cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5756421
title: Supplementary Material for: Longitudinal Analysis of Drusen Volume in Intermediate Age-Related Macular Degeneration Using Two Spectral-Domain Optical Coherence Tomography Scan Patterns

description: <b><i>Purpose:</i></b> To evaluate two different spectral-domain optical coherence tomography (SD-OCT) scan patterns in eyes with intermediate age-related macular degeneration (AMD) for the longitudinal assessment of drusen volume. <b><i>Methods:</i></b> The data of 38 eyes of 38 AMD patients (age 69.97 ± 6.08 years) were included. The longitudinal drusen volume over 4 years was analyzed by annual SD-OCT raster scanning (field size 20 × 15°). Two raster scan patterns (A/B) differed in the distance between neighboring B-scans (240 vs. 30 µm) and in the number of averaged frames (4 vs. 15). <b><i>Results:</i></b> The mean drusen volume at baseline was 0.213 ± 0.100 mm<sup>3</sup> (pattern A) and 0.219 ± 0.103 mm<sup>3</sup> (pattern B) (<i>p</i> = 0.937). Linear mixed-effect models showed no significant difference for the change within 4 years for both pattern A (<i>p</i> = 0.8) and pattern B (<i>p</i> = 0.8). <b><i>Conclusions:</i></b> The results indicate that the performance of interpolation algorithms may be sufficient to balance for less dense raster scanning with regard to quantification of longitudinal drusen volume, which can be used as a surrogate marker for AMD progression in future clinical trials.
DOI: 10.6084/m9.figshare.5756421.v1
title: Supplementary Material for: Longitudinal Analysis of Drusen Volume in Intermediate Age-Related Macular Degeneration Using Two Spectral-Domain Optical Coherence Tomography Scan Patterns

description: <b><i>Purpose:</i></b> To evaluate two different spectral-domain optical coherence tomography (SD-OCT) scan patterns in eyes with intermediate age-related macular degeneration (AMD) for the longitudinal assessment of drusen volume. <b><i>Methods:</i></b> The data of 38 eyes of 38 AMD patients (age 69.97 ± 6.08 years) were included. The longitudinal drusen volume over 4 years was analyzed by annual SD-OCT raster scanning (field size 20 × 15°). Two raster scan patterns (A/B) differed in the distance between neighboring B-scans (240 vs. 30 µm) and in the number of averaged frames (4 vs. 15). <b><i>Results:</i></b> The mean drusen volume at baseline was 0.213 ± 0.100 mm<sup>3</sup> (pattern A) and 0.219 ± 0.103 mm<sup>3</sup> (pattern B) (<i>p</i> = 0.937). Linear mixed-effect models showed no significant difference for the change within 4 years for both pattern A (<i>p</i> = 0.8) and pattern B (<i>p</i> = 0.8). <b><i>Conclusions:</i></b> The results indicate that the performance of interpolation algorithms may be sufficient to balance for less dense raster scanning with regard to quantification of longitudinal drusen volume, which can be used as a surrogate marker for AMD progression in future clinical trials.
DOI: 10.6084/m9.figshare.5756382
title: Relationship between subjective assessment of ram semen wave motion and objective assessment by optical flow and beads motion

description: The optical flow entropy (OFENT) and the optical flow entropy autocorrelation (AUTO) showed a negative nonlinear relation with the wave motion score (WMS) over the 1-5 range (Fig. 3). The average (AVG) and standard deviation of the average speed (STD) parameters describing the speed of the beads showed a positive nonlinear relation with the wave motion score over the 1-5 range (Fig. 4). AVG and STD were significantly higher when the wave motion score was&gt; 4. Cohen's kappa coefficient was calculated to assess the concordance of the ejaculate selection based on the AVG, STD and OFENT parameters or the subjective wave motion score. The thresholds values for AVG, STD and OFENT were, respectively, 1, 0.7 and -2 and gave similar kappa values of 0.49, 0.50 and 0.45 respectively. Regarding the accuracy of detection of bad quality ejaculates and the ability to discard semen with potentially low fertility, the AVG parameter showed the highest sensitivity and specificity with values of 88 % and 77 % respectively. <br>
DOI: 10.21954/ou.rd.5756379
title: Two Week Diabetes Data Set

description: This is a data set of 2 weeks of blood glucose, insulin and carbohydrate intake data used as a standard data set to evaluate diabetes apps.
DOI: 10.6084/m9.figshare.5756373
title: CEN timeseries data

description: testing CEN timeseries
DOI: 10.6084/m9.figshare.5756373.v2
title: CEN timeseries data

description: testing CEN timeseries
DOI: 10.6084/m9.figshare.5756373.v1
title: CEN timeseries data

description: testing CEN timeseries
DOI: 10.6084/m9.figshare.5756319
title: Supplementary Material for: Associations of Fibroblast Growth Factor 23 with Markers of Inflammation and Leukocyte Transmigration in Chronic Kidney Disease

description: <b><i>Background:</i></b> Patients with chronic kidney disease (CKD) show elevated levels of inflammatory markers and have an increased risk of infections as well as cardiovascular morbidity. Recent studies have implied effects of fibroblast growth factor 23 (FGF23) on inflammation in CKD. We analyzed potential correlations between levels of FGF23 with pro-inflammatory chemokines and markers of leukocyte transmigration in CKD patients. <b><i>Methods:</i></b> One hundred three patients with CKD 2–5ND and 54 healthy controls, had biochemical markers in blood and urine analyzed according to routine protocol. Pro-inflammatory cytokines were analyzed by Milliplex technique and leukocyte CD11b adhesion molecule expression was measured by flow cytometry. FGF23 levels were measured with ELISA technique. Treatment of leukocytes from healthy blood donors with FGF23 was performed in vitro and effects analyzed by flow cytometry. <b><i>Results:</i></b> Tumor necrosis factor-alpha, RANTES and interleukin (IL)-12 levels were significantly higher (<i>p</i> = 0.001, <i>p</i> &lt; 0.001, and <i>p</i> &lt; 0.001) in patients with CKD. Elevated FGF23 levels in the CKD group correlated to glomerular filtration rate, parathyroid hormone, urinary albumin excretion and phosphate as well as to IL-12 and RANTES. CD11b expression on resting granulocytes and monocytes, and on activated monocytes, was associated with FGF23<i>.</i> In vitro treatment of leukocytes with FGF23 reduced CD11b expression in resting as well as in formyl-methyinoyl-leucyl-phenylalanine-stimulated granulocytes (<i>p</i> = 0.03). <b><i>Conclusion:</i></b><i></i> FGF23 levels are associated with various inflammatory markers such as pro-inflammatory cytokines and adhesion molecules on innate immune cells. However, further studies are warranted to define the direct role of FGF23 in modulation of the innate immune system in CKD.
DOI: 10.6084/m9.figshare.5756304
title: Cryptosporidium mobile-immobile model

description: The MATLAB source code used to generate the model simulations within Drummond, J.D., F. Boano, E.R. Atwill, X. Li, T. Harter, A.I. Packman (2018). Cryptosporidium oocyst persistence in agricultural streams – a mobile-immobile model framework assessment, Scientific Reports, 8, 4603, doi:10.1038/s41598-018-22784-x.<br>Abstract: Rivers are a means of rapid and long-distance transmission of pathogenic microorganisms from upstream terrestrial sources. Pathogens enter streams and rivers via overland flow, shallow groundwater discharge, and direct inputs. Of concern is the protozoal parasite, Cryptosporidium, which can remain infective for weeks to months under cool and moist conditions, with the infectiousstage (oocysts) largely resistant to chlorination. We applied a mobile-immobile model framework to assess Cryptosporidium transport and retention in streams, that also accounts for inactivation. The model is applied to California’s Central Valley where Cryptosporidium exposure can be at higher risk due to agricultural and wildlife nonpoint sources. The results demonstrate that hyporheic exchange is an important process to include in models characterizing pathogen dynamics in streams, delaying downstream transmission and allowing for immobilization processes, such as reversible filtration in the sediments, to occur. Although in-stream concentrations decrease relatively quickly (within hours), pathogen accumulation of up to 66% of the inputs due to immobilization processes in the sediments and slower moving surface water could result in long retention times (months to years). The modelappropriately estimates baseflow pathogen accumulation and can help predict the potential loads of resuspended pathogens in response to a storm event.
DOI: 10.6084/m9.figshare.5756304.v1
title: Cryptosporidium mobile-immobile model

description: The MATLAB source code used to generate the model simulations within Drummond, J.D., F. Boano, E.R. Atwill, X. Li, T. Harter, A.I. Packman (2018). Cryptosporidium oocyst persistence in agricultural streams – a mobile-immobile model framework assessment, Scientific Reports, 8, 4603, doi:10.1038/s41598-018-22784-x.<br>Abstract: Rivers are a means of rapid and long-distance transmission of pathogenic microorganisms from upstream terrestrial sources. Pathogens enter streams and rivers via overland flow, shallow groundwater discharge, and direct inputs. Of concern is the protozoal parasite, Cryptosporidium, which can remain infective for weeks to months under cool and moist conditions, with the infectiousstage (oocysts) largely resistant to chlorination. We applied a mobile-immobile model framework to assess Cryptosporidium transport and retention in streams, that also accounts for inactivation. The model is applied to California’s Central Valley where Cryptosporidium exposure can be at higher risk due to agricultural and wildlife nonpoint sources. The results demonstrate that hyporheic exchange is an important process to include in models characterizing pathogen dynamics in streams, delaying downstream transmission and allowing for immobilization processes, such as reversible filtration in the sediments, to occur. Although in-stream concentrations decrease relatively quickly (within hours), pathogen accumulation of up to 66% of the inputs due to immobilization processes in the sediments and slower moving surface water could result in long retention times (months to years). The modelappropriately estimates baseflow pathogen accumulation and can help predict the potential loads of resuspended pathogens in response to a storm event.
DOI: 10.6084/m9.figshare.5756280
title: Supplementary Material for: Cooperative Effects of Q10, Vitamin D3, and L-Arginine on Cardiac and Endothelial Cells

description: This work demonstrates the cooperative effect of Q10, vitamin D<sub>3,</sub> and L-arginine on both cardiac and endothelial cells. The effects of Q10, L-arginine, and vitamin D<sub>3</sub> alone or combined on cell viability, nitric oxide, and reactive oxygen species productions in endothelial and cardiac cells were studied. Moreover, the involvement of PI3K/Akt and ERK/MAPK pathways leading to eNOS activation as well as the involvement of vitamin D receptor were also investigated. The same agents were tested in an animal model to verify vasodilation, nitric oxide, and reactive oxygen species production. The data obtained in this work demonstrate for the first time the beneficial and cooperative effect of stimulation with Q10, L-arginine, and vitamin D<sub>3</sub>. Indeed, in cardiac and endothelial cells, Q10, L-arginine, and vitamin D<sub>3</sub> combined were able to induce a nitric oxide production higher than the that induced by the 3 substances alone. The effects on vasodilation induced by cooperative stimulation have been confirmed in an in vivo model as well. The use of a combination of Q10, L-arginine, and vitamin D to counteract increased free radical production could be a potential method to reduce myocardial injury or the effects of aging on the heart.
DOI: 10.6084/m9.figshare.5756280.v1
title: Supplementary Material for: Cooperative Effects of Q10, Vitamin D3, and L-Arginine on Cardiac and Endothelial Cells

description: This work demonstrates the cooperative effect of Q10, vitamin D<sub>3,</sub> and L-arginine on both cardiac and endothelial cells. The effects of Q10, L-arginine, and vitamin D<sub>3</sub> alone or combined on cell viability, nitric oxide, and reactive oxygen species productions in endothelial and cardiac cells were studied. Moreover, the involvement of PI3K/Akt and ERK/MAPK pathways leading to eNOS activation as well as the involvement of vitamin D receptor were also investigated. The same agents were tested in an animal model to verify vasodilation, nitric oxide, and reactive oxygen species production. The data obtained in this work demonstrate for the first time the beneficial and cooperative effect of stimulation with Q10, L-arginine, and vitamin D<sub>3</sub>. Indeed, in cardiac and endothelial cells, Q10, L-arginine, and vitamin D<sub>3</sub> combined were able to induce a nitric oxide production higher than the that induced by the 3 substances alone. The effects on vasodilation induced by cooperative stimulation have been confirmed in an in vivo model as well. The use of a combination of Q10, L-arginine, and vitamin D to counteract increased free radical production could be a potential method to reduce myocardial injury or the effects of aging on the heart.
DOI: 10.6084/m9.figshare.5756277
title: Source-modelling auditory processes of EEG data using EEGLAB and Brainstorm

description: This zip file provides all necessary data, software (Matlab Toolboxes) and analysis scripts for the tutorial article 'Source-modelling auditory processes of EEG data using EEGLAB and Brainstorm' by M Stropahl, AKR Bauer, S Debener, MG Bleichner. Front. Neurosci. - Brain Imaging Methods 2018
DOI: 10.6084/m9.figshare.5756277.v2
title: Source-modelling auditory processes of EEG data using EEGLAB and Brainstorm

description: This zip file provides all necessary data, software (Matlab Toolboxes) and analysis scripts for the tutorial article 'Source-modelling auditory processes of EEG data using EEGLAB and Brainstorm' by M Stropahl, AKR Bauer, S Debener, MG Bleichner. Front. Neurosci. - Brain Imaging Methods 2018
DOI: 10.6084/m9.figshare.5756277.v1
title: Full Dataset

description: This zip file provides all necessary data, software (Matlab Toolboxes) and analysis scripts for the tutorial article 'Source-modelling auditory processes of EEG data using EEGLAB and Brainstorm' by M Stropahl, AKR Bauer, S Debener, MG Bleichner. Front. Neurosci. - Brain Imaging Methods 2018
DOI: 10.6084/m9.figshare.5756103
title: A review of plan library approaches in adaptive radiotherapy of bladder cancer

description: <b>Background:</b> Large variations in the shape and size of the bladder volume are commonly observed in bladder cancer radiotherapy (RT). The clinical target volume (CTV) is therefore frequently inadequately treated and large isotropic margins are inappropriate in terms of dose to organs at risk (OAR); thereby making adaptive radiotherapy (ART) attractive for this tumour site. There are various methods of ART delivery, however, for bladder cancer, plan libraries are frequently used. <b>Material and methods:</b> A review of published studies on plan libraries for bladder cancer using four databases (Pubmed, Science Direct, Embase and Cochrane Library) was conducted. The endpoints selected were accuracy and feasibility of initiation of a plan library strategy into a RT department. <b>Results:</b> Twenty-four articles were included in this review. The majority of studies reported improvement in accuracy with 10 studies showing an improvement in planning target volume (PTV) and CTV coverage with plan libraries, some by up to 24%. Seventeen studies showed a dose reduction to OARs, particularly the small bowel V45Gy, V40Gy, V30Gy and V10Gy, and the rectal V30Gy. However, the occurrence of no suitable plan was reported in six studies, with three studies showing no significant difference between adaptive and non-adaptive strategies in terms of target coverage. In addition, inter-observer variability in plan selection appears to remain problematic. The additional resources, education and technology required for the initiation of plan library selection for bladder cancer may hinder its routine clinical implementation, with eight studies illustrating increased treatment time required. <b>Conclusions:</b> While there is a growing body of evidence in support of plan libraries for bladder RT, many studies differed in their delivery approach. The advent of the clinical use of the MRI-linear accelerator will provide RT departments with the opportunity to consider daily online adaption for bladder cancer as an alternate to plan library approaches.
DOI: 10.6084/m9.figshare.5756103.v1
title: A review of plan library approaches in adaptive radiotherapy of bladder cancer

description: <b>Background:</b> Large variations in the shape and size of the bladder volume are commonly observed in bladder cancer radiotherapy (RT). The clinical target volume (CTV) is therefore frequently inadequately treated and large isotropic margins are inappropriate in terms of dose to organs at risk (OAR); thereby making adaptive radiotherapy (ART) attractive for this tumour site. There are various methods of ART delivery, however, for bladder cancer, plan libraries are frequently used. <b>Material and methods:</b> A review of published studies on plan libraries for bladder cancer using four databases (Pubmed, Science Direct, Embase and Cochrane Library) was conducted. The endpoints selected were accuracy and feasibility of initiation of a plan library strategy into a RT department. <b>Results:</b> Twenty-four articles were included in this review. The majority of studies reported improvement in accuracy with 10 studies showing an improvement in planning target volume (PTV) and CTV coverage with plan libraries, some by up to 24%. Seventeen studies showed a dose reduction to OARs, particularly the small bowel V45Gy, V40Gy, V30Gy and V10Gy, and the rectal V30Gy. However, the occurrence of no suitable plan was reported in six studies, with three studies showing no significant difference between adaptive and non-adaptive strategies in terms of target coverage. In addition, inter-observer variability in plan selection appears to remain problematic. The additional resources, education and technology required for the initiation of plan library selection for bladder cancer may hinder its routine clinical implementation, with eight studies illustrating increased treatment time required. <b>Conclusions:</b> While there is a growing body of evidence in support of plan libraries for bladder RT, many studies differed in their delivery approach. The advent of the clinical use of the MRI-linear accelerator will provide RT departments with the opportunity to consider daily online adaption for bladder cancer as an alternate to plan library approaches.
DOI: 10.6084/m9.figshare.5756088
title: ESM Dataset S2: Clustering Data from Primate social group sizes exhibit a regular scaling pattern with natural attractors

description: Primate groups vary considerably in size across species. Nonetheless, the distribution of mean species group size has a regular scaling pattern with preferred sizes approximating 2.5, 5, 15, 30 and 50 individuals (although strepsirrhines lack the latter two), with a scaling ratio of approximately 2.5 similar to that observed in humans social networks. These clusters appear to form distinct social grades that are associated with rapid evolutionary change, presumably in response to intense environmental selection pressures. These findings may have wider implications for other highly social mammal taxa.
DOI: 10.6084/m9.figshare.5756088.v1
title: ESM Dataset S2: Clustering Data from Primate social group sizes exhibit a regular scaling pattern with natural attractors

description: Primate groups vary considerably in size across species. Nonetheless, the distribution of mean species group size has a regular scaling pattern with preferred sizes approximating 2.5, 5, 15, 30 and 50 individuals (although strepsirrhines lack the latter two), with a scaling ratio of approximately 2.5 similar to that observed in humans social networks. These clusters appear to form distinct social grades that are associated with rapid evolutionary change, presumably in response to intense environmental selection pressures. These findings may have wider implications for other highly social mammal taxa.
DOI: 10.6084/m9.figshare.5756085
title: ESM Dataset S1: Group Size Data from Primate social group sizes exhibit a regular scaling pattern with natural attractors

description: Primate groups vary considerably in size across species. Nonetheless, the distribution of mean species group size has a regular scaling pattern with preferred sizes approximating 2.5, 5, 15, 30 and 50 individuals (although strepsirrhines lack the latter two), with a scaling ratio of approximately 2.5 similar to that observed in humans social networks. These clusters appear to form distinct social grades that are associated with rapid evolutionary change, presumably in response to intense environmental selection pressures. These findings may have wider implications for other highly social mammal taxa.
DOI: 10.6084/m9.figshare.5756085.v1
title: ESM Dataset S1: Group Size Data from Primate social group sizes exhibit a regular scaling pattern with natural attractors

description: Primate groups vary considerably in size across species. Nonetheless, the distribution of mean species group size has a regular scaling pattern with preferred sizes approximating 2.5, 5, 15, 30 and 50 individuals (although strepsirrhines lack the latter two), with a scaling ratio of approximately 2.5 similar to that observed in humans social networks. These clusters appear to form distinct social grades that are associated with rapid evolutionary change, presumably in response to intense environmental selection pressures. These findings may have wider implications for other highly social mammal taxa.