cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4625986.v2
title: Wilken_et_al_Dataset.gp

description: Representative protein sequences of the known Ascomycete mating proteins renamed in the review by Wilken et al. (Fungal Biology Reviews, 2017).<br>
DOI: 10.6084/m9.figshare.4625959
title: Appendix E: Mathematica Analysis Script from Host allometry influences the evolution of parasite host-generalism: theory and meta-analysis

description: An unaltered Mathematica script that reproduces all of the mathematical analyses in the manuscript
DOI: 10.6084/m9.figshare.4625974.v1
title: Supplementary Material for: Therapeutic Advances and New Directions for Triple-Negative Breast Cancer

description: Triple-negative breast cancer (TNBC) is a molecularly diverse grouping with poor prognosis for which chemotherapy remains the foundation of treatment. The molecular heterogeneity of the disease rationalizes its diverse biological behavior and differential response to treatment. Estimates of up to 20% of patients diagnosed have germline mutations in DNA-damage repair-pathway genes, namely BRCA1 and 2, and this can be used to select patients likely to respond to platinums and/or inhibitors of poly(ADP-ribose) polymerase (PARP). Similar strategies can be utilized in other subtypes of TNBC that have ‘BRCA-like’ tumor biology due to the presence of mutations in alternate DNA-damage repair genes. The diverse biological behavior of TNBC and its variable response to chemotherapy were largely decoded following genotyping studies that enabled the identification of distinct molecular subtypes, such that the biological and genetic heterogeneity of the disease could be understood. This subsequently enabled the identification of therapeutic ‘vulnerabilities’ for each subtype that encompass biological processes including proliferation, DNA repair, apoptosis, angiogenesis, immune modulation, and invasion and metastasis. To expedite the development of therapies for high-risk, early-stage breast cancer, we have adopted novel trial designs and re-defined endpoints as surrogates of clinical outcomes. The purpose of this review is to highlight the current standard and experimental treatment options for TNBC.
DOI: 10.6084/m9.figshare.4625941
title: Dative Sickness: A Phylogenetic Analysis of Argument Structure Evolution in Germanic (supplementary materials)

description: Supplementary materials to "Dative Sickness: A Phylogenetic Analysis of Argument Structure Evolution in Germanic"
DOI: 10.6084/m9.figshare.4625947
title: Data supplementary from Host allometry influences the evolution of parasite host-generalism: theory and meta-analysis

description: Data used in analysis
DOI: 10.6084/m9.figshare.4625947.v1
title: Data supplementary from Host allometry influences the evolution of parasite host-generalism: theory and meta-analysis

description: Data used in analysis
DOI: 10.6084/m9.figshare.4625929
title: Nature Reserve Data

description: Plant species richness in China's nature reserves
DOI: 10.6084/m9.figshare.4625929.v1
title: Nature Reserve Data

description: Plant species richness in China's nature reserves
DOI: 10.6084/m9.figshare.4625941.v2
title: Dative Sickness: A Phylogenetic Analysis of Argument Structure Evolution in Germanic (supplementary materials)

description: Supplementary materials to "Dative Sickness: A Phylogenetic Analysis of Argument Structure Evolution in Germanic"
DOI: 10.6084/m9.figshare.4625905
title: Alterations in B cell development, CDR-H3 repertoire and dsDNA-binding antibody production among C57BL/6 <i>ΔD−iD</i> mice congenic for the lupus susceptibility loci <i>sle1, sle2</i> or <i>sle3</i>

description: Systemic lupus erythematosus (SLE) is an autoimmune disease that reflects a failure to block the production of self-reactive antibodies, especially those that bind double-stranded DNA (dsDNA). Backcrossing the lupus-prone NZM2410 genome onto C57BL/6 led to the identification of three genomic intervals, termed <i>sle1, sle2</i> and <i>sle3</i>, which are associated with lupus susceptibility. We previously generated a C57BL/6 strain congenic for an immunoglobulin D<sub>H</sub> locus (<i>ΔD–iD</i>) that enriches for arginine at dsDNA-binding positions. We individually introduced the <i>ΔD–iD</i> allele into the three <i>sle</i> strains to test whether one or more of these susceptibility loci could affect the developmental fate of B cells bearing arginine-enriched CDR-H3s, the CDR-H3 repertoire created by the D<sub>H</sub> and the prevalence of dsDNA-binding antibodies. We found that the combination of the <i>ΔD–iD</i> allele and the <i>sle1</i> locus led to a decrease in mature, recirculating B cell numbers and an increase in marginal zone cell numbers while maintaining a highly charged CDR-H3 repertoire. <i>ΔD–iD</i> and <i>sle2</i> had no effect on peripheral B cell numbers, but the CDR-H3 repertoire was partially normalized. <i>ΔD–iD</i> and <i>sle3</i> led to an increase in marginal zone B cell numbers, with some normalization of hydrophobicity. Mice with <i>ΔD–iD</i> combined with either <i>sle1</i> or <i>sle3</i> had increased production of dsDNA-binding IgM and IgG by 12 months of age. These findings indicate that the peripheral CDR-H3 repertoire can be categorically manipulated by the effects of nonimmunoglobulin genes.
DOI: 10.6084/m9.figshare.4625905.v1
title: Alterations in B cell development, CDR-H3 repertoire and dsDNA-binding antibody production among C57BL/6 <i>ΔD−iD</i> mice congenic for the lupus susceptibility loci <i>sle1, sle2</i> or <i>sle3</i>

description: Systemic lupus erythematosus (SLE) is an autoimmune disease that reflects a failure to block the production of self-reactive antibodies, especially those that bind double-stranded DNA (dsDNA). Backcrossing the lupus-prone NZM2410 genome onto C57BL/6 led to the identification of three genomic intervals, termed <i>sle1, sle2</i> and <i>sle3</i>, which are associated with lupus susceptibility. We previously generated a C57BL/6 strain congenic for an immunoglobulin D<sub>H</sub> locus (<i>ΔD–iD</i>) that enriches for arginine at dsDNA-binding positions. We individually introduced the <i>ΔD–iD</i> allele into the three <i>sle</i> strains to test whether one or more of these susceptibility loci could affect the developmental fate of B cells bearing arginine-enriched CDR-H3s, the CDR-H3 repertoire created by the D<sub>H</sub> and the prevalence of dsDNA-binding antibodies. We found that the combination of the <i>ΔD–iD</i> allele and the <i>sle1</i> locus led to a decrease in mature, recirculating B cell numbers and an increase in marginal zone cell numbers while maintaining a highly charged CDR-H3 repertoire. <i>ΔD–iD</i> and <i>sle2</i> had no effect on peripheral B cell numbers, but the CDR-H3 repertoire was partially normalized. <i>ΔD–iD</i> and <i>sle3</i> led to an increase in marginal zone B cell numbers, with some normalization of hydrophobicity. Mice with <i>ΔD–iD</i> combined with either <i>sle1</i> or <i>sle3</i> had increased production of dsDNA-binding IgM and IgG by 12 months of age. These findings indicate that the peripheral CDR-H3 repertoire can be categorically manipulated by the effects of nonimmunoglobulin genes.
DOI: 10.34740/kaggle/dsv/1459060
title: COVID-19 cases by Continent
DOI: 10.6084/m9.figshare.4625131
title: 16-ch TCSPC single-molecule measurement of dsDNA using line-excitation

description: Data files in Photon-HDF5 format for freely-diffusing single-molecule measurements of a 80-base-pair dsDNA labeled with ATTO550.<br>Copyright 2017 The Regents of the University of California<br>
DOI: 10.6084/m9.figshare.4625131.v2
title: 16-ch TCSPC single-molecule measurement of dsDNA using line-excitation

description: Data files in Photon-HDF5 format for freely-diffusing single-molecule measurements of a 80-base-pair dsDNA labeled with ATTO550.<br>Copyright 2017 The Regents of the University of California<br>
DOI: 10.6084/m9.figshare.4625131.v1
title: 16-ch TCSPC single-molecule measurement of dsDNA using line-excitation

description: Data files in Photon-HDF5 format for freely-diffusing single-molecule measurements of a 80-base-pair dsDNA labeled with ATTO550.
DOI: 10.6084/m9.figshare.4625074
title: FMO2 Pieda HOP files

description: Input and output files from FMO2 PIEDA calculations
DOI: 10.6084/m9.figshare.4625074.v1
title: FMO2 Pieda HOP files

description: Input and output files from FMO2 PIEDA calculations
DOI: 10.6084/m9.figshare.4624891
title: Highly selective separation and recovery of Pd(II) from the automotive catalyst residue with the thiocarbamoyl substituted azothiacalix[4]arene derivative

description: New ligand, namely, 5, 11, 17, 23-tetrakis-((<i>p</i>-chlorophenyl) azo)-25,26,27,28-tetrakis ((dimethylthio carbamoyl)oxy) thiacalix[4]arene (CADTTCA), has been investigated for separation and recovery of Pd(II) through solvent extraction technique. Experimental parameters such as contact time, diluents, effect of H<sup>+</sup> and Cl<sup>−</sup> concentration, and acid durability have been thoroughly investigated. The loading capacity toward Pd(II) was determined to be 113 mg/L using 0.25 mM CADTTCA. The extractant showed high selectivity and extractability for Pd(II) than the other metal ions present in automotive catalyst residue (ACR) solution containing platinum group (PGMs) metal ions (i.e., Pd(II), Pt(IV), Rh(II), La(III), Al(III) and Ce(III)). The recovery percentage of Pd(II) was 98% after five extraction-scrubbing-stripping cycles. The probable extraction mechanisms were established through the FT-IR spectral analysis.
DOI: 10.6084/m9.figshare.4624891.v2
title: Highly selective separation and recovery of Pd(II) from the automotive catalyst residue with the thiocarbamoyl substituted azothiacalix[4]arene derivative

description: New ligand, namely, 5, 11, 17, 23-tetrakis-((<i>p</i>-chlorophenyl) azo)-25,26,27,28-tetrakis ((dimethylthio carbamoyl)oxy) thiacalix[4]arene (CADTTCA), has been investigated for separation and recovery of Pd(II) through solvent extraction technique. Experimental parameters such as contact time, diluents, effect of H<sup>+</sup> and Cl<sup>−</sup> concentration, and acid durability have been thoroughly investigated. The loading capacity toward Pd(II) was determined to be 113 mg/L using 0.25 mM CADTTCA. The extractant showed high selectivity and extractability for Pd(II) than the other metal ions present in automotive catalyst residue (ACR) solution containing platinum group (PGMs) metal ions (i.e., Pd(II), Pt(IV), Rh(II), La(III), Al(III) and Ce(III)). The recovery percentage of Pd(II) was 98% after five extraction-scrubbing-stripping cycles. The probable extraction mechanisms were established through the FT-IR spectral analysis.
DOI: 10.6084/m9.figshare.4624876
title: Predicting the equilibrium solubility of solid polycyclic aromatic hydrocarbons and dibenzothiophene using a combination of MOSCED plus molecular simulation or electronic structure calculations

description: Methods to predict the equilibrium solubility of non-electrolyte solids are important for the design of novel separation processes. Here we demonstrate how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here SMD or SM8, can be used to predict parameters for the MOdified Separation of Cohesive Energy Density (MOSCED) method. The method is applied to the solutes naphthalene, anthracene, phenanthrene, pyrene and dibenzothiophene, compounds of interested to the petroleum industry and for environmental remediation. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. Comparing to a total of 422 non-aqueous and 193 aqueous experimental solubilities, we find the proposed method is able to well correlate the data. The use of MOSCED is additionally advantageous as it is a solubility parameter-based method useful for intuitive solvent selection and formulation.
DOI: 10.6084/m9.figshare.4624879
title: Effects of strain and sex on the behaviour of free-range slow-growing chickens raised in a hot environment

description: Behaviour is a good indicator of the well-being of chickens. The objective of the study was to compare foraging behaviour in males and females of three indigenous chicken strains under generally hot free-range conditions. Behavioural activities were monitored in 21-wk-old Potchefstroom Koekoek (PK), Ovambo (OV) and Naked Neck (NN) chickens. Birds were separated by sex and allocated to four pens of <i>Chloris gayana</i>. Three birds per pen were randomly chosen and marked with paint 20 min before observation. Temperature humidity index (THI) was calculated and main effects analysed using the general linear models procedure. Naked Necks spent more time walking than OV and PK. Strain did not affect other behaviours. Females spent more time foraging, while males dominated standing and walking. There was negative correlation between THI and time spent foraging. There was interaction between strain and sex on time spent standing. Foraging and drinking behaviours were more prominent in the morning (07:00 h) and late afternoon (17:00 h) compared to the 12:00-h period, whereas preening and dust-bathing were dominant around mid-day. Strain, sex and THI influence behaviour in free-range chickens. Breeding programmes should be cognizant of these attributes in order to produce hardier birds in view of worsening climatic uncertainties.
DOI: 10.6084/m9.figshare.4624876.v1
title: Predicting the equilibrium solubility of solid polycyclic aromatic hydrocarbons and dibenzothiophene using a combination of MOSCED plus molecular simulation or electronic structure calculations

description: Methods to predict the equilibrium solubility of non-electrolyte solids are important for the design of novel separation processes. Here we demonstrate how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here SMD or SM8, can be used to predict parameters for the MOdified Separation of Cohesive Energy Density (MOSCED) method. The method is applied to the solutes naphthalene, anthracene, phenanthrene, pyrene and dibenzothiophene, compounds of interested to the petroleum industry and for environmental remediation. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. Comparing to a total of 422 non-aqueous and 193 aqueous experimental solubilities, we find the proposed method is able to well correlate the data. The use of MOSCED is additionally advantageous as it is a solubility parameter-based method useful for intuitive solvent selection and formulation.
DOI: 10.6084/m9.figshare.4624879.v1
title: Effects of strain and sex on the behaviour of free-range slow-growing chickens raised in a hot environment

description: Behaviour is a good indicator of the well-being of chickens. The objective of the study was to compare foraging behaviour in males and females of three indigenous chicken strains under generally hot free-range conditions. Behavioural activities were monitored in 21-wk-old Potchefstroom Koekoek (PK), Ovambo (OV) and Naked Neck (NN) chickens. Birds were separated by sex and allocated to four pens of <i>Chloris gayana</i>. Three birds per pen were randomly chosen and marked with paint 20 min before observation. Temperature humidity index (THI) was calculated and main effects analysed using the general linear models procedure. Naked Necks spent more time walking than OV and PK. Strain did not affect other behaviours. Females spent more time foraging, while males dominated standing and walking. There was negative correlation between THI and time spent foraging. There was interaction between strain and sex on time spent standing. Foraging and drinking behaviours were more prominent in the morning (07:00 h) and late afternoon (17:00 h) compared to the 12:00-h period, whereas preening and dust-bathing were dominant around mid-day. Strain, sex and THI influence behaviour in free-range chickens. Breeding programmes should be cognizant of these attributes in order to produce hardier birds in view of worsening climatic uncertainties.
DOI: 10.6084/m9.figshare.4624858
title: Structural and mechanistic insights into nuclear transport and delivery of the critical pluripotency factor Oct4 to DNA

description: Oct4 is a master regulator of the induction and maintenance of cellular pluripotency, and has crucial roles in early stages of differentiation. It is the only factor that cannot be substituted by other members of the same protein family to induce pluripotency. However, although Oct4 nuclear transport and delivery to target DNA are critical events for reprogramming to pluripotency, little is known about the molecular mechanism. Oct4 is imported to the nucleus by the classical nuclear transport mechanism, which requires importin α as an adaptor to bind the nuclear localization signal (NLS). Although there are structures of complexes of the NLS of transcription factors (TFs) in complex with importin α, there are no structures available for complexes involving intact TFs. We have therefore modeled the structure of the complex of the whole Oct4 POU domain and importin α2 using protein-protein docking and molecular dynamics. The model explains how the Ebola virus VP24 protein has a negative effect on the nuclear import of STAT1 by importin α but not on Oct4, and how Nup 50 facilitates cargo release from importin α. The model demonstrates the structural differences between the Oct4 importin α bound and DNA bound crystal states. We propose that the ‘expanded linker’ between the two DNA-binding domains of Oct4 is an intrinsically disordered region and that its conformational changes have a key role in the recognition/binding to both DNA and importin α. Moreover, we propose that this structural change enables efficient delivery to DNA after release from importin α.
DOI: 10.6084/m9.figshare.4624858.v1
title: Structural and mechanistic insights into nuclear transport and delivery of the critical pluripotency factor Oct4 to DNA

description: Oct4 is a master regulator of the induction and maintenance of cellular pluripotency, and has crucial roles in early stages of differentiation. It is the only factor that cannot be substituted by other members of the same protein family to induce pluripotency. However, although Oct4 nuclear transport and delivery to target DNA are critical events for reprogramming to pluripotency, little is known about the molecular mechanism. Oct4 is imported to the nucleus by the classical nuclear transport mechanism, which requires importin α as an adaptor to bind the nuclear localization signal (NLS). Although there are structures of complexes of the NLS of transcription factors (TFs) in complex with importin α, there are no structures available for complexes involving intact TFs. We have therefore modeled the structure of the complex of the whole Oct4 POU domain and importin α2 using protein-protein docking and molecular dynamics. The model explains how the Ebola virus VP24 protein has a negative effect on the nuclear import of STAT1 by importin α but not on Oct4, and how Nup 50 facilitates cargo release from importin α. The model demonstrates the structural differences between the Oct4 importin α bound and DNA bound crystal states. We propose that the ‘expanded linker’ between the two DNA-binding domains of Oct4 is an intrinsically disordered region and that its conformational changes have a key role in the recognition/binding to both DNA and importin α. Moreover, we propose that this structural change enables efficient delivery to DNA after release from importin α.
DOI: 10.6084/m9.figshare.4624711
title: Review of ecological integrity assessments for fresh waters

description: These are the complete set of documents reviewed as frameworks for assessment of ecological integrity of freshwaters between 1985 and 2015. Within the 87 documents, we identified 89 approaches (named "frameworks") for assessing integrity in freshwaters; these frameworks were contrasted using attributes that described the types of metrics used, the results, applications, ecosystem type, and statistics applied. <br>This dataset was the result of a comprehensive literature review using the following steps: Our protocols for search and selection generally followed those outlined by Pullin and Stewart (2006) for systematic review. We used Thomson ISI’s Web of Science, Science Direct, JSTOR, and Google Scholar search engines to generate an initial set of potential assessment publications through 2015 using combinations of the words: ecological integrity, ecological condition, ecosystem health, assessment, bioassessment, freshwater, wetland, riparian, lake, river, stream, watershed. We used these same combinations in standard search engines to identify relevant grey literature, as well as additions discovered through citations within publications. This resulted in an initial pool of documents (<i>n</i>=370), which related to the assessment at least one type of freshwater system - wetlands, lakes, streams, riparian areas, or watersheds - in North America. We then screened this document pool against the following review criteria: <i>1) </i>condition or integrity were considered an endpoint for the assessment, <i>2)</i> the total geographic scale assessed was greater than or equal to a watershed, <i>3)</i> the methods and products were described sufficiently to assess a majority of attributes, and <i>4)</i> the methods could be considered generalizable and applicable at different scales, geographic locations, or with respect to other management or conservation goals.<br>The dataset forms the frameworks reviewed in "Past, Present, and Future of Ecological Integrity Assessments" in the journal <i>Frontiers in Ecology and the Environment</i>
DOI: 10.6084/m9.figshare.4624711.v1
title: Review of ecological integrity assessments for fresh waters

description: These are the complete set of documents reviewed as frameworks for assessment of ecological integrity of freshwaters between 1985 and 2015. Within the 87 documents, we identified 89 approaches (named "frameworks") for assessing integrity in freshwaters; these frameworks were contrasted using attributes that described the types of metrics used, the results, applications, ecosystem type, and statistics applied. <br>This dataset was the result of a comprehensive literature review using the following steps: Our protocols for search and selection generally followed those outlined by Pullin and Stewart (2006) for systematic review. We used Thomson ISI’s Web of Science, Science Direct, JSTOR, and Google Scholar search engines to generate an initial set of potential assessment publications through 2015 using combinations of the words: ecological integrity, ecological condition, ecosystem health, assessment, bioassessment, freshwater, wetland, riparian, lake, river, stream, watershed. We used these same combinations in standard search engines to identify relevant grey literature, as well as additions discovered through citations within publications. This resulted in an initial pool of documents (<i>n</i>=370), which related to the assessment at least one type of freshwater system - wetlands, lakes, streams, riparian areas, or watersheds - in North America. We then screened this document pool against the following review criteria: <i>1) </i>condition or integrity were considered an endpoint for the assessment, <i>2)</i> the total geographic scale assessed was greater than or equal to a watershed, <i>3)</i> the methods and products were described sufficiently to assess a majority of attributes, and <i>4)</i> the methods could be considered generalizable and applicable at different scales, geographic locations, or with respect to other management or conservation goals.<br>The data forms the basis of the publication "Past, Present, and Future of Ecological Integrity Assessments" in the journal <i>Frontiers in Ecology and the Environment</i>