cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7016390.v2
title: Supplementary Material for: MACUSTAR: Development and Clinical Validation of Functional, Structural, and Patient-Reported Endpoints in Intermediate Age-Related Macular Degeneration

description: <b><i>Purpose:</i></b> Currently, no outcome measures are clinically validated and accepted as clinical endpoints by regulatory agencies for drug development in intermediate age-related macular degeneration (iAMD). The MACUSTAR Consortium, a public-private research group funded by the European Innovative Medicines Initiative intends to close this gap. <b><i>Procedures:</i></b> Development of study protocol and statistical analysis plan including predictive modelling of multimodal endpoints based on a review of the literature and expert consensus. <b><i>Results:</i></b> This observational study consists of a cross-sectional and a longitudinal part. Functional outcome measures assessed under low contrast and low luminance have the potential to detect progression of visual deficit within iAMD and to late AMD. Structural outcome measures will be multimodal and investigate topographical relationships with function. Current patient-reported outcome measures (PROMs) are not acceptable to regulators and may not capture the functional deficit specific to iAMD with needed precision, justifying development of novel PROMs for iAMD. The total sample size will be <i>n</i> = 750, consisting mainly of subjects with iAMD (<i>n</i> = 600). <b><i>Conclusions:</i></b> As clinical endpoints currently accepted by regulators cannot detect functional loss or patient-relevant impact in iAMD, we will clinically validate novel candidate endpoints for iAMD.
DOI: 10.6084/m9.figshare.7016390.v1
title: Supplementary Material for: MACUSTAR: Development and Clinical Validation of Functional, Structural, and Patient-Reported Endpoints in Intermediate Age-Related Macular Degeneration

description: <b><i>Purpose:</i></b> Currently, no outcome measures are clinically validated and accepted as clinical endpoints by regulatory agencies for drug development in intermediate age-related macular degeneration (iAMD). The MACUSTAR Consortium, a public-private research group funded by the European Innovative Medicines Initiative intends to close this gap. <b><i>Procedures:</i></b> Development of study protocol and statistical analysis plan including predictive modelling of multimodal endpoints based on a review of the literature and expert consensus. <b><i>Results:</i></b> This observational study consists of a cross-sectional and a longitudinal part. Functional outcome measures assessed under low contrast and low luminance have the potential to detect progression of visual deficit within iAMD and to late AMD. Structural outcome measures will be multimodal and investigate topographical relationships with function. Current patient-reported outcome measures (PROMs) are not acceptable to regulators and may not capture the functional deficit specific to iAMD with needed precision, justifying development of novel PROMs for iAMD. The total sample size will be <i>n</i> = 750, consisting mainly of subjects with iAMD (<i>n</i> = 600). <b><i>Conclusions:</i></b> As clinical endpoints currently accepted by regulators cannot detect functional loss or patient-relevant impact in iAMD, we will clinically validate novel candidate endpoints for iAMD.
DOI: 10.17045/sthlmuni.7016369
title: Open data: Frequency mismatch negativity and visual load

description: Wiens, S., van Berlekom, E., Szychowska, M., & Eklund, R. (2019). Visual Perceptual Load Does Not Affect the Frequency Mismatch Negativity. Frontiers in Psychology, 10(1970). doi:10.3389/fpsyg.2019.01970<br><br>We manipulated visual perceptual load (high and low load) while we recorded electroencephalography. Event-related potentials (ERPs) were computed from these data.<br><br>OSF_*.pdf contains the preregistration at open science framework (osf).<br>https://doi.org/10.17605/OSF.IO/EWG9X<br><br>ERP_2019_rawdata_bdf.zip contains the raw eeg data files that were recorded with a biosemi system (www.biosemi.com). The files can be opened in matlab with the fieldtrip toolbox. <br>https://www.mathworks.com/products/matlab.html<br>http://www.fieldtriptoolbox.org/<br><br>ERP_2019_visual_load_fieldtrip_scripts.zip contains all the matlab scripts that were used to process the ERP data with the toolbox fieldtrip. http://www.fieldtriptoolbox.org/<br><br>ERP_2019_fieldtrip_mat_*.zip contain the final, preprocessed individual data files. They can be opened with matlab.<br><br>ERP_2019_visual_load_python_scripts.zip contains the python scripts for the main task. They need python (https://www.python.org/) and psychopy (http://www.psychopy.org/)<br><br>ERP_2019_visual_load_wmc_R_scripts.zip contains the R scripts to process the working memory capacity (wmc) data. https://www.r-project.org/.<br><br>ERP_2019_visual_load_R_scripts.zip contains the R scripts to analyze the data and the output files with figures (eg scatterplots). https://www.r-project.org/.<br>
DOI: 10.6084/m9.figshare.7016372
title: Varicella Zoster FastQC data

description: FastQC reports - Varicella Zoster Virus long-read sequencing dataset
DOI: 10.17045/sthlmuni.7016369.v1
title: Open data: Frequency mismatch negativity and visual load

description: Wiens, S., van Berlekom, E., Szychowska, M., & Eklund, R. (2019). Visual Perceptual Load Does Not Affect the Frequency Mismatch Negativity. Frontiers in Psychology, 10(1970). doi:10.3389/fpsyg.2019.01970<br><br>osf_.pdf contains the preregistration at open science framework (osf).<br>https://doi.org/10.17605/OSF.IO/EWG9X<br><br>bdf.zip contains the raw eeg data files that were recorded with a biosemi system (www.biosemi.com). The files can be opened in matlab with the fieldtrip toolbox. http://www.fieldtriptoolbox.org/<br><br>fieldtrip.zip contains all the matlab scripts that were used to process the erp data with the toolbox fieldtrip. http://www.fieldtriptoolbox.org/<br><br>fieldtrip_mat_*.zip contain the final, preprocessed individual data files. They can be opened with matlab.<br><br>R_scripts.zip contains the R scripts to analyze the data and the output files with figures (eg scatterplots).<br>
DOI: 10.6084/m9.figshare.7016306
title: CGU-BES Dataset for Fall and Activity of Daily Life

description: Fifteen healthy participants (11 males, 4 females; 21.8±1.8 yr; 167.7±6.0 cm; 63.0±10.1 kg) performed simulated falls and activities of daily living (ADLs). Every participant performed four simulated falls and eight other types of functional movements, all starting from walking. The four kinds of simulated falls are defined as a forward fall, a backward fall, a lateral fall toward the right-hand side, and a lateral fall toward the left-hand side. The eight types of ADLs are defined as continuous walk, hands raised and lowered, a forward jump, an upward jump, crouch, forward lying down, backward lying down, and stroll followed by standing then sitting. The protocol of this study was approved by the Research Ethics Committee of the Chang Gung Medical Foundation (IRB#101-0830B). All kinematic data were collected by a wearable wireless sensor system. The system contained a tri-axial accelerometer with a full-scale range of ±3.6 g with ±0.3% nonlinearity and a sensitivity of 300 mV/g (ADXL330, Analog Device, Cambridge, MA, USA), a tri-axial gyroscope with a full-scale range of ±400 degrees/sec (dps) and a sensitivity of 3.2 mV/dps (LYPR540AH, STMicroelectronics, Geneva, Switzerland), a microcontroller (MSP430F5438, Texas Instruments, Dallas, TX, USA), and a Bluetooth module (BTC-1022, Atech OEM Inc., Taipei, Taiwan). The sensor was attached to the anterior aspect of the chest using an elastic band. Trunk accelerations and angular velocities were digitized in parallel through a built-in 12-bit analog-digital converter, at a sampling rate of 200 Hz. The digital series were transmitted via Bluetooth to a personal computer.
DOI: 10.6084/m9.figshare.7016303
title: Physical and geometric determinants of transport in feto-placental microvascular networks: Supplementary Datasets

description: The raw geometric data of Specimen 1 is given in the files Specimen1_Vasculature.stl and Specimen1_Villi.stl. The geometries can be previewed in 3D by clicking on the file names. Further raw villous geometries are available upon request.<br>The files with "N_" in the filename are for computation of the advective-diffusive transport at varying inlet-outlet pressure drops. To evaluate these files, first one must run the flow study, after that the transport study, as the latter uses solutions of the former.<br>The files with "Nmax_" in their fine name are for calculation of the transport capacity, which is purely a diffusion problem. These files can be evaluated simply by running the transport study.<br>The simulations in files "...N_HIGHRES" and "Nmax_HIGHRES" underly Fig. 4, Fig. S3 and Fig. 5A&B. In particular, the geometry is sliced into nine distinct capillaries shown in Fig. 4. To evaluate the fluxes of individual capillaries correctly (and to account for solute concentration boundary layers, should they arise) the pre-programmed mesh settings are at a high resolution: Mesh1 (Stokes problem) has approx. 3mio tetrahedral elements, Mesh 2 (Transport problem) approx. 60mio tetrahedral elements. See details in the supplementary information.<br>The simulations in files "...N_original" and "Nmax_original" (8 in total) underly Figs 2 & 3. The purpose of these files is to calculate transport across an entire network, which is why they do not require as high a resolution: The Stokes meshes have approximately 300k tetrahedral elements and the transport meshes between 3mio and 12mio elements. <br>All Comsol files which do <i>not</i> include "with_solutions" in their file name are saved with compact history, and all meshes and solutions are cleared. For easier reproducibility, the two files marked "with_solutions" contain meshes and solutions, so in order to reproduce the blue curves in Fig. 2 and most of the results of the supplementary information, one can directly evaluate the solutions stored in the "with_solutions" files. <br>Code that creates Fig. 5 is contained in "Fig5-dicrete-network-model_figshare.zip". To produce all the subparts of Fig. 5, run the Mathematica file "Fig5-discrete_network_model.nb" from top to bottom (Evaluation-&gt;Evaluate Notebook). It requires an instllation of Matlab and a link between Mathematica and Matlab to be established via MatLink (http://matlink.org/).
DOI: 10.6084/m9.figshare.7016303.v1
title: Physical and geometric determinants of transport in feto-placental microvascular networks: Supplementary Datasets

description: The raw geometric data of Specimen 1 is given in the files Specimen1_Vasculature.stl and Specimen1_Villi.stl. The geometries can be previewed in 3D by clicking on the file names. Further raw villous geometries are available upon request.<br>The files with "N_" in the filename are for computation of the advective-diffusive transport at varying inlet-outlet pressure drops. To evaluate these files, first one must run the flow study, after that the transport study, as the latter uses solutions of the former.<br>The files with "Nmax_" in their fine name are for calculation of the transport capacity, which is purely a diffusion problem. These files can be evaluated simply by running the transport study.<br>The simulations in files "...N_HIGHRES" and "Nmax_HIGHRES" underly Fig. 4, Fig. S3 and Fig. 5A&B. In particular, the geometry is sliced into nine distinct capillaries shown in Fig. 4. To evaluate the fluxes of individual capillaries correctly (and to account for solute concentration boundary layers, should they arise) the pre-programmed mesh settings are at a high resolution: Mesh1 (Stokes problem) has approx. 3mio tetrahedral elements, Mesh 2 (Transport problem) approx. 60mio tetrahedral elements. See details in the supplementary information.<br>The simulations in files "...N_original" and "Nmax_original" (8 in total) underly Figs 2 & 3. The purpose of these files is to calculate transport across an entire network, which is why they do not require as high a resolution: The Stokes meshes have approximately 300k tetrahedral elements and the transport meshes between 3mio and 12mio elements. <br>All Comsol files which do <i>not</i> include "with_solutions" in their file name are saved with compact history, and all meshes and solutions are cleared. For easier reproducibility, the two files marked "with_solutions" contain meshes and solutions, so in order to reproduce the blue curves in Fig. 2 and most of the results of the supplementary information, one can directly evaluate the solutions stored in the "with_solutions" files.
DOI: 10.6084/m9.figshare.7016204
title: GO_meera_R.mucronata.txt

description: Gene Ontology annotations for <i>de novo</i> assembled transcriptome of a mangrove species, <i>Rhizophora mucronata</i> was retrieved from gene ontology consortium based on UniProtKB keyword mapping. The total number of GO terms identified in molecular function (F), biological process (P) and cellular component (C) category are 2436, 1995 and 1435 respectively.
DOI: 10.6084/m9.figshare.7016192
title: Supplementary Material for: Hybrid NOTES: Complete Endoscopic Resection of the Gastric Wall Assisted by Laparoscopy in a Gastric Fundus Gastrointestinal Stromal Tumor

description: Medicine
DOI: 10.6084/m9.figshare.7016189
title: Data.rar

description: Data used for WRR journal: "Uncertainty Quantification for Subsurface Flow and Transport: Coping with Nonlinearity/Irregularity via Polynomial Chaos Surrogate and Machine Learning" [Paper #2018WR022676RR]
DOI: 10.6084/m9.figshare.7016192.v1
title: Supplementary Material for: Hybrid NOTES: Complete Endoscopic Resection of the Gastric Wall Assisted by Laparoscopy in a Gastric Fundus Gastrointestinal Stromal Tumor

description: Medicine
DOI: 10.6084/m9.figshare.7016189.v1
title: Data.rar

description: Data used for WRR journal: "Uncertainty Quantification for Subsurface Flow and Transport: Coping with Nonlinearity/Irregularity via Polynomial Chaos Surrogate and Machine Learning" [Paper #2018WR022676RR]
DOI: 10.6084/m9.figshare.7016141
title: 23 Religiousness.xlsx

description: Data on change in religiosity.<br>
DOI: 10.6084/m9.figshare.7016132
title: Does bad posture affect the standing balance?

description: <b>Introduction</b>: Bad posture is a well-known problem in children and adolescents, and it has a negative effect in adulthood. It can be hypothesized that due to bad posture, changes in the body’s position cause changes in standing balance. <b>Objective</b>: The objective of the study is to determine the influence of bad posture on the standing balance of school-aged children based on independent time–distance- and frequency-based foot centre-of-pressure parameters. <b>Subjects and Methods</b>: Subjects included 171 children (113 with neutral posture (70 boys and 73 girls), mean age: 10.7 ± 1.1 years (range: 9–13), and 68 with bad posture (22 boys and 46 girls), mean age: 10.7 ± 1.2 (range: 9–13)). The parameters were derived from the motion of the centre of pressure on a platform equipped with pressure sensors, on which the subjects were standing for 60 s with both feet and open eyes. <b>Results</b>: When comparing the two groups, the load distribution difference between the legs and the medium–high-frequency band power ratio in the mediolateral direction showed a significant difference out of 17 centre-of-pressure parameters. However, the other 15 parameters did not show any significant differences. <b>Conclusion</b>: There is no clearly significant degradation of postural control in children with bad posture, as the effects of altered posture are continuously corrected by the central nervous system. The asymmetric load between the two sides may further degrade muscular imbalance; thus, correcting bad posture is an important task of physiotherapy.
DOI: 10.6084/m9.figshare.7016132.v1
title: Does bad posture affect the standing balance?

description: <b>Introduction</b>: Bad posture is a well-known problem in children and adolescents, and it has a negative effect in adulthood. It can be hypothesized that due to bad posture, changes in the body’s position cause changes in standing balance. <b>Objective</b>: The objective of the study is to determine the influence of bad posture on the standing balance of school-aged children based on independent time–distance- and frequency-based foot centre-of-pressure parameters. <b>Subjects and Methods</b>: Subjects included 171 children (113 with neutral posture (70 boys and 73 girls), mean age: 10.7 ± 1.1 years (range: 9–13), and 68 with bad posture (22 boys and 46 girls), mean age: 10.7 ± 1.2 (range: 9–13)). The parameters were derived from the motion of the centre of pressure on a platform equipped with pressure sensors, on which the subjects were standing for 60 s with both feet and open eyes. <b>Results</b>: When comparing the two groups, the load distribution difference between the legs and the medium–high-frequency band power ratio in the mediolateral direction showed a significant difference out of 17 centre-of-pressure parameters. However, the other 15 parameters did not show any significant differences. <b>Conclusion</b>: There is no clearly significant degradation of postural control in children with bad posture, as the effects of altered posture are continuously corrected by the central nervous system. The asymmetric load between the two sides may further degrade muscular imbalance; thus, correcting bad posture is an important task of physiotherapy.
DOI: 10.6084/m9.figshare.7016105
title: Data Sepsis 2017 upload.xlsx

description: Dataset on Neutrophil to Lymphocyte Ratio as a Predictor of 28-Day-Mortality in Septic Patients: A Retrospective Cohort Study<br>
DOI: 10.6084/m9.figshare.7015973
title: Table S1 from Ecological specialization is associated with genetic structure in the ant-associated butterfly family Lycaenidae

description: Specimen data including GenBank Accession numbers and BOLD access codes for the species used in the analysis.
DOI: 10.6084/m9.figshare.7015973.v1
title: Table S1 from Ecological specialization is associated with genetic structure in the ant-associated butterfly family Lycaenidae

description: Specimen data including GenBank Accession numbers and BOLD access codes for the species used in the analysis.
DOI: 10.6084/m9.figshare.7015967
title: Appendix S1 from Ecological specialization is associated with genetic structure in the ant-associated butterfly family Lycaenidae

description: R scripts used in this study.
DOI: 10.6084/m9.figshare.7015967.v1
title: Appendix S1 from Ecological specialization is associated with genetic structure in the ant-associated butterfly family Lycaenidae

description: R scripts used in this study.
DOI: 10.6084/m9.figshare.7015937
title: Data from Strategic decision making about travel during disease outbreaks: a game theoretical approach

description: Visitors can play an important role in the spread of infections. Here, we incorporate an epidemic model into a game theoretical framework to investigate the effects of travel strategies on infection control. Potential visitors must decide whether to travel to a destination that is at risk of infectious disease outbreaks. We compare the individually optimal (Nash equilibrium) strategy to the group optimal strategy that maximizes the overall population utility. Economic epidemiological models often find that individual and group optimal strategies are very different. By contrast, we find perfect agreement between individual and group optimal strategies across a wide parameter regime. For more limited regimes where disagreement does occur, the disagreement is (i) generally very extreme; (ii) highly sensitive to small changes in infection transmissibility and visitor costs/benefits; and (iii) can manifest either in a higher travel volume for individual optimal than group optimal strategies, or vice versa. The simulations show qualitative agreement with the 2003 severe acute respiratory syndrome outbreak in Beijing, China. We conclude that a conflict between individual and group optimal visitor travel strategies during outbreaks may not generally be a problem, although extreme differences could emerge suddenly under certain changes in economic and epidemiological conditions.
DOI: 10.6084/m9.figshare.7015937.v1
title: Data from Strategic decision making about travel during disease outbreaks: a game theoretical approach

description: Visitors can play an important role in the spread of infections. Here, we incorporate an epidemic model into a game theoretical framework to investigate the effects of travel strategies on infection control. Potential visitors must decide whether to travel to a destination that is at risk of infectious disease outbreaks. We compare the individually optimal (Nash equilibrium) strategy to the group optimal strategy that maximizes the overall population utility. Economic epidemiological models often find that individual and group optimal strategies are very different. By contrast, we find perfect agreement between individual and group optimal strategies across a wide parameter regime. For more limited regimes where disagreement does occur, the disagreement is (i) generally very extreme; (ii) highly sensitive to small changes in infection transmissibility and visitor costs/benefits; and (iii) can manifest either in a higher travel volume for individual optimal than group optimal strategies, or vice versa. The simulations show qualitative agreement with the 2003 severe acute respiratory syndrome outbreak in Beijing, China. We conclude that a conflict between individual and group optimal visitor travel strategies during outbreaks may not generally be a problem, although extreme differences could emerge suddenly under certain changes in economic and epidemiological conditions.
DOI: 10.6084/m9.figshare.7015658
title: DATASET BPH and BENIGN

description: This data contains insect images.
DOI: 10.6084/m9.figshare.7015658.v1
title: DATASET BPH and BENIGN

description: This data contains insect images.
DOI: 10.6084/m9.figshare.7015607
title: Additional file 9: of Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors

description: Script 2. Script designed to obtain the most abundant OTUs for each sample type: water, larva and adult. (TXT 803 bytes)
DOI: 10.6084/m9.figshare.7015604
title: Additional file 8: of Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors

description: Script 1. Script designed to regroup OTUs in either unique or shared among sample types: water, larva and adult. (TXT 1 kb)
DOI: 10.6084/m9.figshare.7015607.v1
title: Additional file 9: of Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors

description: Script 2. Script designed to obtain the most abundant OTUs for each sample type: water, larva and adult. (TXT 803 bytes)
DOI: 10.6084/m9.figshare.7015604.v1
title: Additional file 8: of Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors

description: Script 1. Script designed to regroup OTUs in either unique or shared among sample types: water, larva and adult. (TXT 1 kb)
DOI: 10.6084/m9.figshare.7015565
title: Additional file 2: of Role of milk and dairy intake in cognitive function in older adults: a systematic review and meta-analysis

description: Analytical dataset. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7015565.v1
title: Additional file 2: of Role of milk and dairy intake in cognitive function in older adults: a systematic review and meta-analysis

description: Analytical dataset. (XLSX 9 kb)
DOI: 10.5281/zenodo.4005762
title: tutorial ethiopia

description: PhyloPhlAn metagenomic database "tutorial ethiopia"
DOI: 10.5281/zenodo.4005761
title: tutorial ethiopia

description: PhyloPhlAn metagenomic database "tutorial ethiopia"
DOI: 10.6084/m9.figshare.7015523
title: Additional file 2: of Effects of capitation payment on utilization and claims expenditure under National Health Insurance Scheme: a cross-sectional study of three regions in Ghana

description: Raw dataset on utilization and claims expenditure. (XLSX 157 kb)