cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.877061
title: A method for quantifying, visualising, and analysing gastropod shell form

description: Supplementary materials Abstract Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genus Opisthostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approaches for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.
DOI: 10.6084/m9.figshare.877048
title: Optical Binding Movies

description: Evanescent wave optical binding of 1 micron diameter silica microspheres
DOI: 10.6084/m9.figshare.877092.v1
title: 1. From Punch-Drunk to C.T.E: Critchley’s Missing Text

description: Archival research
DOI: 10.6084/m9.figshare.877048.v2
title: Optical Binding Movies

description: Evanescent wave optical binding of 1 micron diameter silica microspheres
DOI: 10.6084/m9.figshare.877048.v1
title: new fileset

description: Evanescent wave optical binding of 1 micron diameter silica microspheres
DOI: 10.6084/m9.figshare.877037
title: Data files Prmt7 and adipocyte differentiation

description: Dataset 1: Dataset for Fig.1B<br>Quantification of Prmt7 protein levels in differentiating C3H10T1/2 cells. Column A describes the time when cells were harvested. Columns B to E show the signal intensities of Prmt7 and PI3K from two independent experiments, quantified by ImageJ. Columns F and G show the ratio of Prmt7 levels to PI3K levels for each sample in each experiment. Columns H and I show relative Prmt7 levels where the day 0 sample in each experiment is normalized to 1. Column J shows the mean of the relative Prmt7 levels from the two independent experiments. Dataset 2: Dataset for Fig.2B<br>Quantification of Prmt7 protein levels in the knockdown and over-expression C3H10T1/2 cells. Column A shows the names of the cells. Columns B to E show the signal intensities of Prmt7 and PI3K from two independent experiments, quantified by ImageJ. Columns F and G show the ratio of Prmt7 levels to PI3K levels for each sample in each experiment. Columns H and I show relative Prmt7 levels where the shControl and the pBABE vector sample in each experiment is normalized to 1. Column J shows the mean of the relative Prmt7 levels from the two independent experiments. Dataset 3: Dataset for Fig.3<br>Cell counting results. Column A shows the time when cell numbers were counted. Column B shows the names of the cells. Columns C to F show the numbers of the cells (x105) from two independent experiments with two replicates in each experiment. Column G shows the mean of the cell numbers. Column H shows the standard deviation (SD) of the cell numbers. Dataset 4: Dataset for Fig.4B<br>Quantification of Oil-Red O staining on day 6 post-differentiated C3H10T1/2 cells. Column A shows the names of the cells. Columns B to Column E show the values of OD500 from two independent experiments with two replicates in each experiment. Column F represents the mean of the OD500 values. Column F shows the mean values. Column G shows the standard deviation (SD) of the OD500 values. Dataset 5: Dataset for Fig.4D<br>Real-time qPCR results for the expression of selected genes in day 6 post-differentiated C3H10T1/2 cells. Column A shows to the names of the transcripts. Column B shows the names of the cells. Column C indicates the experiment number. Columns D and E show raw Ct values from two replicates from each sample. Column F shows the mean raw Ct value. Columns G to K show the following values: delta Ct (Ct – Ct5S rRNA), delta delta Ct (dCt - dCtshCtrl), fold change (2^(-ddCt)), the mean of the fold change, and the standard deviation (SD) of the fold change.
DOI: 10.6084/m9.figshare.877042
title: Sanitizing with quality score

description: Publicly available RNA-Seq data (SRR100067) from wild type Neurospora crassa 74-OR23-1VA were obtained from the NCBI, http://www.ncbi.nlm.nih.gov/Traces/sra to generate these datasets
DOI: 10.6084/m9.figshare.877061.v5
title: A method for quantifying, visualising, and analysing gastropod shell form

description: Liew, T. S., & Schilthuizen, M. (2013). A method for quantifying, visualising, and analysing gastropod shell form (No. e157v1). PeerJ PrePrints. Supplementary materials Abstract Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genus Opisthostoma, which exhibit great variability in shell form. The outcome suggests that our method is more robust, reproducible, and versatile than the conventional traditional and geometric morphometric approaches for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.
DOI: 10.6084/m9.figshare.877037.v1
title: Data files Prmt7 and adipocyte differentiation

description: Dataset 1: Dataset for Fig.1B<br>Quantification of Prmt7 protein levels in differentiating C3H10T1/2 cells. Column A describes the time when cells were harvested. Columns B to E show the signal intensities of Prmt7 and PI3K from two independent experiments, quantified by ImageJ. Columns F and G show the ratio of Prmt7 levels to PI3K levels for each sample in each experiment. Columns H and I show relative Prmt7 levels where the day 0 sample in each experiment is normalized to 1. Column J shows the mean of the relative Prmt7 levels from the two independent experiments. Dataset 2: Dataset for Fig.2B<br>Quantification of Prmt7 protein levels in the knockdown and over-expression C3H10T1/2 cells. Column A shows the names of the cells. Columns B to E show the signal intensities of Prmt7 and PI3K from two independent experiments, quantified by ImageJ. Columns F and G show the ratio of Prmt7 levels to PI3K levels for each sample in each experiment. Columns H and I show relative Prmt7 levels where the shControl and the pBABE vector sample in each experiment is normalized to 1. Column J shows the mean of the relative Prmt7 levels from the two independent experiments. Dataset 3: Dataset for Fig.3<br>Cell counting results. Column A shows the time when cell numbers were counted. Column B shows the names of the cells. Columns C to F show the numbers of the cells (x105) from two independent experiments with two replicates in each experiment. Column G shows the mean of the cell numbers. Column H shows the standard deviation (SD) of the cell numbers. Dataset 4: Dataset for Fig.4B<br>Quantification of Oil-Red O staining on day 6 post-differentiated C3H10T1/2 cells. Column A shows the names of the cells. Columns B to Column E show the values of OD500 from two independent experiments with two replicates in each experiment. Column F represents the mean of the OD500 values. Column F shows the mean values. Column G shows the standard deviation (SD) of the OD500 values. Dataset 5: Dataset for Fig.4D<br>Real-time qPCR results for the expression of selected genes in day 6 post-differentiated C3H10T1/2 cells. Column A shows to the names of the transcripts. Column B shows the names of the cells. Column C indicates the experiment number. Columns D and E show raw Ct values from two replicates from each sample. Column F shows the mean raw Ct value. Columns G to K show the following values: delta Ct (Ct – Ct5S rRNA), delta delta Ct (dCt - dCtshCtrl), fold change (2^(-ddCt)), the mean of the fold change, and the standard deviation (SD) of the fold change.
DOI: 10.6084/m9.figshare.877042.v2
title: Sanitizing with quality score

description: Publicly available RNA-Seq data (SRR100067) from wild type Neurospora crassa 74-OR23-1VA were obtained from the NCBI, http://www.ncbi.nlm.nih.gov/Traces/sra to generate these datasets
DOI: 10.6084/m9.figshare.877061.v6
title: A method for quantifying, visualising, and analysing gastropod shell form

description: Liew, T. S., & Schilthuizen, M. (2013). A method for quantifying, visualising, and analysing gastropod shell form (No. e157v1). PeerJ PrePrints. Supplementary materials Abstract Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genus Opisthostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approaches for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.
DOI: 10.6084/m9.figshare.877042.v1
title: Sanitizing with quality score: implication for de novo transcriptome reconstruction of Illumina reads

description: Publicly available RNA-Seq data (SRR100067) from wild type Neurospora crassa 74-OR23-1VA were obtained from the NCBI, http://www.ncbi.nlm.nih.gov/Traces/sra to generate these datasets
DOI: 10.6084/m9.figshare.877031
title: Code for thesis

description: Code for thesis
DOI: 10.6084/m9.figshare.877061.v7
title: A method for quantifying, visualising, and analysing gastropod shell form

description: Liew, T. S., & Schilthuizen, M. (2014). A method for quantifying, visualising, and analysing gastropod shell form (No. e157v3). PeerJ PrePrints. https://peerj.com/preprints/157v3/ Supplementary materials Abstract Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genus Opisthostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approaches for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.
DOI: 10.6084/m9.figshare.877018
title: Data Sets Tm values for HRM assay specificity

description: Data Set 1. Tm Values for HRM duplex assay specificity<br>This data set contains the individual Tm values for the specificity testing of the vaginal/skin, blood/menstrual and saliva/semen HRM duplex assay specificity presented in Table 2. Individual donors are listed according to body fluid or tissue type with the Tm values (oC) recorded under each biomarker. IL19 = vaginal biomarker, ALAS2 = blood , HTN3 = saliva biomarker, IL1F7 = skin biomarker, MMP10 = menstrual blood, TGM4 = semen biomarker, n.d. = not detected in body fluid of interest, empty cell = no detection Data Set 2. Tm Values for ‘All Body Fluids’ Hexaplex Assay Specificity<br>This data set contains the individual Tm values for specificity testing of the ‘all body fluids’ hexaplex HRM assay presented in Table 4. Individual donors are listed according to body fluid or tissue type with the observed Tm values recorded under each biomarker. n.d. = not detected in body fluid of interest
DOI: 10.6084/m9.figshare.877031.v1
title: Code for thesis

description: Code for thesis
DOI: 10.6084/m9.figshare.877018.v1
title: Data Sets Tm values for HRM assay specificity

description: Data Set 1. Tm Values for HRM duplex assay specificity<br>This data set contains the individual Tm values for the specificity testing of the vaginal/skin, blood/menstrual and saliva/semen HRM duplex assay specificity presented in Table 2. Individual donors are listed according to body fluid or tissue type with the Tm values (oC) recorded under each biomarker. IL19 = vaginal biomarker, ALAS2 = blood , HTN3 = saliva biomarker, IL1F7 = skin biomarker, MMP10 = menstrual blood, TGM4 = semen biomarker, n.d. = not detected in body fluid of interest, empty cell = no detection Data Set 2. Tm Values for ‘All Body Fluids’ Hexaplex Assay Specificity<br>This data set contains the individual Tm values for specificity testing of the ‘all body fluids’ hexaplex HRM assay presented in Table 4. Individual donors are listed according to body fluid or tissue type with the observed Tm values recorded under each biomarker. n.d. = not detected in body fluid of interest
DOI: 10.6084/m9.figshare.877061.v8
title: A method for quantifying, visualising, and analysing gastropod shell form

description: Supplementary materials Abstract Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genus Opisthostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approaches for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.
DOI: 10.6084/m9.figshare.875630.v1
title: Effect of PEG on the intracellular localisation of HA2 fusion peptides functionalised gold nanoparticles; nanoparticles capped with HA2, PEG and CALNN (Figure 2C-D dataset)

description: Gold nanoparticles were capped with 10% CCALNN-dHA2, 20% CCALNN-PEG and 70% CALNN peptides. HeLa cells were incubated with these gold nanoparticles. 42 TEM images are shown. The first 29 images (1-29) were used for the quantification shown in Fig 2 of the article. The full experimental details can be found in the article.
DOI: 10.6084/m9.figshare.877061.v9
title: A method for quantifying, visualising, and analysing gastropod shell form

description: Supplementary materials Abstract Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genus Opisthostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approaches for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.
DOI: 10.6084/m9.figshare.875584.v1
title: Effect of PEG on the intracellular localisation of HA2 fusion peptides functionalised gold nanoparticles; nanoparticles capped with HA2 and CALNN (Figure 2A-B dataset)

description: Gold nanoparticles were capped with 10% CCALNN-dHA2 and 90% CALNN peptides. HeLa cells were incubated with these gold nanoparticles. 36 TEM images are shown. The first 30 images (1-30) were used for the quantification shown in Fig 2 of the article. The full experimental details can be found in the article.
DOI: 10.6084/m9.figshare.875546
title: Analiza ryzyka przedsiębiorstwa X z branży wytwarzania i przetwarzania produktów rafinacji ropy naftowej

description: Aim of the study <em><strong>"Analysis of the company's risk X with industry production and processing of refined petroleum products"</strong></em> was to conduct a study on the analysis of financial condition on the basis of calculations and analyzes. By applying the <strong>Financial Health Index</strong> allow comparison of solvency, financial flexibility and generally understood condition in 2006-2007.
DOI: 10.6084/m9.figshare.877061.v11
title: A method for quantifying, visualising, and analysing gastropod shell form

description: Supplementary materials Abstract Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genus Opisthostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approaches for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.
DOI: 10.6084/m9.figshare.877061.v10
title: A method for quantifying, visualising, and analysing gastropod shell form

description: Supplementary materials Abstract Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genus Opisthostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approaches for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.