparticle mesh EwaldQfraction of native contactsRMSDroot mean square deviationRMSFroot mean square fluctuation<i>R</i><sub>g</sub>radius of gyrationSASAsolvent Accessible Surface AreascSASAthe side chain SASATrptryptophan β-lactoglobulin dimethyl sulfoxide free-energy landscape guanidinium chloride intermediate state molten globule state particle mesh Ewald fraction of native contacts root mean square deviation root mean square fluctuation radius of gyration solvent Accessible Surface Area the side chain SASA tryptophan Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11368677
title: An atypical heterotrimeric Gα protein has substantially reduced nucleotide binding but retains nucleotide-independent interactions with its cognate RGS protein and Gβγ dimer

description: Plants uniquely have a family of proteins called extra-large G proteins (XLG) that share homology in their C-terminal half with the canonical Gα subunits; we carefully detail here that Arabidopsis XLG2 lacks critical residues requisite for nucleotide binding and hydrolysis which is consistent with our quantitative analyses. Based on microscale thermophoresis, Arabidopsis XLG2 binds GTPγS with an affinity 100 times lower than that to canonical Gα subunits. This means that given the concentration range of guanine nucleotide in plant cells, XLG2 is not likely bound by GTP <i>in vivo</i>. Homology modeling and molecular dynamics simulations provide a plausible mechanism for the poor nucleotide binding affinity of XLG2. Simulations indicate substantially stronger salt bridge networks formed by several key amino-acid residues of AtGPA1 which are either misplaced or missing in XLG2. These residues in AtGPA1 not only maintain the overall shape and integrity of the apoprotein cavity but also increase the frequency of favorable nucleotide-protein interactions in the nucleotide-bound state. Despite this loss of nucleotide dependency, XLG2 binds the RGS domain of AtRGS1 with an affinity similar to the Arabidopsis AtGPA1 in its apo-state and about 2 times lower than AtGPA1 in its transition state. In addition, XLG2 binds the Gβγ dimer with an affinity similar to that of AtGPA1. XLG2 likely acts as a dominant negative Gα protein to block G protein signaling. We propose that XLG2, independent of guanine nucleotide binding, regulates the active state of the canonical G protein pathway directly by sequestering Gβγ and indirectly by promoting heterodimer formation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11368677.v2
title: An atypical heterotrimeric Gα protein has substantially reduced nucleotide binding but retains nucleotide-independent interactions with its cognate RGS protein and Gβγ dimer

description: Plants uniquely have a family of proteins called extra-large G proteins (XLG) that share homology in their C-terminal half with the canonical Gα subunits; we carefully detail here that Arabidopsis XLG2 lacks critical residues requisite for nucleotide binding and hydrolysis which is consistent with our quantitative analyses. Based on microscale thermophoresis, Arabidopsis XLG2 binds GTPγS with an affinity 100 times lower than that to canonical Gα subunits. This means that given the concentration range of guanine nucleotide in plant cells, XLG2 is not likely bound by GTP <i>in vivo</i>. Homology modeling and molecular dynamics simulations provide a plausible mechanism for the poor nucleotide binding affinity of XLG2. Simulations indicate substantially stronger salt bridge networks formed by several key amino-acid residues of AtGPA1 which are either misplaced or missing in XLG2. These residues in AtGPA1 not only maintain the overall shape and integrity of the apoprotein cavity but also increase the frequency of favorable nucleotide-protein interactions in the nucleotide-bound state. Despite this loss of nucleotide dependency, XLG2 binds the RGS domain of AtRGS1 with an affinity similar to the Arabidopsis AtGPA1 in its apo-state and about 2 times lower than AtGPA1 in its transition state. In addition, XLG2 binds the Gβγ dimer with an affinity similar to that of AtGPA1. XLG2 likely acts as a dominant negative Gα protein to block G protein signaling. We propose that XLG2, independent of guanine nucleotide binding, regulates the active state of the canonical G protein pathway directly by sequestering Gβγ and indirectly by promoting heterodimer formation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11297591
title: Identification of the phospholipid binding regions of the envelope E protein of flaviviruses by molecular dynamics

description: The <i>Flavivirus</i> genus comprise several important human pathogens, including dengue, West Nile, Yellow fever, Japanese encephalitis, Zika, and tick-borne encephalitis viruses. These enveloped viruses affect more than 2 billion people in the world, mainly in less developed countries. Although some vaccines exist for some flaviviruses, these vaccines are not universally available due to many factors and since their infections are a world-wide public health issue, the development of antiviral molecules is fundamental. Flavivirus membranes, through the help of the envelope E glycoprotein, fuse with endosomal compartments in a pH-dependent way to release their genome into the cytoplasm and require specific lipids, such as bis(monoacylglycero)phosphate (BMP), for efficient fusion. The fundamental role the envelope E protein has on viral entry and membrane fusion suggest that it is an essential antiviral target. In this work, we have used atomistic molecular dynamics simulations to study the binding of the head-group of BMP to the tip of the envelope E proteins of ZIKV, DENV, TBEV and JEV viruses whose three-dimensional structures are known. Our results indicate that, apart from the fusion loop, there are different amino acid residues in different regions of the envelope E proteins of flaviviruses capable of binding the head-group of BMP. These regions should work together to accomplish the binding and fusion of the envelope and endosomal membranes and represent a new target to develop and design potent and effective antiviral agents capable of blocking flavivirus-endosome membrane fusion.
DOI: 10.17632/vfd44g4nvn.1
title: Data for: Knowledge, Attitudes and Mental Health of College Students during the COVID-19 quarantine in China

description: Investigation and Analysis on Mental Health of College Students.
DOI: 10.18462/iir.iccc.2020.289682
title: Implementation of a technology platform to develop sustainable strategies in order to reduce Food Loss and Waste across the continuum of food distribution in Canada.
DOI: 10.18462/iir.iccc.2020.290095
title: Salting of mackerel fillets in refrigerated brine.
DOI: 10.5281/zenodo.4066185
title: Pulsation-driven Mass Loss from Massive Stars behind Stellar Mergers in Metal-poor Dense Clusters

description: MESA inlists, run_star_extras, and data associated with Nakauchi, Inayoshi, Omukai 2020. MESA version 12115.
DOI: 10.5281/zenodo.4066184
title: Pulsation-driven Mass Loss from Massive Stars behind Stellar Mergers in Metal-poor Dense Clusters

description: MESA inlists, run_star_extras, and data associated with Nakauchi, Inayoshi, Omukai 2020. MESA version 12115.
DOI: 10.18462/iir.iccc.2020.284549
title: Enzymatic hydrolysis of cod heads – effect of freezing and thawing on the quality and composition of protein hydrolysates.
DOI: 10.5281/zenodo.4066583
title: Assessment of fat-free mass from bioelectrical impedance analysis in men and women with Prader-Willi syndrome: cross-sectional study

description: We have recently shown that population-specific formulae are required to estimate fat-free mass (FFM) from bioelectrical impedance analysis (BIA) in obese women with Prader-Willi syndrome (PWS) matched by age and percent fat mass (FM) to non-PWS women. The present cross-sectional study was aimed at developing generalised BIA equations that could be used in PWS subjects independently of sex and FM. We used dual-energy X-ray absorptiometry to measure FFM and BIA to measure whole-body impedance at 50 kHz (Z<sub>50</sub>) in 34 women and 21 men with PWS. The impedance index, that is, height (cm)<sup>2</sup>/Z<sub>50</sub> (Ω), explained 77% (BCa-bootstrapped 95% CI 65 to 85%) of the variance of FFM with a root mean squared error of the estimate of 3.7 kg (BCa-bootstrapped 95% CI 3.2 to 4.5 kg). BIA can be used to estimate FFM in obese and non-obese PWS men and women by means of population-specific equations.
DOI: 10.5281/zenodo.4066582
title: Assessment of fat-free mass from bioelectrical impedance analysis in men and women with Prader-Willi syndrome: cross-sectional study

description: We have recently shown that population-specific formulae are required to estimate fat-free mass (FFM) from bioelectrical impedance analysis (BIA) in obese women with Prader-Willi syndrome (PWS) matched by age and percent fat mass (FM) to non-PWS women. The present cross-sectional study was aimed at developing generalised BIA equations that could be used in PWS subjects independently of sex and FM. We used dual-energy X-ray absorptiometry to measure FFM and BIA to measure whole-body impedance at 50 kHz (Z<sub>50</sub>) in 34 women and 21 men with PWS. The impedance index, that is, height (cm)<sup>2</sup>/Z<sub>50</sub> (Ω), explained 77% (BCa-bootstrapped 95% CI 65 to 85%) of the variance of FFM with a root mean squared error of the estimate of 3.7 kg (BCa-bootstrapped 95% CI 3.2 to 4.5 kg). BIA can be used to estimate FFM in obese and non-obese PWS men and women by means of population-specific equations.
DOI: 10.6084/m9.figshare.1577614
title: MDV files for alaising study

description: Please download from ARM archive
DOI: 10.6084/m9.figshare.1577603
title: Outdoor wood furnaces create significant indoor particulate pollution in neighboring homes

description: <i>Context</i>: The use of outdoor wood furnaces (OWFs) is common in many parts of the United States. Little published information exists on the concentrations of outdoor and indoor fine particulates found near OWFs.<i>Objective</i>: To compare PM<sub>2.5</sub> (cts) and PM<sub>0.5</sub> (cts) particle concentrations inside four Connecticut homes located 30.5–259 m from OWFs, and inside six Connecticut control homes located more than 2 km from the nearest OWF.<i>Materials and methods</i>: PM<sub>2.5</sub> (cts) and PM<sub>0.5</sub> (cts) measurements were made with a Dylos light-scattering particulate counter.<i>Results</i>: Mean PM<sub>2.5</sub> (cts) concentrations were 4.21 times as great in the four OWF exposed homes than the six control homes (0.302 × 10<sup>6</sup> counts/m<sup>3</sup> versus 0.0718 counts × 10<sup>6</sup>/m<sup>3</sup><i>p</i> 2.5 (cts) concentrations inside the four OWF exposed homes roughly corresponds to a mass PM<sub>2.5</sub> of 37 µg/m<sup>3</sup>, which is above the US EPA 24-h PM<sub>2.5</sub> limit of 35 µg/m<sup>3</sup>. Mean PM<sub>0.5</sub> (cts) concentrations were 3.44 times as great in the four OWF exposed homes than in the six control homes (0.657 versus 0.191 × 10<sup>6</sup>/m<sup>3</sup><i>p</i> 2.5 (cts) and PM<sub>0.5</sub> (cts) concentrations were significantly higher in the house 259 m from an OWF as compared with the mean of the six control homes.<i>Conclusion</i>: Existing regulations, such as the present Connecticut law requiring a 61 meter distance between an OWF and neighboring homes, are not adequate to protect the health of neighboring residents.
DOI: 10.6084/m9.figshare.1577602
title: Use of novel inhalation kinetic studies to refine physiologically-based pharmacokinetic models for ethanol in non-pregnant and pregnant rats

description: Ethanol (EtOH) exposure induces a variety of concentration-dependent neurological and developmental effects in the rat. Physiologically-based pharmacokinetic (PBPK) models have been used to predict the inhalation exposure concentrations necessary to produce blood EtOH concentrations (BEC) in the range associated with these effects. Previous laboratory reports often lacked sufficient detail to adequately simulate reported exposure scenarios associated with BECs in this range, or lacked data on the time-course of EtOH in target tissues (e.g. brain, liver, eye, fetus). To address these data gaps, inhalation studies were performed at 5000, 10 000, and 21 000 ppm (6 h/d) in non-pregnant female Long-Evans (LE) rats and at 21 000 ppm (6.33 h/d) for 12 d of gestation in pregnant LE rats to evaluate our previously published PBPK models at toxicologically-relevant blood and tissue concentrations. Additionally, nose-only and whole-body plethysmography studies were conducted to refine model descriptions of respiration and uptake within the respiratory tract. The resulting time-course and plethysmography data from these <i>in vivo</i> studies were compared to simulations from our previously published models, after which the models were recalibrated to improve descriptions of tissue dosimetry by accounting for dose-dependencies in pharmacokinetic behavior. Simulations using the recalibrated models reproduced these data from non-pregnant, pregnant, and fetal rats to within a factor of 2 or better across datasets, resulting in a suite of model structures suitable for simulation of a broad range of EtOH exposure scenarios.
DOI: 10.6084/m9.figshare.1577603.v1
title: Outdoor wood furnaces create significant indoor particulate pollution in neighboring homes

description: <i>Context</i>: The use of outdoor wood furnaces (OWFs) is common in many parts of the United States. Little published information exists on the concentrations of outdoor and indoor fine particulates found near OWFs.<i>Objective</i>: To compare PM<sub>2.5</sub> (cts) and PM<sub>0.5</sub> (cts) particle concentrations inside four Connecticut homes located 30.5–259 m from OWFs, and inside six Connecticut control homes located more than 2 km from the nearest OWF.<i>Materials and methods</i>: PM<sub>2.5</sub> (cts) and PM<sub>0.5</sub> (cts) measurements were made with a Dylos light-scattering particulate counter.<i>Results</i>: Mean PM<sub>2.5</sub> (cts) concentrations were 4.21 times as great in the four OWF exposed homes than the six control homes (0.302 × 10<sup>6</sup> counts/m<sup>3</sup> versus 0.0718 counts × 10<sup>6</sup>/m<sup>3</sup><i>p</i> 2.5 (cts) concentrations inside the four OWF exposed homes roughly corresponds to a mass PM<sub>2.5</sub> of 37 µg/m<sup>3</sup>, which is above the US EPA 24-h PM<sub>2.5</sub> limit of 35 µg/m<sup>3</sup>. Mean PM<sub>0.5</sub> (cts) concentrations were 3.44 times as great in the four OWF exposed homes than in the six control homes (0.657 versus 0.191 × 10<sup>6</sup>/m<sup>3</sup><i>p</i> 2.5 (cts) and PM<sub>0.5</sub> (cts) concentrations were significantly higher in the house 259 m from an OWF as compared with the mean of the six control homes.<i>Conclusion</i>: Existing regulations, such as the present Connecticut law requiring a 61 meter distance between an OWF and neighboring homes, are not adequate to protect the health of neighboring residents.
DOI: 10.6084/m9.figshare.1577614.v1
title: MDV files for alaising study

description: Please download from ARM archive