cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25392/leicester.data.7718453.v1
title: Motion integration is anisotropic during smooth pursuit eye movements

description: Four movies showing of how motion coherence depends on the direction of smooth pursuit eye movements. We used a multiple-aperture array, with drift speeds being attributed to correspond to (100% coherence) to a single global motion direction or randomly to some proportion.<br>Participant's task is to track the black dot and discriminate between upward or downward motion of the surrounding. All movies show global motion that is a slightly downward from horizontal. The elements are low contrast(necessary for motion to cohere) and therefore may only be visible in full screen mode or close to the screen.<b></b><i></i><sub></sub><sup></sup><br><b></b><i></i><sub></sub><sup></sup><br>Movie 1: Global motion (50% coherent) opposite to the motion of the pursuit target (black dot)<br> Movie 2: Global motion (100% coherent) opposite to the motion of the pursuit target (black dot) <br>Movie 3: Global motion (50% coherent) in the direction of the pursuit target (black dot) <b></b><i></i><sub></sub><sup></sup><br>Movie 4: Global motion (100% coherent) in the direction of the the pursuit target (black dot)<br>
DOI: 10.6084/m9.figshare.7718462.v1
title: Quantifying the impact of tissue metabolism on solute transport in feto-placental microvascular networks

description: The raw geometric data which we use is given as STL files; the capillary surfaces surfaces end in "_Vasculature.stl" (four files) and villous surfaces end in "_Villi.stl" (four files). The geometries can be previewed in 3D by clicking on the file names.<br>Fig4_nonlinear_metabolism.mph: Simulations underlying Fig 4. Coupled transport problem, no boundary layers, mesh ~315k tetrahedral elements.<br>specimen3_FL_stripped.mph & specimen3_DL_stripped.mph: Simulations for calculating flow-limited and diffusion-limited metabolic scale functions G & F, respectively. This underlies Figs. 1, 2, 3 and 7. The mesh has approx. 19.7mio tetrahedral elements and is particularly well resolved at and near the villous surface to ensure that boundary layers for strong metabolism are resolved. Each simulation (to solve for solute in metabolising tissue) ran for approximately 10h. The meshing process itself ran for several hours. We used a powerful computer (128 GB RAM, 16 core CPU). The solutions and meshes were stripped from the Comsol files to comply with figshare's 5GB file size limitation. <br>specimen3_fully_coupled.mph: Simulations for calculating fully coupled problem with linear uptake kinetics, which underlies Fig. 2 (dots). The mesh has approximately 4.1mio tetrahedral elements.<br><br>*.nb and *.xlsx: Codes and data needed to Figures 2, 3, 4 and 7. The *.nb files were created in Mathematica 11.0.1.0, relying on the numerical data contained in the Excel (*.xlsx) files <i><b>which must be in the same folder as the *.nb files</b></i>. To reproduce the figures, open a Mathematica file and then go to Evaluation -&gt; Evaluate notebook, which will run all codes automatically and assemble all figures/subfigures. When switching between *.nb files, make sure to either close Mathematica or go to Evaluation -&gt; Quit Kernel -&gt; Local.
DOI: 10.7284/101505
title: Multiplexed data collected during research cruise AT15-53 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/101504
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT15-53 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/101502
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT15-53 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/101503
title: Multibeam Echosounder data collected during research cruise AT15-53 using a SeaBeam 2112 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/101509
title: Multiplexed data collected during research cruise AT15-54 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/101508
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT15-54 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7718366
title: Supplementary Material for: Development of HiSQOL: A Hidradenitis Suppurativa-Specific Quality of Life Instrument

description: <b><i>Background:</i></b> Hidradenitis suppurativa (HS) is a chronic and painful skin disease. In addition, HS lesions may be associated with pus and odour, potentially leading to significant stigma and, consequently, greatly affected quality of life (QOL). QOL is a multidimensional construct, which can be measured in various ways. However, generic or dermatologic QOL measures may not capture changes in QOL particularly affected in HS. Accordingly, patients and experts included in the HIdradenitis SuppuraTiva cORe outcomes set International Collaboration (HISTORIC) agreed that future clinical HS trials should measure HS-specific QOL. <b><i>Objectives:</i></b> To develop an HS-specific QOL instrument (HiSQOL, Hidradenitis Suppurativa Quality of life). <b><i>Method:</i></b> The initial phases of the questionnaire development, described in this study, included item generation by patient interviews, development of a pilot questionnaire, questionnaire refinement, and pilot testing. <b><i>Results:</i></b> For item generation, 21 patients were interviewed individually or in focus groups. Analysis of the interviews identified 105 candidate items and, next, a pilot questionnaire was developed. Finally, item reduction and two rounds of pilot testing resulted in a 23-item questionnaire representing physical, psychological, and social QOL dimensions. <b><i>Conclusions:</i></b> We have comprehensively explored on HS’s possible effect on the QOL of the affected individuals and identified a 23-item HS-specific QOL questionnaire. The questionnaire proved to be feasible, acceptable, and comprehensible in the second round of pilot testing. With HiSQOL, researchers can measure HS-specific QOL in future clinical trials, potentially enabling them to discover more effective treatment options. It is envisaged, that after thorough validation in a trial setting, a streamlined version of HISQOL may also become available for clinical use in daily practice.
DOI: 10.7284/101506
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT15-54 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7718354
title: KDS1 genome from Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: insights from a natural arms-race

description: CRISPR-Cas systems function as adaptive immune systems by acquiring nucleotide sequences called spacers that mediate sequence-specific defence against competitors. Uniquely, the phage ICP1 encodes a Type I-F CRISPR-Cas system that is deployed to target and overcome PLE, a mobile genetic element with anti-phage activity in <i>Vibrio cholerae</i>. Here, we exploit the arms race between ICP1 and PLE to examine spacer acquisition and interference under laboratory conditions to reconcile findings from wild populations. Natural ICP1 isolates encode multiple spacers directed against PLE, but we find that single spacers do not equally interfere with PLE mobilization. High-throughput sequencing to assay spacer acquisition reveals that ICP1 can also acquire spacers that target the <i>V. cholerae</i> chromosome. We find that targeting the <i>V. cholerae</i> chromosome proximal to PLE is sufficient to block PLE and is dependent on Cas2-3 helicase activity. We propose a model in which indirect chromosomal spacers are able to circumvent PLE by Cas2-3-mediated processive degradation of the <i>V. cholerae</i> chromosome before PLE mobilization. Generally, laboratory-acquired spacers are much more diverse than the subset of spacers maintained by ICP1 in nature, showing how evolutionary pressures can constrain CRISPR-Cas targeting in ways that are often not appreciated through <i>in vitro</i> analyses.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718354.v1
title: KDS1 genome from Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: insights from a natural arms-race

description: CRISPR-Cas systems function as adaptive immune systems by acquiring nucleotide sequences called spacers that mediate sequence-specific defence against competitors. Uniquely, the phage ICP1 encodes a Type I-F CRISPR-Cas system that is deployed to target and overcome PLE, a mobile genetic element with anti-phage activity in <i>Vibrio cholerae</i>. Here, we exploit the arms race between ICP1 and PLE to examine spacer acquisition and interference under laboratory conditions to reconcile findings from wild populations. Natural ICP1 isolates encode multiple spacers directed against PLE, but we find that single spacers do not equally interfere with PLE mobilization. High-throughput sequencing to assay spacer acquisition reveals that ICP1 can also acquire spacers that target the <i>V. cholerae</i> chromosome. We find that targeting the <i>V. cholerae</i> chromosome proximal to PLE is sufficient to block PLE and is dependent on Cas2-3 helicase activity. We propose a model in which indirect chromosomal spacers are able to circumvent PLE by Cas2-3-mediated processive degradation of the <i>V. cholerae</i> chromosome before PLE mobilization. Generally, laboratory-acquired spacers are much more diverse than the subset of spacers maintained by ICP1 in nature, showing how evolutionary pressures can constrain CRISPR-Cas targeting in ways that are often not appreciated through <i>in vitro</i> analyses.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.7284/101507
title: Gravimeter data collected during research cruise AT15-54 using a Bell BGM-3 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/112015
title: Multibeam Echosounder data collected during research cruise AT15-54 using a SeaBeam 2112 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108563
title: Singlebeam Echosounder data collected during research cruise AT15-54 using a Knudsen 320B/R instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7718312
title: S7 ARG_ACR from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.7284/101516
title: Multiplexed data collected during research cruise AT15-55 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7718312.v1
title: S7 ARG_ACR from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.7284/101515
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT15-55 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7718297
title: S10 Summary_blast_anti-CRISPR from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718297.v1
title: S10 Summary_blast_anti-CRISPR from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718285
title: S9 anti-CRISPR list from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.7284/101514
title: Gravimeter data collected during research cruise AT15-55 using a Bell BGM-3 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7718285.v1
title: S9 anti-CRISPR list from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.7284/101520
title: Multiplexed data collected during research cruise AT15-56 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/101519
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT15-56 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/101517
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT15-56 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition