cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3082039.v4
title: Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome

description: The sequence of cattle genome provided a valuable opportunity to systematically link genetic and metabolic traits of cattle. The objectives of this study were 1) to reconstruct genome-scale cattle-specific metabolic pathways based on the most recent and updated cattle genome build and 2) to identify duplicated metabolic genes in the cattle genome for better understanding of metabolic adaptations in cattle. A bioinformatic pipeline of an organism for amalgamating genomic annotations from multiple sources was updated. Using this, an amalgamated cattle genome database based on UMD_3.1, was created. The amalgamated cattle genome database is composed of a total of 33,292 genes: 19,123 consensus genes between NCBI and Ensembl databases, 8,410 and 5,493 genes only found in NCBI or Ensembl, respectively, and 266 genes from NCBI scaffolds. A metabolic reconstruction of the cattle genome and cattle pathway genome database (PGDB) was also developed using Pathway Tools, followed by an intensive manual curation. The manual curation filled or revised 68 pathway holes, deleted 36 metabolic pathways, and added 23 metabolic pathways. Consequently, the curated cattle PGDB contains 304 metabolic pathways, 2,460 reactions including 2,371 enzymatic reactions, and 4,012 enzymes. Furthermore, this study identified eight duplicated genes in 12 metabolic pathways in the cattle genome compared to human and mouse. Some of these duplicated genes are related with specific hormone biosynthesis and detoxifications. The updated genome-scale metabolic reconstruction is a useful tool for understanding biology and metabolic characteristics in cattle. There has been significant improvements in the quality of cattle genome annotations and the MetaCyc database. The duplicated metabolic genes in the cattle genome compared to human and mouse implies evolutionary changes in the cattle genome and provides a useful information for further research on understanding metabolic adaptations of cattle. <br>
DOI: 10.6084/m9.figshare.3082039.v3
title: Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome

description: The sequence of cattle genome provided a valuable opportunity to systematically link genetic and metabolic traits of cattle. The objectives of this study were 1) to reconstruct genome-scale cattle-specific metabolic pathways based on the most recent and updated cattle genome build and 2) to identify duplicated metabolic genes in the cattle genome for better understanding of metabolic adaptations in cattle. A bioinformatic pipeline of an organism for amalgamating genomic annotations from multiple sources was updated. Using this, an amalgamated cattle genome database based on UMD_3.1, was created. The amalgamated cattle genome database is composed of a total of 33,292 genes: 19,123 consensus genes between NCBI and Ensembl databases, 8,410 and 5,493 genes only found in NCBI or Ensembl, respectively, and 266 genes from NCBI scaffolds. A metabolic reconstruction of the cattle genome and cattle pathway genome database (PGDB) was also developed using Pathway Tools, followed by an intensive manual curation. The manual curation filled or revised 68 pathway holes, deleted 36 metabolic pathways, and added 23 metabolic pathways. Consequently, the curated cattle PGDB contains 304 metabolic pathways, 2,460 reactions including 2,371 enzymatic reactions, and 4,012 enzymes. Furthermore, this study identified eight duplicated genes in 12 metabolic pathways in the cattle genome compared to human and mouse. Some of these duplicated genes are related with specific hormone biosynthesis and detoxifications. The updated genome-scale metabolic reconstruction is a useful tool for understanding biology and metabolic characteristics in cattle. There has been significant improvements in the quality of cattle genome annotations and the MetaCyc database. The duplicated metabolic genes in the cattle genome compared to human and mouse implies evolutionary changes in the cattle genome and provides a useful information for further research on understanding metabolic adaptations of cattle. <br>
DOI: 10.6084/m9.figshare.3081970
title: The simultaneous mass and energy evaporation (SM2E) model

description: In this article, the Simultaneous Mass and Energy Evaporation (SM2E) model is presented. The SM2E model is based on theoretical models for mass and energy transfer. The theoretical models systematically under or over predicted at various flow conditions: laminar, transition, and turbulent. These models were harmonized with experimental measurements to eliminate systematic under or over predictions; a total of 113 measured evaporation rates were used. The SM2E model can be used to estimate evaporation rates for pure liquids as well as liquid mixtures at laminar, transition, and turbulent flow conditions. However, due to limited availability of evaporation data, the model has so far only been tested against data for pure liquids and binary mixtures. The model can take evaporative cooling into account and when the temperature of the evaporating liquid or liquid mixture is known (e.g., isothermal evaporation), the SM2E model reduces to a mass transfer-only model.
DOI: 10.6084/m9.figshare.3081970.v1
title: The simultaneous mass and energy evaporation (SM2E) model

description: In this article, the Simultaneous Mass and Energy Evaporation (SM2E) model is presented. The SM2E model is based on theoretical models for mass and energy transfer. The theoretical models systematically under or over predicted at various flow conditions: laminar, transition, and turbulent. These models were harmonized with experimental measurements to eliminate systematic under or over predictions; a total of 113 measured evaporation rates were used. The SM2E model can be used to estimate evaporation rates for pure liquids as well as liquid mixtures at laminar, transition, and turbulent flow conditions. However, due to limited availability of evaporation data, the model has so far only been tested against data for pure liquids and binary mixtures. The model can take evaporative cooling into account and when the temperature of the evaporating liquid or liquid mixture is known (e.g., isothermal evaporation), the SM2E model reduces to a mass transfer-only model.
DOI: 10.6084/m9.figshare.3081814
title: Data used in PLoS One article "Complexity, Predictability and Time Homogeneity of Syntax in the Songs of Cassin’s Vireo (Vireo cassini)" by Hedley (2016)

description: Textgrid files for use in Praat with corresponding wav files, containing annotations identifying phrase-types delivered by Cassin's Vireos, with their timing and sequential order. See Textgrids ReadMe.txt for additional details.
DOI: 10.6084/m9.figshare.3081784
title: Corticosteroid-free treatment of tocilizumab monotherapy for microscopic polyangiitis: a single-arm, single-center, clinical trial

description: <i>Objectives</i>: To assess the efficacy of tocilizumab (TCZ) monotherapy for the remission induction of microscopic polyangiitis (MPA) in a prospective single-arm, single-center, cohort, pilot study. <i>Methods</i>: Eligible patients were aged between 20 and 80 years and were newly diagnosed with MPA according to Watts’ classification algorithm. Seven patients received 8 mg/kg of intravenous TCZ fortnightly for the first 2 months (5 courses), and monthly for the next 10 months (10 courses). One year after TCZ monotherapy, the patients were followed-up without any treatment. The protocol did not permit the use corticosteroids or any other immunosuppressants. Complete remission (CR) was defined as the Birmingham Vasculitis Activity Score of 0 at two consecutive visits made at least a month apart. <i>Results</i>: CR was achieved in two of six patients (33.3%) at 6 months and three patients (50.0%) at 12 months. Two patients were withdrawn: one because of inefficacy at 6 weeks and the other because of flare at 6 months. One patient voluntarily withdrew after CR at 3 months. Four patients (66.7%) could be kept drug-free after 1 year of TCZ without relapse for 6–15 months at the last visit. <i>Conclusion</i>: TCZ monotherapy may be an alternative treatment strategy in some patients with MPA.
DOI: 10.6084/m9.figshare.3081784.v1
title: Corticosteroid-free treatment of tocilizumab monotherapy for microscopic polyangiitis: a single-arm, single-center, clinical trial

description: <i>Objectives</i>: To assess the efficacy of tocilizumab (TCZ) monotherapy for the remission induction of microscopic polyangiitis (MPA) in a prospective single-arm, single-center, cohort, pilot study. <i>Methods</i>: Eligible patients were aged between 20 and 80 years and were newly diagnosed with MPA according to Watts’ classification algorithm. Seven patients received 8 mg/kg of intravenous TCZ fortnightly for the first 2 months (5 courses), and monthly for the next 10 months (10 courses). One year after TCZ monotherapy, the patients were followed-up without any treatment. The protocol did not permit the use corticosteroids or any other immunosuppressants. Complete remission (CR) was defined as the Birmingham Vasculitis Activity Score of 0 at two consecutive visits made at least a month apart. <i>Results</i>: CR was achieved in two of six patients (33.3%) at 6 months and three patients (50.0%) at 12 months. Two patients were withdrawn: one because of inefficacy at 6 weeks and the other because of flare at 6 months. One patient voluntarily withdrew after CR at 3 months. Four patients (66.7%) could be kept drug-free after 1 year of TCZ without relapse for 6–15 months at the last visit. <i>Conclusion</i>: TCZ monotherapy may be an alternative treatment strategy in some patients with MPA.
DOI: 10.6084/m9.figshare.3081781
title: Cost-effectiveness of non-vitamin K antagonist oral anticoagulants for stroke prevention in non-valvular atrial fibrillation: a systematic and qualitative review

description: The introduction of non-vitamin K antagonist oral anticoagulants (NOACs) into clinical practice represented a major change in the treatment of non-valvular atrial fibrillation (NVAF); drugs as effective as the gold standard were available, rapidly functioning and without major interferences with drugs and foods. However, a huge increase in the economic burden of NVAF was predicted, and many cost-effectiveness analyses were developed to aid policy makers and clinicians in implementing strategies for the prevention of stroke in NVAF. The present systematic review identified 54 studies from 21 different countries, reporting the incremental cost-effectiveness of dabigatran, apixaban, rivaroxaban and edoxaban. A critical appraisal of the studies was conducted in order to highlight consolidated results and biases.
DOI: 10.6084/m9.figshare.3081781.v1
title: Cost-effectiveness of non-vitamin K antagonist oral anticoagulants for stroke prevention in non-valvular atrial fibrillation: a systematic and qualitative review

description: The introduction of non-vitamin K antagonist oral anticoagulants (NOACs) into clinical practice represented a major change in the treatment of non-valvular atrial fibrillation (NVAF); drugs as effective as the gold standard were available, rapidly functioning and without major interferences with drugs and foods. However, a huge increase in the economic burden of NVAF was predicted, and many cost-effectiveness analyses were developed to aid policy makers and clinicians in implementing strategies for the prevention of stroke in NVAF. The present systematic review identified 54 studies from 21 different countries, reporting the incremental cost-effectiveness of dabigatran, apixaban, rivaroxaban and edoxaban. A critical appraisal of the studies was conducted in order to highlight consolidated results and biases.
DOI: 10.6084/m9.figshare.3081664
title: DFToutputfilesSennJACS2016.zip

description: Output files and pseudopotentials for density functional theory (DFT) calculations associated with the publication 'Symmetry Switching of Negative Thermal Expansion by Chemical Control' by Mark Senn et al. The DFT calculations were performed with the Abinit code version 7.2.2 which is available at http://www.abinit.org/downloads/packages/7-2.2
DOI: 10.6084/m9.figshare.3081664.v1
title: DFToutputfilesSennJACS2016.zip

description: Output files and pseudopotentials for density functional theory (DFT) calculations associated with the publication 'Symmetry Switching of Negative Thermal Expansion by Chemical Control' by Mark Senn et al. The DFT calculations were performed with the Abinit code version 7.2.2 which is available at http://www.abinit.org/downloads/packages/7-2.2
DOI: 10.6084/m9.figshare.3081610
title: Raw data for meta-analysis of replications project

description: Raw data for meta-analysis of replications project.
DOI: 10.6084/m9.figshare.3081640
title: The NPM software dependency network (npmjs.com)

description: The public software repository npm (http://npmjs.com) is one of the biggest ones. This dataset contains dependencies among packages in npm and is represented in edgelist format. It has 154744 nodes (software packages) and 517098 directed edges (dependencies).
DOI: 10.6084/m9.figshare.3081400
title: Research Data Preservation. The rewards of doing things better.

description: Presentation at the Association of Learned and Professional Society Publishers (ALPSP) event "Standing on the Digits of Giants: Research data, preservation and innovation". March 2016. Zip file is in bagit format and includes the presentation in PDF and powerpoint, associated technical and descriptive metadata, and a small dataset used in one of the figures.<br>
DOI: 10.6084/m9.figshare.3081400.v1
title: Research Data Preservation. The rewards of doing things better.

description: Presentation at the Association of Learned and Professional Society Publishers (ALPSP) event "Standing on the Digits of Giants: Research data, preservation and innovation". March 2016. Zip file is in bagit format and includes the presentation in PDF and powerpoint, associated technical and descriptive metadata, and a small dataset used in one of the figures.<br>
DOI: 10.6084/m9.figshare.3081277
title: Uranium distribution as a proxy for basin-scale fluid flow in distributive fluvial systems

description: Table S1
DOI: 10.6084/m9.figshare.3081277.v1
title: Uranium distribution as a proxy for basin-scale fluid flow in distributive fluvial systems

description: Table S1
DOI: 10.6084/m9.figshare.3081220
title: Far-field super-resolution imaging of resonant multiples

description: sonar_survey.mat/ Readme_sonar are for the sonar survey results shown in Figure 4. <br><br>exploration_survey.mat/ Readme_exploration are for the exploration survey results in Figure 5.<br>
DOI: 10.6084/m9.figshare.3081208
title: dataset_Rödel.et.al.xlsx

description: Rödel, H.G., Zapka, M., Stefanski, V. & von Holst, D. (2016) Data from: Reproductive effort alters immune parameters measured post-partum in European rabbits under semi-natural conditions. <i>Functional Ecology</i>
DOI: 10.6084/m9.figshare.3081208.v1
title: dataset_Rödel.et.al.xlsx

description: Rödel, H.G., Zapka, M., Stefanski, V. & von Holst, D. (2016) Data from: Reproductive effort alters immune parameters measured post-partum in European rabbits under semi-natural conditions. <i>Functional Ecology</i>
DOI: 10.6084/m9.figshare.3081220.v1
title: Sonar survey

description: Sonar survey data in Figure 4<br>
DOI: 10.6084/m9.figshare.3081028
title: Mesograzer identity, not host algae, determines consumer stable isotope ratios

description: Species-specific foraging habits or feeding preferences influence the overall trophic functioning in consumer assemblages. We set out to assess the <i>in situ</i> trophic diversity in a mesograzer assemblage (isopods, amphipods and gastropods) associated with marine littoral macroalgae. More specifically, we set out to establish whether stable isotope ratios of carbon (δ<sup>13</sup>C) and nitrogen (δ<sup>15</sup>N) are dependent on primary consumer identity or expressed in relation to the identity of the algal host, i.e<i>.</i> the habitat of the consumer. Consumer locations in bivariate isotope space revealed significant differences among grazer taxa, but no effect of the algal host. This suggests that grazer-specific foraging is more important in driving the qualitative range of feeding in the consumer assemblage than host diversity <i>per se</i> within a macrohabitat, such as a bay or a lagoon. The stable isotope ratios of the mesoherbivores were in line with expectations based on the known feeding ecology of the grazers. However, the trophic diversity suggested by stable isotope analysis implies that even an established concept such as the mesograzer guild may encompass simplifications in terms of functional group membership.
DOI: 10.6084/m9.figshare.3081040
title: Observed water content of bromeliads

description: Observed water content of bromeliads after a drought. Ilha do Cardoso, Brasil 25^o^<br>03' S, 47^o^ 53' W)<br>
DOI: 10.6084/m9.figshare.3081028.v1
title: Mesograzer identity, not host algae, determines consumer stable isotope ratios

description: Species-specific foraging habits or feeding preferences influence the overall trophic functioning in consumer assemblages. We set out to assess the <i>in situ</i> trophic diversity in a mesograzer assemblage (isopods, amphipods and gastropods) associated with marine littoral macroalgae. More specifically, we set out to establish whether stable isotope ratios of carbon (δ<sup>13</sup>C) and nitrogen (δ<sup>15</sup>N) are dependent on primary consumer identity or expressed in relation to the identity of the algal host, i.e<i>.</i> the habitat of the consumer. Consumer locations in bivariate isotope space revealed significant differences among grazer taxa, but no effect of the algal host. This suggests that grazer-specific foraging is more important in driving the qualitative range of feeding in the consumer assemblage than host diversity <i>per se</i> within a macrohabitat, such as a bay or a lagoon. The stable isotope ratios of the mesoherbivores were in line with expectations based on the known feeding ecology of the grazers. However, the trophic diversity suggested by stable isotope analysis implies that even an established concept such as the mesograzer guild may encompass simplifications in terms of functional group membership.
DOI: 10.6084/m9.figshare.3080995
title: Structural basis to characterise transactivation domain of BRCA1

description: Familial inheritance of breast and ovarian cancer is attributed to mutations discovered in functional domains of BRCA1 gene. BRCA1 is a multifunctional protein responsible for maintaining the genomic integrity and has transcriptional regulatory function encoded in its C-terminal region. The different amino-terminal e extensions to BRCA1 BRCT domain are responsible for transcription activation. However, only BRCA1 BRCT (1649–1859) amino acids have been explored for its structural characteristics. Noting the importance of extended region to the N-terminus of BRCT different regions of BRCA1 which demonstrates maximum transactivation activity has been explored for their structure and functional activity. Secondary and tertiary structural analysis revealed a limited alpha-helical content with well-folded tertiary structure. <i>In silico</i> tools were used to corroborate the <i>in vitro</i> results. Amino acids composition and sequence analysis display a propensity for intrinsic disorder and coiled-coil formation in BRCA1 (1396–1863) (BRCA1-TAD). The results presented in this paper suggest the extreme flexibility in coiled-coil motif might be an important requirement in the establishment of protein–protein interaction networks for BRCA1.
DOI: 10.6084/m9.figshare.3080995.v1
title: Structural basis to characterise transactivation domain of BRCA1

description: Familial inheritance of breast and ovarian cancer is attributed to mutations discovered in functional domains of BRCA1 gene. BRCA1 is a multifunctional protein responsible for maintaining the genomic integrity and has transcriptional regulatory function encoded in its C-terminal region. The different amino-terminal e extensions to BRCA1 BRCT domain are responsible for transcription activation. However, only BRCA1 BRCT (1649–1859) amino acids have been explored for its structural characteristics. Noting the importance of extended region to the N-terminus of BRCT different regions of BRCA1 which demonstrates maximum transactivation activity has been explored for their structure and functional activity. Secondary and tertiary structural analysis revealed a limited alpha-helical content with well-folded tertiary structure. <i>In silico</i> tools were used to corroborate the <i>in vitro</i> results. Amino acids composition and sequence analysis display a propensity for intrinsic disorder and coiled-coil formation in BRCA1 (1396–1863) (BRCA1-TAD). The results presented in this paper suggest the extreme flexibility in coiled-coil motif might be an important requirement in the establishment of protein–protein interaction networks for BRCA1.
DOI: 10.6084/m9.figshare.3080980
title: Graphite Nanosheet as Low Shrinkage Additive, Curing Accelerator, and Conducting Filler for Unsaturated Polyester Resin

description: The effect of graphite nanosheets on electrical properties, curing behavior, and polymerization shrinkage of unsaturated polyester resin has been investigated. A solution of polystyrene was used as low profile additive to reduce shrinkage. The results showed that graphite nanosheets have been well dispersed/distributed in the unsaturated polyester matrix where they have high aspect ratio and high surface area. Graphite nanosheet exhibited an accelerating effect on the curing of unsaturated polyester and reduced the polymerization shrinkage as low as 3.6%. Despite large reduction of flexural properties by low profile additive, graphite nanosheet considerably increased the flexural strength and modulus of unsaturated polyester/low profile additive by 47 and 103%, respectively. Therefore, graphite nanosheet can be used as a new low profile additive for unsaturated polyester resins where it is also able to improve mechanical properties and curing rate.
DOI: 10.6084/m9.figshare.3080974
title: Synthesis, Characterization and Adsorptive Properties of Quaternized 2-Dimethylaminoethyl Methacrylate Based Polymer–Clay Nanocomposites

description: [2-(Methacryloyloxy)ethyl]dimethylhexadecylammonium bromide (QDMA) was synthesized by means of quaternization of 2-dimethylaminoethyl methacrylate. Poly(QDMA) and poly(QDMA)-bentonite nanocomposites containing different amount of bentonite were prepared by in situ suspension polymerization and characterized. Adsorption behaviors of these materials towards acid orange 8 and <i>p</i>-nitrophenol were investigated with respect to solution pH. For both adsorbate, adsorption capacities of some nanocomposites were found to be higher than those of bentonite and poly(QDMA). Effects of various parameters such as contact time, initial adsorbate concentration, and temperature on the adsorption of acid orange 8 and <i>p</i>-nitrophenol onto NC3 from aqueous solutions were also evaluated.