cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5107501.v1
title: Raw Data TRAIL.xlsx

description: Cp raw data from real time RT-PCR experiments are included in this excel file<br>
DOI: 10.6084/m9.figshare.5107498.v1
title: Supplementary Material for: Drug Discovery to Halt the Progression of Acute Kidney Injury to Chronic Kidney Disease: A Case for Phenotypic Drug Discovery in Acute Kidney Injury

description: The cellular responses that occur following acute kidney injury (AKI) are complex and dynamic, involving multiple cells types and molecular pathways. For this reason, early selection of defined molecular targets for therapeutic intervention is unlikely to be effective in complex in vivo models of AKI, let alone Phase 3 clinical trials in patients with even more complex AKI pathobiology. Phenotypic screening using zebrafish provides an attractive alternative that does not require prior knowledge of molecular targets and may identify compounds that modify multiple targets that might be missed in more traditional target-based screens. In this review, we discuss results of an academic drug discovery campaign that used zebrafish as a primary screening tool to discover compounds with favorable absorption, metabolism, and toxicity that enhance repair when given late after injury in multiple models of AKI. We discuss how this screening campaign is being integrated into a more comprehensive, phenotypic, and target-based screen for lead compound optimization.
DOI: 10.6084/m9.figshare.5107333
title: Dataset for: Molecular and Functional Characterization of the Voltage-Gated Proton Channel in Zebrafish Neutrophils

description: Voltage-gated proton channels (Hv1/VSOP) are expressed in various cells types, including phagocytes, and are involved in diverse physiological processes. Although hvcn1, the gene encoding Hv1, has been identified across a wide range of species, most of the knowledge about its physiological function and expression profile is limited to mammals. In the present study, we investigated the basic properties of DrHv1, the Hv1 ortholog in zebrafish (<i>Danio rerio</i>) which is an excellent animal model owing to the transparency, as well as its functional expression in native cells. Electrophysiological analysis using a heterologous expression system confirmed the properties of a voltage-gated proton channel are conserved in DrHv1 with differences in threshold and activation kinetics as compared to mouse (<i>Mus musculus</i>) Hv1 (mHv1). RT-PCR analysis revealed that hvcn1 is expressed in zebrafish neutrophils, as is the case in mammals. Subsequent electrophysiological analysis confirmed the functional expression of DrHv1 in zebrafish neutrophils, which suggests Hv1 function in phagocytes is conserved among vertebrates. We also found that DrHv1 is comparatively resistant to extracellular Zn<sup>2+</sup>, which is a potent inhibitor of mammalian Hv1, and this phenomenon appears to reflect variation in the Zn<sup>2+</sup>-coordinating residue (histidine) within the extracellular linker region in mammalian Hv1. Notably, the serum Zn<sup>2+</sup> concentration is much higher in zebrafish than in mouse, raising the possibility that Zn<sup>2+</sup> sensitivity was acquired in accordance with a change in the serum Zn<sup>2+</sup> concentration. The present study highlights the biological variation and importance of Hv1 in different animal species.
DOI: 10.6084/m9.figshare.5107447
title: A New Perspective on the Interplay between Self-Control and Cognitive Performance: Modeling Progressive Depletion Patterns

description: Dataset for investigating the interplay between ego depletion, trait self-control and their interaction on mathematical performance over the course ot testing. <br>
DOI: 10.6084/m9.figshare.5107360
title: Dataset for: Estimation of smooth ROC curves for biomarkers with limits of detection

description: Protein biomarkers found in plasma are commonly used for cancer screening and early detection. Measurements obtained by such markers are often based on different assays that may not support detection of accurate measurements due to a limit of detection (LOD). The $ROC$ curve is the most popular statistical tool for the evaluation of a continuous biomarker. However, in situations where LODs exist, the empirical $ROC$ curve fails to provide a valid estimate for the whole spectrum of the false positive rate (FPR). Hence, crucial information regarding the performance of the marker in high sensitivity and/or high specificity values is not revealed. In this paper, we address this problem and propose methods for constructing $ROC$ curve estimates for all possible $FPR$ values. We explore flexible parametric methods, transformations to normality, and robust kernel-based and spline-based approaches. We evaluate our methods though simulations and illustrate them in colorectal and pancreatic cancer data.
DOI: 10.6084/m9.figshare.5107333.v1
title: Dataset for: Molecular and Functional Characterization of the Voltage-Gated Proton Channel in Zebrafish Neutrophils

description: Voltage-gated proton channels (Hv1/VSOP) are expressed in various cells types, including phagocytes, and are involved in diverse physiological processes. Although hvcn1, the gene encoding Hv1, has been identified across a wide range of species, most of the knowledge about its physiological function and expression profile is limited to mammals. In the present study, we investigated the basic properties of DrHv1, the Hv1 ortholog in zebrafish (<i>Danio rerio</i>) which is an excellent animal model owing to the transparency, as well as its functional expression in native cells. Electrophysiological analysis using a heterologous expression system confirmed the properties of a voltage-gated proton channel are conserved in DrHv1 with differences in threshold and activation kinetics as compared to mouse (<i>Mus musculus</i>) Hv1 (mHv1). RT-PCR analysis revealed that hvcn1 is expressed in zebrafish neutrophils, as is the case in mammals. Subsequent electrophysiological analysis confirmed the functional expression of DrHv1 in zebrafish neutrophils, which suggests Hv1 function in phagocytes is conserved among vertebrates. We also found that DrHv1 is comparatively resistant to extracellular Zn<sup>2+</sup>, which is a potent inhibitor of mammalian Hv1, and this phenomenon appears to reflect variation in the Zn<sup>2+</sup>-coordinating residue (histidine) within the extracellular linker region in mammalian Hv1. Notably, the serum Zn<sup>2+</sup> concentration is much higher in zebrafish than in mouse, raising the possibility that Zn<sup>2+</sup> sensitivity was acquired in accordance with a change in the serum Zn<sup>2+</sup> concentration. The present study highlights the biological variation and importance of Hv1 in different animal species.
DOI: 10.6084/m9.figshare.5107360.v1
title: Dataset for: Estimation of smooth ROC curves for biomarkers with limits of detection

description: Protein biomarkers found in plasma are commonly used for cancer screening and early detection. Measurements obtained by such markers are often based on different assays that may not support detection of accurate measurements due to a limit of detection (LOD). The $ROC$ curve is the most popular statistical tool for the evaluation of a continuous biomarker. However, in situations where LODs exist, the empirical $ROC$ curve fails to provide a valid estimate for the whole spectrum of the false positive rate (FPR). Hence, crucial information regarding the performance of the marker in high sensitivity and/or high specificity values is not revealed. In this paper, we address this problem and propose methods for constructing $ROC$ curve estimates for all possible $FPR$ values. We explore flexible parametric methods, transformations to normality, and robust kernel-based and spline-based approaches. We evaluate our methods though simulations and illustrate them in colorectal and pancreatic cancer data.
DOI: 10.6084/m9.figshare.5107330
title: Virus genomes in extended database - (Item K)

description: Viral genome sequences (7214) as part of the microbial genomes database used in the study:<br><b><br>Kirstahler P, Bjerrum SS, Friis-Møller A, </b><b>la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) </b>Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid. <b>Scientific Reports</b>, doi:10.1038/s41598-018-22416-4.
DOI: 10.6084/m9.figshare.5107330.v2
title: Virus genomes in extended database - (Item K)

description: Viral genome sequences (7214) as part of the microbial genomes database used in the study:<br><b><br>Kirstahler P, Bjerrum SS, Friis-Møller A, </b><b>la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) </b>Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid. <b>Scientific Reports</b>, doi:10.1038/s41598-018-22416-4.
DOI: 10.6084/m9.figshare.5107330.v1
title: Virus genomes in extended database - (Item G)

description: Viral genome sequences (7214) as part of the microbial genomes database used in the study:<br><b><br>Kirstahler P, Bjerrum SS, Friis-Møller A, </b><b>la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2017) </b>Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.<b> Journal </b>Vol:Issue page-page.
DOI: 10.6084/m9.figshare.5107300
title: Table S3 from CEP19 cooperates with FOP and CEP350 to drive early steps in the ciliogenesis programme

description: Primary cilia are microtubule-based sensory organelles necessary for efficient transduction of extracellular cues. To initiate cilia formation, ciliary vesicles (CVs) are transported to the vicinity of the centrosome where they dock to the distal end of the mother centriole and fuse to initiate cilium assembly. However, to this date, the early steps in cilia formation remain incompletely understood. Here, we demonstrate functional interplay between CEP19, FOP and CEP350 in ciliogenesis. Using three-dimensional structured-illumination microscopy (3D-SIM) imaging, we mapped the relative spatial distribution of these proteins at the distal end of the mother centriole and show that CEP350/FOP act upstream of CEP19 in their recruitment hierarchy. We demonstrate that CEP19 CRISPR KO cells are severely impaired in their ability to form cilia, analogous to the loss of function of CEP19 binding partners FOP and CEP350. Using GFP-tagged deletion constructs of CEP19, we show that the C-terminus of CEP19 is required for both its localization to centrioles and for its function in ciliogenesis. Critically, this region also mediates the interaction between CEP19 and FOP/CEP350. Interestingly, a morbid obesity-associated R82* truncated mutant of CEP19 cannot ciliate nor interact with FOP and CEP350, indicative of a putative role for CEP19 in ciliopathies. Finally, analysis of CEP19 KO cells using thin-section electron microscopy revealed marked defects in the docking of CVs to the distal end of the mother centrioles. Together, these data demonstrate a role for the CEP19, FOP and CEP350 module in ciliogenesis and the possible effect of disrupting their functions in ciliopathies.
DOI: 10.6084/m9.figshare.5107294
title: Table S2 from CEP19 cooperates with FOP and CEP350 to drive early steps in the ciliogenesis programme

description: Primary cilia are microtubule-based sensory organelles necessary for efficient transduction of extracellular cues. To initiate cilia formation, ciliary vesicles (CVs) are transported to the vicinity of the centrosome where they dock to the distal end of the mother centriole and fuse to initiate cilium assembly. However, to this date, the early steps in cilia formation remain incompletely understood. Here, we demonstrate functional interplay between CEP19, FOP and CEP350 in ciliogenesis. Using three-dimensional structured-illumination microscopy (3D-SIM) imaging, we mapped the relative spatial distribution of these proteins at the distal end of the mother centriole and show that CEP350/FOP act upstream of CEP19 in their recruitment hierarchy. We demonstrate that CEP19 CRISPR KO cells are severely impaired in their ability to form cilia, analogous to the loss of function of CEP19 binding partners FOP and CEP350. Using GFP-tagged deletion constructs of CEP19, we show that the C-terminus of CEP19 is required for both its localization to centrioles and for its function in ciliogenesis. Critically, this region also mediates the interaction between CEP19 and FOP/CEP350. Interestingly, a morbid obesity-associated R82* truncated mutant of CEP19 cannot ciliate nor interact with FOP and CEP350, indicative of a putative role for CEP19 in ciliopathies. Finally, analysis of CEP19 KO cells using thin-section electron microscopy revealed marked defects in the docking of CVs to the distal end of the mother centrioles. Together, these data demonstrate a role for the CEP19, FOP and CEP350 module in ciliogenesis and the possible effect of disrupting their functions in ciliopathies.
DOI: 10.6084/m9.figshare.5107297
title: Table S4 from CEP19 cooperates with FOP and CEP350 to drive early steps in the ciliogenesis programme

description: Primary cilia are microtubule-based sensory organelles necessary for efficient transduction of extracellular cues. To initiate cilia formation, ciliary vesicles (CVs) are transported to the vicinity of the centrosome where they dock to the distal end of the mother centriole and fuse to initiate cilium assembly. However, to this date, the early steps in cilia formation remain incompletely understood. Here, we demonstrate functional interplay between CEP19, FOP and CEP350 in ciliogenesis. Using three-dimensional structured-illumination microscopy (3D-SIM) imaging, we mapped the relative spatial distribution of these proteins at the distal end of the mother centriole and show that CEP350/FOP act upstream of CEP19 in their recruitment hierarchy. We demonstrate that CEP19 CRISPR KO cells are severely impaired in their ability to form cilia, analogous to the loss of function of CEP19 binding partners FOP and CEP350. Using GFP-tagged deletion constructs of CEP19, we show that the C-terminus of CEP19 is required for both its localization to centrioles and for its function in ciliogenesis. Critically, this region also mediates the interaction between CEP19 and FOP/CEP350. Interestingly, a morbid obesity-associated R82* truncated mutant of CEP19 cannot ciliate nor interact with FOP and CEP350, indicative of a putative role for CEP19 in ciliopathies. Finally, analysis of CEP19 KO cells using thin-section electron microscopy revealed marked defects in the docking of CVs to the distal end of the mother centrioles. Together, these data demonstrate a role for the CEP19, FOP and CEP350 module in ciliogenesis and the possible effect of disrupting their functions in ciliopathies.
DOI: 10.6084/m9.figshare.5107300.v1
title: Table S3 from CEP19 cooperates with FOP and CEP350 to drive early steps in the ciliogenesis programme

description: Primary cilia are microtubule-based sensory organelles necessary for efficient transduction of extracellular cues. To initiate cilia formation, ciliary vesicles (CVs) are transported to the vicinity of the centrosome where they dock to the distal end of the mother centriole and fuse to initiate cilium assembly. However, to this date, the early steps in cilia formation remain incompletely understood. Here, we demonstrate functional interplay between CEP19, FOP and CEP350 in ciliogenesis. Using three-dimensional structured-illumination microscopy (3D-SIM) imaging, we mapped the relative spatial distribution of these proteins at the distal end of the mother centriole and show that CEP350/FOP act upstream of CEP19 in their recruitment hierarchy. We demonstrate that CEP19 CRISPR KO cells are severely impaired in their ability to form cilia, analogous to the loss of function of CEP19 binding partners FOP and CEP350. Using GFP-tagged deletion constructs of CEP19, we show that the C-terminus of CEP19 is required for both its localization to centrioles and for its function in ciliogenesis. Critically, this region also mediates the interaction between CEP19 and FOP/CEP350. Interestingly, a morbid obesity-associated R82* truncated mutant of CEP19 cannot ciliate nor interact with FOP and CEP350, indicative of a putative role for CEP19 in ciliopathies. Finally, analysis of CEP19 KO cells using thin-section electron microscopy revealed marked defects in the docking of CVs to the distal end of the mother centrioles. Together, these data demonstrate a role for the CEP19, FOP and CEP350 module in ciliogenesis and the possible effect of disrupting their functions in ciliopathies.
DOI: 10.6084/m9.figshare.5107294.v1
title: Table S2 from CEP19 cooperates with FOP and CEP350 to drive early steps in the ciliogenesis programme

description: Primary cilia are microtubule-based sensory organelles necessary for efficient transduction of extracellular cues. To initiate cilia formation, ciliary vesicles (CVs) are transported to the vicinity of the centrosome where they dock to the distal end of the mother centriole and fuse to initiate cilium assembly. However, to this date, the early steps in cilia formation remain incompletely understood. Here, we demonstrate functional interplay between CEP19, FOP and CEP350 in ciliogenesis. Using three-dimensional structured-illumination microscopy (3D-SIM) imaging, we mapped the relative spatial distribution of these proteins at the distal end of the mother centriole and show that CEP350/FOP act upstream of CEP19 in their recruitment hierarchy. We demonstrate that CEP19 CRISPR KO cells are severely impaired in their ability to form cilia, analogous to the loss of function of CEP19 binding partners FOP and CEP350. Using GFP-tagged deletion constructs of CEP19, we show that the C-terminus of CEP19 is required for both its localization to centrioles and for its function in ciliogenesis. Critically, this region also mediates the interaction between CEP19 and FOP/CEP350. Interestingly, a morbid obesity-associated R82* truncated mutant of CEP19 cannot ciliate nor interact with FOP and CEP350, indicative of a putative role for CEP19 in ciliopathies. Finally, analysis of CEP19 KO cells using thin-section electron microscopy revealed marked defects in the docking of CVs to the distal end of the mother centrioles. Together, these data demonstrate a role for the CEP19, FOP and CEP350 module in ciliogenesis and the possible effect of disrupting their functions in ciliopathies.
DOI: 10.6084/m9.figshare.5107297.v1
title: Table S4 from CEP19 cooperates with FOP and CEP350 to drive early steps in the ciliogenesis programme

description: Primary cilia are microtubule-based sensory organelles necessary for efficient transduction of extracellular cues. To initiate cilia formation, ciliary vesicles (CVs) are transported to the vicinity of the centrosome where they dock to the distal end of the mother centriole and fuse to initiate cilium assembly. However, to this date, the early steps in cilia formation remain incompletely understood. Here, we demonstrate functional interplay between CEP19, FOP and CEP350 in ciliogenesis. Using three-dimensional structured-illumination microscopy (3D-SIM) imaging, we mapped the relative spatial distribution of these proteins at the distal end of the mother centriole and show that CEP350/FOP act upstream of CEP19 in their recruitment hierarchy. We demonstrate that CEP19 CRISPR KO cells are severely impaired in their ability to form cilia, analogous to the loss of function of CEP19 binding partners FOP and CEP350. Using GFP-tagged deletion constructs of CEP19, we show that the C-terminus of CEP19 is required for both its localization to centrioles and for its function in ciliogenesis. Critically, this region also mediates the interaction between CEP19 and FOP/CEP350. Interestingly, a morbid obesity-associated R82* truncated mutant of CEP19 cannot ciliate nor interact with FOP and CEP350, indicative of a putative role for CEP19 in ciliopathies. Finally, analysis of CEP19 KO cells using thin-section electron microscopy revealed marked defects in the docking of CVs to the distal end of the mother centrioles. Together, these data demonstrate a role for the CEP19, FOP and CEP350 module in ciliogenesis and the possible effect of disrupting their functions in ciliopathies.
DOI: 10.6084/m9.figshare.5107276
title: Supplementary Material for: Use of the Myocardial Performance Index in Decreased Fetal Movement Assessment: A Case-Control Study

description: <b><i>Objectives:</i></b> To determine whether there are any fetal cardiac function changes, as measured by the myocardial performance index (MPI), in pregnancies complicated by decreased fetal movement (DFM). <b><i>Methods:</i></b> We performed a prospective cross-sectional case-control study of 50 DFM and 50 uncomplicated third-trimester pregnancies matched within 2 gestational weeks. Routine ultrasound growth and well-being parameters as well as MPI were measured. Average MPI measurements and its component values were compared between the DFM and the control group, as were demographics, other ultrasound data, and perinatal outcomes. <b><i>Results:</i></b> Average left MPI (LMPI) and right MPI (RMPI) was similar between groups (LMPI: 0.54 ± 0.08 [DFM], 0.53 ± 0.08 [controls], <i>p</i> = 0.76; RMPI: 0.60 ± 0.12 (DFM), 0.59 ± 0.11 [controls], <i>p</i> = 0.79). However, subgroup analysis of DFM fetuses with (<i>n</i> = 20) or without (<i>n</i> = 30) any adverse perinatal outcome demonstrated modestly higher average RMPI and LMPI in the adverse perinatal outcome group (RMPI: 0.64 ± 0.08 vs. 0.57 ± 0.13, <i>p</i> = 0.02; LMPI: 0.56 ± 0.07 vs. 0.52 ± 0.07, <i>p</i> = 0.052). <b><i>Conclusion:</i></b> The MPI did not demonstrate clinically usable differences between the overall DFM population and controls. However, higher LMPI and RMPI values in the exploratory subgroup of DFM fetuses with adverse perinatal outcomes may warrant further exploration of the MPI in DFM.
DOI: 10.6084/m9.figshare.5107276.v1
title: Supplementary Material for: Use of the Myocardial Performance Index in Decreased Fetal Movement Assessment: A Case-Control Study

description: <b><i>Objectives:</i></b> To determine whether there are any fetal cardiac function changes, as measured by the myocardial performance index (MPI), in pregnancies complicated by decreased fetal movement (DFM). <b><i>Methods:</i></b> We performed a prospective cross-sectional case-control study of 50 DFM and 50 uncomplicated third-trimester pregnancies matched within 2 gestational weeks. Routine ultrasound growth and well-being parameters as well as MPI were measured. Average MPI measurements and its component values were compared between the DFM and the control group, as were demographics, other ultrasound data, and perinatal outcomes. <b><i>Results:</i></b> Average left MPI (LMPI) and right MPI (RMPI) was similar between groups (LMPI: 0.54 ± 0.08 [DFM], 0.53 ± 0.08 [controls], <i>p</i> = 0.76; RMPI: 0.60 ± 0.12 (DFM), 0.59 ± 0.11 [controls], <i>p</i> = 0.79). However, subgroup analysis of DFM fetuses with (<i>n</i> = 20) or without (<i>n</i> = 30) any adverse perinatal outcome demonstrated modestly higher average RMPI and LMPI in the adverse perinatal outcome group (RMPI: 0.64 ± 0.08 vs. 0.57 ± 0.13, <i>p</i> = 0.02; LMPI: 0.56 ± 0.07 vs. 0.52 ± 0.07, <i>p</i> = 0.052). <b><i>Conclusion:</i></b> The MPI did not demonstrate clinically usable differences between the overall DFM population and controls. However, higher LMPI and RMPI values in the exploratory subgroup of DFM fetuses with adverse perinatal outcomes may warrant further exploration of the MPI in DFM.
DOI: 10.6084/m9.figshare.5107207
title: Time-budget data from 'Bright birds are cautious' from Bright birds are cautious: seasonally conspicuous plumage prompts risk avoidance in male superb fairy-wrens

description: Time-budget data
DOI: 10.6084/m9.figshare.5107204
title: Supplemental Table S3 from Transcriptional response to West Nile virus infection in the zebra finch (<i>Taeniopygia guttata</i>)

description: Spreadsheet of differentially expressed genes (adjusted p value &lt; 0.10) from the DEseq2 analysis.