cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/109505
title: Expendable Probe data collected during research cruise KN207-02 using a Sippican MK21 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504715.v1
title: Three-way interaction model with switching mechanism as an effective strategy for tracing functionally-related genes

description: <b>Introduction</b>: Identification of functionally-related genes is an important step in understanding biological systems. The most popular strategy to infer functional dependence is to study pairwise correlations between gene expression levels. However, certain functionally-related genes may have a low expression correlation due to their nonlinear interactions. The use of a three-way interaction (3WI) model with switching mechanism (SM) is a relatively new strategy to trace functionally-related genes. The 3WI model traces the dynamic and nonlinear nature of the co-expression relationship of two genes by introducing their link to the expression level of a third gene. <b>Areas covered</b>: In this paper, we reviewed a variety of existing methods for tracing the 3WIs. Furthermore, we provide a comprehensive review of the previous biological studies based on 3WI models. <b>Expert commentary</b>: Comparison of features of these methods indicates that the modified liquid association algorithm has the best efficiency for tracing 3WI between others. The limited number of biological studies based on the 3WI suggests that high computational demand of the available algorithms is a major challenge to apply this approach for analyzing high-throughput omics data.
DOI: 10.7284/109506
title: Gravimeter data collected during research cruise KN207-02 using a Bell BGM-3 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504712
title: Epitope-driven common subunit vaccine design against <i>H. pylori</i> strains

description: The developing potent vaccine is a pre-emptive strategy to tackle drug abuses and maladies of multidrug-resistant <i>Helicobacter pylori</i> strains. Ongoing vaccine studies are being conducted, however, development is in its infancy as ineffective vaccine targets might be. So, the linear perspective may indicate the need for potent subunit vaccine variants. Here, surface-exposed membrane proteins out of 826 common proteins of 53 <i>H. pylori</i> strains were chosen for analysis, as a follow-up to previous studies; these proteins are responsible for antigenicity to elicit the immune response. Antigenic determinant regions on prognostic targets were evaluated in the successive peptide screening using experimental T-cell epitope positive control and optimized with eminent immunoinformatics algorithms. In the milieu of docking, an ensemble of 2200 multiple conformers of complexes of modeled peptide and human leukocyte antigen- antigenD Related Beta-chain (HLA-DRB) was generated. Prioritized physics-based Molecular Mechanics-Generalized Born Surface Area approach coupled with bond length monitoring paved the improvement of prediction accuracy with binding potency estimations. Δ<i>G</i><sub>bind</sub> free energy, interaction patterns, enrichment factor contributions and root-mean-square deviation predictions evidenced the existence of better binding affinities of four novel peptides hits with predominant allotype HLA-DR alleles than co-crystal controls. Moreover, conformational plasticity and stability assessments of the better ranked complex epitope-2 (86-FRRNPNINV-94) – HLA-DRB5*0101 formulated in dynamic simulations of 10,416 trajectories depicted stable interaction profile that correlated with docking endpoints. Thus, the proposed novel vaccine cocktails of the study would be ideal candidates and provide new insights for T-cell driven subunit vaccine design against <i>H. pylori</i> strains Communicated by Ramaswamy H. Sarma
DOI: 10.7284/106806
title: Multibeam Echosounder data collected during research cruise KN207-02 using a SeaBeam 3012-P1 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504712.v1
title: Epitope-driven common subunit vaccine design against <i>H. pylori</i> strains

description: The developing potent vaccine is a pre-emptive strategy to tackle drug abuses and maladies of multidrug-resistant <i>Helicobacter pylori</i> strains. Ongoing vaccine studies are being conducted, however, development is in its infancy as ineffective vaccine targets might be. So, the linear perspective may indicate the need for potent subunit vaccine variants. Here, surface-exposed membrane proteins out of 826 common proteins of 53 <i>H. pylori</i> strains were chosen for analysis, as a follow-up to previous studies; these proteins are responsible for antigenicity to elicit the immune response. Antigenic determinant regions on prognostic targets were evaluated in the successive peptide screening using experimental T-cell epitope positive control and optimized with eminent immunoinformatics algorithms. In the milieu of docking, an ensemble of 2200 multiple conformers of complexes of modeled peptide and human leukocyte antigen- antigenD Related Beta-chain (HLA-DRB) was generated. Prioritized physics-based Molecular Mechanics-Generalized Born Surface Area approach coupled with bond length monitoring paved the improvement of prediction accuracy with binding potency estimations. Δ<i>G</i><sub>bind</sub> free energy, interaction patterns, enrichment factor contributions and root-mean-square deviation predictions evidenced the existence of better binding affinities of four novel peptides hits with predominant allotype HLA-DR alleles than co-crystal controls. Moreover, conformational plasticity and stability assessments of the better ranked complex epitope-2 (86-FRRNPNINV-94) – HLA-DRB5*0101 formulated in dynamic simulations of 10,416 trajectories depicted stable interaction profile that correlated with docking endpoints. Thus, the proposed novel vaccine cocktails of the study would be ideal candidates and provide new insights for T-cell driven subunit vaccine design against <i>H. pylori</i> strains
DOI: 10.7284/109507
title: Singlebeam Echosounder data collected during research cruise KN207-02 using a Knudsen 320B/R instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504712.v3
title: Epitope-driven common subunit vaccine design against <i>H. pylori</i> strains

description: The developing potent vaccine is a pre-emptive strategy to tackle drug abuses and maladies of multidrug-resistant <i>Helicobacter pylori</i> strains. Ongoing vaccine studies are being conducted, however, development is in its infancy as ineffective vaccine targets might be. So, the linear perspective may indicate the need for potent subunit vaccine variants. Here, surface-exposed membrane proteins out of 826 common proteins of 53 <i>H. pylori</i> strains were chosen for analysis, as a follow-up to previous studies; these proteins are responsible for antigenicity to elicit the immune response. Antigenic determinant regions on prognostic targets were evaluated in the successive peptide screening using experimental T-cell epitope positive control and optimized with eminent immunoinformatics algorithms. In the milieu of docking, an ensemble of 2200 multiple conformers of complexes of modeled peptide and human leukocyte antigen- antigenD Related Beta-chain (HLA-DRB) was generated. Prioritized physics-based Molecular Mechanics-Generalized Born Surface Area approach coupled with bond length monitoring paved the improvement of prediction accuracy with binding potency estimations. Δ<i>G</i><sub>bind</sub> free energy, interaction patterns, enrichment factor contributions and root-mean-square deviation predictions evidenced the existence of better binding affinities of four novel peptides hits with predominant allotype HLA-DR alleles than co-crystal controls. Moreover, conformational plasticity and stability assessments of the better ranked complex epitope-2 (86-FRRNPNINV-94) – HLA-DRB5*0101 formulated in dynamic simulations of 10,416 trajectories depicted stable interaction profile that correlated with docking endpoints. Thus, the proposed novel vaccine cocktails of the study would be ideal candidates and provide new insights for T-cell driven subunit vaccine design against <i>H. pylori</i> strains Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7504712.v2
title: Epitope-driven common subunit vaccine design against <i>H. pylori</i> strains

description: The developing potent vaccine is a pre-emptive strategy to tackle drug abuses and maladies of multidrug-resistant <i>Helicobacter pylori</i> strains. Ongoing vaccine studies are being conducted, however, development is in its infancy as ineffective vaccine targets might be. So, the linear perspective may indicate the need for potent subunit vaccine variants. Here, surface-exposed membrane proteins out of 826 common proteins of 53 <i>H. pylori</i> strains were chosen for analysis, as a follow-up to previous studies; these proteins are responsible for antigenicity to elicit the immune response. Antigenic determinant regions on prognostic targets were evaluated in the successive peptide screening using experimental T-cell epitope positive control and optimized with eminent immunoinformatics algorithms. In the milieu of docking, an ensemble of 2200 multiple conformers of complexes of modeled peptide and human leukocyte antigen- antigenD Related Beta-chain (HLA-DRB) was generated. Prioritized physics-based Molecular Mechanics-Generalized Born Surface Area approach coupled with bond length monitoring paved the improvement of prediction accuracy with binding potency estimations. Δ<i>G</i><sub>bind</sub> free energy, interaction patterns, enrichment factor contributions and root-mean-square deviation predictions evidenced the existence of better binding affinities of four novel peptides hits with predominant allotype HLA-DR alleles than co-crystal controls. Moreover, conformational plasticity and stability assessments of the better ranked complex epitope-2 (86-FRRNPNINV-94) – HLA-DRB5*0101 formulated in dynamic simulations of 10,416 trajectories depicted stable interaction profile that correlated with docking endpoints. Thus, the proposed novel vaccine cocktails of the study would be ideal candidates and provide new insights for T-cell driven subunit vaccine design against <i>H. pylori</i> strains Communicated by Ramaswamy H. Sarma
DOI: 10.7284/106822
title: Multiplexed data collected during research cruise KN207-03 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504646
title: Pre-crystallization phase formation of thermolysin hexamers in solution close to crystallization conditions

description: Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7504646.v1
title: Pre-crystallization phase formation of thermolysin hexamers in solution close to crystallization conditions

description: Communicated by Ramaswamy H. Sarma
DOI: 10.7284/109509
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN207-03 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504637
title: Relavant data underlying the findings described in the manuscript.xlsx

description: Quantitative identification and long-term trend analysis of baseflow nitrogen load export from an agricultural watershed, China<br>
DOI: 10.6084/m9.figshare.7504637.v1
title: Relavant data underlying the findings described in the manuscript.xlsx

description: Quantitative identification and long-term trend analysis of baseflow nitrogen load export from an agricultural watershed, China<br>
DOI: 10.6084/m9.figshare.7504628
title: Differently Eurosceptic: radical right populist parties and their supporters

description: Since the 2008 crisis, radical right populist (RRP) party positions on European integration have hardened and/or increased in salience. But do their supporters align with them on this? And what role does Euroscepticism play in driving support for these parties? Using data from the ‘euandi’ voting advice application, we examine how close over 8000 RRP supporters in the UK, France, the Netherlands, Austria, Sweden and Belgium were in 2014 to their parties on European integration and, for comparison, immigration. We find that, while they closely aligned on immigration, which remains a stronger predictor of support, they did not on European integration. We conclude, firstly, that increased salience of this issue does not necessarily lead to stronger linkages between parties and voters and that the consequences of positional congruence depend on salience congruence. Secondly, our findings suggest that RRP parties enjoy flexibility on European integration and can shift positions if necessary.
DOI: 10.6084/m9.figshare.7504628.v1
title: Differently Eurosceptic: radical right populist parties and their supporters

description: Since the 2008 crisis, radical right populist (RRP) party positions on European integration have hardened and/or increased in salience. But do their supporters align with them on this? And what role does Euroscepticism play in driving support for these parties? Using data from the ‘euandi’ voting advice application, we examine how close over 8000 RRP supporters in the UK, France, the Netherlands, Austria, Sweden and Belgium were in 2014 to their parties on European integration and, for comparison, immigration. We find that, while they closely aligned on immigration, which remains a stronger predictor of support, they did not on European integration. We conclude, firstly, that increased salience of this issue does not necessarily lead to stronger linkages between parties and voters and that the consequences of positional congruence depend on salience congruence. Secondly, our findings suggest that RRP parties enjoy flexibility on European integration and can shift positions if necessary.
DOI: 10.7284/109508
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise KN207-03 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504607
title: Differentially expressed genes

description: This file contains three DEG set from A vs. B, A vs. C, A vs. D
DOI: 10.7284/109510
title: Gravimeter data collected during research cruise KN207-03 using a Bell BGM-3 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504607.v2
title: Differentially expressed genes

description: This file contains three DEG set from A vs. B, A vs. C, A vs. D
DOI: 10.6084/m9.figshare.7504607.v1
title: Differentially expressed genes

description: This file contains three DEG set from A vs. B, A vs. C, A vs. D
DOI: 10.7284/106823
title: Multiplexed data collected during research cruise KN207-04 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109511
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN207-04 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109512
title: Gravimeter data collected during research cruise KN207-04 using a Bell BGM-3 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504565
title: The data of the study related to aerobic exercise and intestinal microbiota.xlsx

description: These data are about our study related to aerobic exercise and intestinal microbiota.This study aimed to examine whether exercise intervention modifies the composition of intestinal microbiota in healthy elderly women.
DOI: 10.7284/109684
title: Multiplexed data collected during research cruise KN208 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504547
title: Gossypium.geneStructure.optimize

description: Optimization of gene structure
DOI: 10.6084/m9.figshare.7504565.v1
title: The data of the study related to aerobic exercise and intestinal microbiota.xlsx

description: These data are about our study related to aerobic exercise and intestinal microbiota.This study aimed to examine whether exercise intervention modifies the composition of intestinal microbiota in healthy elderly women.
DOI: 10.6084/m9.figshare.7504547.v1
title: Gossypium.geneStructure.optimize

description: Optimization of gene structure
DOI: 10.7284/109683
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN208 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504523
title: DEGs of A vs C

description: Differential expressed genes between cotton (Gossypium hirsutum) treated by low temperature 10 °C and that of control
DOI: 10.6084/m9.figshare.7504526
title: DEGs of A vs D

description: Differential expressed genes between cotton (Gossypium hirsutum) treated by low temperature 15 °C and that of control
DOI: 10.7284/109682
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise KN208 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504523.v1
title: DEGs of A vs C

description: Differential expressed genes between cotton (Gossypium hirsutum) treated by low temperature 10 °C and that of control
DOI: 10.6084/m9.figshare.7504526.v2
title: DEGs of A vs D

description: Differential expressed genes between cotton (Gossypium hirsutum) treated by low temperature 15 °C and that of control
DOI: 10.6084/m9.figshare.7504520
title: DEGs of A vs B

description: Differential expressed genes between cotton (Gossypium hirsutum) treated by low temperature 4 °C and that of control
DOI: 10.6084/m9.figshare.7504526.v1
title: DEGs of A vs D

description: Differential expressed genes between cotton (Gossypium hirsutum) treated by low temperature 15 °C and that of control
DOI: 10.7284/109686
title: Multibeam Echosounder data collected during research cruise KN208 using a SeaBeam 3012-P1 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504520.v1
title: DEGs of A vs B

description: Differential expressed genes between cotton (Gossypium hirsutum) treated by low temperature 4 °C and that of control
DOI: 10.7284/109685
title: Singlebeam Echosounder data collected during research cruise KN208 using a Knudsen 320B/R instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109689
title: Multiplexed data collected during research cruise KN209-01 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504508
title: Visualization of Land Mine Danger, Svilaja Region (Croatia)

description: Mines remaining from the Homeland War are a huge problem in Croatia. The joint work of experts in humanitarian demining and military doctrines in certain geographical areas, and scientists of various profiles, has resulted in a concept for producing mine danger maps, which show areas and levels of potential hazards from mines, i.e. suspected hazardous areas. This paper presents the concept for producing mine danger maps for a suspected hazardous area (Svilaja, Croatia). The input data comprise information stored in mine information systems and additional data collected on the suspected hazardous area (e.g. bunkers and shelters for tanks, artillery and people). The resulting maps (Main Map) seek to improve the identification of areas where there is no threat so that parts of suspected hazardous areas can be proposed for mine reduction, or suspected hazardous areas can be better defined.
DOI: 10.7284/109688
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN209-01 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504508.v1
title: Visualization of Land Mine Danger, Svilaja Region (Croatia)

description: Mines remaining from the Homeland War are a huge problem in Croatia. The joint work of experts in humanitarian demining and military doctrines in certain geographical areas, and scientists of various profiles, has resulted in a concept for producing mine danger maps, which show areas and levels of potential hazards from mines, i.e. suspected hazardous areas. This paper presents the concept for producing mine danger maps for a suspected hazardous area (Svilaja, Croatia). The input data comprise information stored in mine information systems and additional data collected on the suspected hazardous area (e.g. bunkers and shelters for tanks, artillery and people). The resulting maps (Main Map) seek to improve the identification of areas where there is no threat so that parts of suspected hazardous areas can be proposed for mine reduction, or suspected hazardous areas can be better defined.
DOI: 10.6084/m9.figshare.7504517.v4
title: Table S1. qRT-PCR primers used in validation of transcriptomic profiling for stress of low-temperature gradients in cotton (Gossypium hirsutum)

description: <b>qRT-PCR primers used in transcriptomic profiling for stress of low-temperature gradients in cotton (</b><b><i>Gossypium hirsutum</i></b><b>)</b><br>
DOI: 10.7284/109687
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise KN209-01 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109691
title: Multibeam Echosounder data collected during research cruise KN209-01 using a SeaBeam 3012-P1 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109690
title: Singlebeam Echosounder data collected during research cruise KN209-01 using a Knudsen 320B/R instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504481
title: Composts of poultry litter or dairy manure differentially affect survival of enteric bacteria in fields with spinach

description: OTU tables and representative sequences generated via Illumina miSeq of soil and compost microbial communities in agricultural soil.
DOI: 10.6084/m9.figshare.7504454
title: sAxl in LN - Dataset.xlsx

description: Soluble (s)Axl in patients with lupus nephritis. Dataset.
DOI: 10.6084/m9.figshare.7504475
title: All8Rats-rn6_gVCFpool.6nt.Pooled.chrs1-20.X.Y.M.qual30.dp10.vcf.gz

description: This file contains variant calls (on rn6 genome coordinates) for eight inbred rat strains (variant calling and alignment was performed using UnifiedGenotyper and BWA respectively). <br>
DOI: 10.6084/m9.figshare.7504451
title: Assembled transcripts of largemouth bass

description: These transcripts of largemouth bass were assembled with Trinity. A total of 18 liver libraries were constructed and sequenced.