cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24962586.v1
title: Supplementary tables: Ataluren delays loss of ambulation and respiratory decline in nonsense mutation Duchenne muscular dystrophy patients

description: <b>These are peer-reviewed supplementary tables for the article 'Ataluren delays loss of ambulation and respiratory decline in nonsense mutation Duchenne muscular dystrophy patients' published in the </b><b><i>Journal of Comparative Effectiveness Research</i></b><b>. </b><b>Supplementary Table 1. </b>Baseline demographics and disease characteristics for Study 019 patients with nmDMD who received ataluren (40 mg/kg/day) plus SoC in at least Study 019 (N = 59) and for propensity-score matched patients with DMD receiving SoC alone in the CINRG DNHS (N = 59), using age at diagnosis for both datasets as the fourth covariate for matching, for the sensitivity analysis of age at LoA. <b>Supplementary Table 2. </b>Baseline demographics and disease characteristics for non-ambulatory Study 019 patients with nmDMD who received ataluren 40 mg/kg/day plus SoC in at least this study (N = 45) and propensity-score matched patients with DMD who received SoC alone in the CINRG DNHS (N = 45), using age at diagnosis for both datasets as the fourth covariate for matching, for the sensitivity analysis of age at decline in respiratory function. <b>Supplementary Table 3. </b>Treatment-emergent adverse events† experienced by patients in the as-treated population of Study 019 (N = 94). <b>Supplementary Table 4. </b>Lipid profile of patients in the as-treated population of Study 019 (N = 94) at baseline and Week 240. <b>Supplementary Table 5.</b> Hypertensive status of patients in the as-treated population of Study 019 (N = 94) from baseline to Week 240. <b>Supplementary Table 6. </b>ECG results of patients of patients in the as-treated population of Study 019 (N = 94) from screening to post-treatment. <b>Supplementary Table 7. </b>Hepatic and renal abnormalities in patients in the as-treated population of Study 019 (N = 94) from screening to post-treatment. <b>Summary: Aim:</b> We investigated the effect of ataluren plus standard of care (SoC) on age at loss of ambulation (LoA) and respiratory decline in patients with nonsense mutation Duchenne muscular dystrophy (nmDMD) versus patients with DMD on SoC alone. <b>Patients & methods: </b>Study 019 was a long-term Phase III study of ataluren safety in nmDMD patients with a history of ataluren exposure. Propensity score matching identified Study 019 and CINRG DNHS patients similar in disease progression predictors. <b>Results & conclusion: </b>Ataluren plus SoC was associated with a 2.2-year delay in age at LoA (p = 0.0006), and a 3.0-year delay in decline of predicted forced vital capacity to &lt;60% in nonambulatory patients (p = 0.0004), versus SoC. Ataluren plus SoC delays disease progression and benefits ambulatory and nonambulatory patients with nmDMD. ClinicalTrials.gov registration: NCT01557400.
DOI: 10.5281/zenodo.10467053
title: Dataset for: Feasibility study to improve clinical trial transparency with individualized report cards at a large university medical center

description: This deposit contains data associated with a feasibility study evaluating the use of individualized report cards to improve trial transparency at the Charité - Universitätsmedizin Berlin. It primarily includes large raw data files and other files compiled by, or used in the project code repository: https://github.com/quest-bih/tv-ct-transparency/. These data are deposited for documentation and computational reproducibility; they do not reflect the most current/accurate data available from each source.

The deposit contains:

Survey data (`survey-data.csv`): Participant responses for an anonymous survey conducted to assess the usefulness of the report cards and infosheet. The survey was administered in LimeSurvey and hosted on a server at the QUEST Center for Responsible Research at the Berlin Institute of Health at Charité – Universitätsmedizin Berlin. Any information that could potentially identify participants, such as IP address and free-text fields (e.g., corrections, comments) were removed. This file serves as input for the analysis of the survey data.
DOI: 10.5281/zenodo.10467054
title: Dataset for: Feasibility study to improve clinical trial transparency with individualized report cards at a large university medical center

description: This deposit contains data associated with a feasibility study evaluating the use of individualized report cards to improve trial transparency at the Charité - Universitätsmedizin Berlin. It primarily includes large raw data files and other files compiled by, or used in the project code repository: https://github.com/quest-bih/tv-ct-transparency/. These data are deposited for documentation and computational reproducibility; they do not reflect the most current/accurate data available from each source.

The deposit contains:

Survey data (`survey-data.csv`): Participant responses for an anonymous survey conducted to assess the usefulness of the report cards and infosheet. The survey was administered in LimeSurvey and hosted on a server at the QUEST Center for Responsible Research at the Berlin Institute of Health at Charité – Universitätsmedizin Berlin. Any information that could potentially identify participants, such as IP address and free-text fields (e.g., corrections, comments) were removed. This file serves as input for the analysis of the survey data.
DOI: 10.13020/h56h-bd77
title: Deep Brain Stimulation (DBS) and Implant-friendly (IF) Mode Calculator

description: The purpose of this study is to present a strategy to calculate the implant-friendly (IF) excitation modes—which mitigate the radiofrequency (RF) heating at the contacts of deep brain stimulation (DBS) electrodes—of multi-channel RF coils at 7T. 
Methods: 
An induced RF current on an implantable electrode generates a scattered magnetic field whose left-handed circularly polarizing component (B1+) is approximated using a -mapping technique and subsequently utilized as a gauge for the electrode’s induced current. Using this approach, the relative induced currents due to each channel of a multi-channel RF coil on the DBS electrode were calculated. The IF modes of the corresponding multi-channel coil were determined by calculating the null space of the relative induced currents. The proposed strategy was tested and validated for unilateral and bilateral commercial DBS electrodes (directional lead, Infinity DBS system, Abbott Laboratories) placed inside a uniform phantom by performing heating and imaging studies on a 7T MRI scanner using a 16-channel transceive RF coil.
Results: 
Individual IF modes nor shim solutions obtained from IF modes did not induce significant temperature increase when used for a high-power Turbo Spin Echo sequence. In contrast, shimming with the scanner’s toolbox (i.e., based on per-channel B1+ fields) resulted in a more than 2°C temperature increase for the same amount of input power.
Conclusion: 
A strategy for calculating the IF modes of a multi-channel RF coil is presented. This strategy was validated using a 16-channel RF coil at 7T for unilateral and bilateral commercial DBS electrodes inside a uniform phantom.
description: Repository includes MATLAB codes. Raw input and and output files may be requested by emailing the author. The code that supports the findings of this study is openly available at https://github.com/AliSaMRI/DBS_IF_Mode_Calculator
DOI: 10.6073/pasta/c666da6e4172781b4c8938dc23a41ee4
title: Barn Tower Meteorological Station at Harvard Forest since 2015

description: The Barn Tower (40 m) was installed in 2009 to support meteorological and phenological measurements and to provide a relay point for the Harvard Forest field wireless network. A wind instrument was later installed at the top of the tower to provide continuous measurements of wind speed and direction.
DOI: 10.6084/m9.figshare.24962514
title: Summary-Abstract

description: Summary:Background: This scoping review explores childhood pregnancy (&lt;15 years), emphasizing regional variations, economic influences, and key metrics such as fertility rates, abortion, reproductive health services, antenatal care, migration, and education and workforce participation among children.Objectives: The primary goal is a comprehensive investigation into childhood pregnancy to construct archetypes based on migration, ethnicity, and income status. The specific objectives include identifying population differences and generating hypotheses on the role of political decisions. Eligibility Criteria: Inclusive of diverse study methodologies, the review encompasses academic publications, reports, and data from governmental and non-governmental organizations, focusing on the intersections of politics, migration, ethnicity, and income for girls aged less than 15 facing pregnancy.Sources of Evidence: Evidence is sourced from selected studies, prioritizing insights into childhood pregnancy's intersections with political, migratory, ethnic, and economic factors.Charting Methods: Utilizing a narrative synthesis approach, the review systematically gathers and analyzes data, focusing on regional disparities, economic contexts, and relevant metrics.Results: The synthesis reveals complex dimensions of childhood pregnancy, providing insights into regional disparities, economic contexts, and specific challenges faced by different populations. Explanatory archetypes are constructed to illustrate how migration, ethnicity, and income contribute to varying experiences.Conclusions: The review concludes by emphasizing the importance of understanding, offering valuable insights for informed interventions, and guiding future research. Archetypes contribute to evidence-based strategies for addressing the unique circumstances faced by diverse groups of girls in Colombia, aiming to mitigate the impact of childhood pregnancy.
DOI: 10.6084/m9.figshare.24962514.v1
title: Summary-Abstract

description: Summary:Background: This scoping review explores childhood pregnancy (&lt;15 years), emphasizing regional variations, economic influences, and key metrics such as fertility rates, abortion, reproductive health services, antenatal care, migration, and education and workforce participation among children.Objectives: The primary goal is a comprehensive investigation into childhood pregnancy to construct archetypes based on migration, ethnicity, and income status. The specific objectives include identifying population differences and generating hypotheses on the role of political decisions. Eligibility Criteria: Inclusive of diverse study methodologies, the review encompasses academic publications, reports, and data from governmental and non-governmental organizations, focusing on the intersections of politics, migration, ethnicity, and income for girls aged less than 15 facing pregnancy.Sources of Evidence: Evidence is sourced from selected studies, prioritizing insights into childhood pregnancy's intersections with political, migratory, ethnic, and economic factors.Charting Methods: Utilizing a narrative synthesis approach, the review systematically gathers and analyzes data, focusing on regional disparities, economic contexts, and relevant metrics.Results: The synthesis reveals complex dimensions of childhood pregnancy, providing insights into regional disparities, economic contexts, and specific challenges faced by different populations. Explanatory archetypes are constructed to illustrate how migration, ethnicity, and income contribute to varying experiences.Conclusions: The review concludes by emphasizing the importance of understanding, offering valuable insights for informed interventions, and guiding future research. Archetypes contribute to evidence-based strategies for addressing the unique circumstances faced by diverse groups of girls in Colombia, aiming to mitigate the impact of childhood pregnancy.
DOI: 10.6084/m9.figshare.24962589
title: Supplementary materials: Impact analysis of expanding narrow-spectrum antibiotic use for children with ear, sinus and throat infections

description: <b>These are peer-reviewed supplementary tables for the article '</b><b>Impact analysis of expanding narrow-spectrum antibiotic use for children with ear, sinus and throat infections</b><b>' published in the</b><b> </b><b><i>Journal of Comparative Effectiveness Research</i></b><b>.</b><b>Table A-1. </b>Complete Set of Parameters Used in the Model.<b>Table A-2. </b>Ranges Used for One-Way Sensitivity Analysis and Distributions Used for Probabilistic Sensitivity Analysis.<b>Summary: Aim:</b> Estimate the impacts treating acute respiratory tract infections (ARTIs) in children aged 6 months through 12 years with narrow-spectrum antibiotics. <b>Materials & methods:</b> Decision-tree model to estimate children’s health, healthcare utilization and costs, and caregiver’s time and costs for using narrow-spectrum antibiotics in eligible children with an ARTI, compared with current use of narrow- and broad-spectrum antibiotics. <b>Results:</b> Reduced adverse drug reactions by 35,750 (14%) cases) and 4750 (12%) fewer emergency department visits, 300 (12%) fewer hospitalizations, and 50,500 (10%) avoided outpatient visits. Annual healthcare costs fell by US$120 million (22%). Total societal costs declined by US$131 million (20%). <b>Conclusion:</b> National implementation of narrow-spectrum antibiotics to treat ARTIs in children improves patient outcomes and reduces caregiver burden and annual healthcare costs.<br>
DOI: 10.6084/m9.figshare.24962589.v1
title: Supplementary materials: Impact analysis of expanding narrow-spectrum antibiotic use for children with ear, sinus and throat infections

description: <b>These are peer-reviewed supplementary tables for the article '</b><b>Impact analysis of expanding narrow-spectrum antibiotic use for children with ear, sinus and throat infections</b><b>' published in the</b><b> </b><b><i>Journal of Comparative Effectiveness Research</i></b><b>.</b><b>Table A-1. </b>Complete Set of Parameters Used in the Model.<b>Table A-2. </b>Ranges Used for One-Way Sensitivity Analysis and Distributions Used for Probabilistic Sensitivity Analysis.<b>Summary: Aim:</b> Estimate the impacts treating acute respiratory tract infections (ARTIs) in children aged 6 months through 12 years with narrow-spectrum antibiotics. <b>Materials & methods:</b> Decision-tree model to estimate children’s health, healthcare utilization and costs, and caregiver’s time and costs for using narrow-spectrum antibiotics in eligible children with an ARTI, compared with current use of narrow- and broad-spectrum antibiotics. <b>Results:</b> Reduced adverse drug reactions by 35,750 (14%) cases) and 4750 (12%) fewer emergency department visits, 300 (12%) fewer hospitalizations, and 50,500 (10%) avoided outpatient visits. Annual healthcare costs fell by US$120 million (22%). Total societal costs declined by US$131 million (20%). <b>Conclusion:</b> National implementation of narrow-spectrum antibiotics to treat ARTIs in children improves patient outcomes and reduces caregiver burden and annual healthcare costs.<br>
DOI: 10.6073/pasta/79b535cdb660fa5019dff7c27a1439ea
title: PRP01 Konza prairie long term restoration study of aboveground annual net primary productivity (ANPP)

description: The experiment is a randomized complete block design with four whole plot hetereogeneity treatments replicated within each of four blocks (n=16 whole plots). The whole plot treatments were created using different combinations of soil depth and nutrient manipulations. The control plots contained no depth or nutrient manipulations. The 'maximum hetereogeneity' plots contained three 2 m x 8 m vertical strips assigned to ambient, enriched and reduced N treatments and four 2 m x 6 m horizontal strips assigned to deep and shallow soil to result in six treatment combinations. The maximum heterogeneity plots are a split-block design. Each plot contained 12 subplots (2 m x 2 m) for sampling. All of the plots had surface soil temporarily removed to a depth of approximately 25 cm and natural limestone slabs were laid in strips assigned to the shallow soil treatment. The soil from all plots was then replaced, leveled, and disked (2-3 cm deep). In February 1998, we incorporated sawdust (49% C; C:N ratio=122) into the strips assigned to the reduced-N treatment. The average C concentration and bulk density in the surface 15 cm following long-term cultivation was 1.5% and 1.2 g cm-3, respectively. Sawdust was tilled into the soil at a rate of 5.5 kg dry wt./m2 to achieve a C concentration representative of native prairie soil (approx.3% C). Surface applications of granular sugar were initiated in 2004 at a rate of 200 g sucrose m-2 (84.22 g C/m2) 3-4 times each growing season. Strips assigned to the enriched-N treatment were fertilized with 5 g N m2/y (applied as ammonium-nitrate) in July of the first growing season and early June of each subsequent year.
DOI: 10.5281/zenodo.3888587
title: 6DMG: A 6D Motion Gesture Database

description: Motion-based control is gaining popularity, and motion gestures form a complementary modality in human-computer interactions. To achieve more robust user independent motion gesture recognition in a manner analogous to automatic speech recognition, we need a deeper understanding of the motions in gesture, which arouses the need for a 6D motion gesture database. In this work, we present a database that contains comprehensive motion data, including the position, orientation, acceleration, and angular speed, for a set of common motion gestures performed by different users. We hope this motion gesture database can be a useful platform for researchers and developers to build their recognition algorithms as well as a common test bench for performance comparisons. Associated codes with the dataset along with instructions may be found on our GitHub page at https://github.com/olivesgatech/6DMG.
DOI: 10.5281/zenodo.10471794
title: 6DMG:  A 6D Motion Gesture Database

description: Motion-based control is gaining popularity, and motion gestures form a complementary modality in human-computer interactions. To achieve more robust user independent motion gesture recognition in a manner analogous to automatic speech recognition, we need a deeper understanding of the motions in gesture, which arouses the need for a 6D motion gesture database. In this work, we present a database that contains comprehensive motion data, including the position, orientation, acceleration, and angular speed, for a set of common motion gestures performed by different users. We hope this motion gesture database can be a useful platform for researchers and developers to build their recognition algorithms as well as a common test bench for performance comparisons. Associated codes with the dataset along with instructions may be found on our GitHub page at https://github.com/olivesgatech/6DMG.
DOI: 10.5281/zenodo.3888586
title: 6DMG:  A 6D Motion Gesture Database

description: Motion-based control is gaining popularity, and motion gestures form a complementary modality in human-computer interactions. To achieve more robust user independent motion gesture recognition in a manner analogous to automatic speech recognition, we need a deeper understanding of the motions in gesture, which arouses the need for a 6D motion gesture database. In this work, we present a database that contains comprehensive motion data, including the position, orientation, acceleration, and angular speed, for a set of common motion gestures performed by different users. We hope this motion gesture database can be a useful platform for researchers and developers to build their recognition algorithms as well as a common test bench for performance comparisons. Associated codes with the dataset along with instructions may be found on our GitHub page at https://github.com/olivesgatech/6DMG.
DOI: 10.25345/c58k75716
title: MassIVE MSV000093791 - Quantitative analysis of ribosomal protein expression in bacteria
title: Analysis of ribosomal proteins purified as ribosome particles. Two set of samples were analyzed: 1) ribosomes purified from bacteria expressing sgRNA that does not target any ribosomal RNA gene (control); 2) ribosomes purified from bacteria expressing sgRNA targeting three ribosomal RNA genes. The aim of the project is to quantify the peptides and compare both sets of samples. The ribosomal peptides prepared from the bacteria expressing the sgRNA targeting the rRNA genes are expected to be less abundant than in the control samples. The two sample sets are the following: A-D (four biological replicates) are the samples from the bacteria expressing functional sgRNA downregulating three rRNA genes. E-H (four biologicial replicates) are the control samples from the bacteria expressing sgRNA that do not target any rRNA gene. All the sampes were spiked with an almost equivalent amount of ribosomes from a WT strain grown in almost 100% 13C and 15N labelled minimum medium. Ribosomes were purified according to published protocols. Basically, the ribosome particles are sedimented by ultra-centrifugation in a saccharose-rich medium. The recovered pellets were resuspended for electrophoretic migration (stacking gel only) for later in-gel trypsinolysis. The obtained peptides were extracted from the gel according to standard procedures and analyzed by LC-MS/MS on a QExactivePlus Orbitrap mass spectrometer (Thermo scientific). The raw data were converted to mzXML (raw data files) and processed using our proteomics software suite (i2MassChroQ, see http://pappso.inrae.fr/en/bioinfo/). The database search engine was X!Tandem, that produces, for each MS run file analyzed, a corresponding XML file, that we submit here as the database search identification data files). The X!Tandem program was first configured to run without accounting for labelled peptides (one set of "light-only" XML files were thus generated by X!Tandem). Then, X!Tandem was configured to account for all the residues labelled 100% with 13C and 15N (one set of "heavy-only" XML files were thus generated by X!Tandem). We loaded first the "light-only" X!Tandem-generated XML files in i2MassChroq, checked the quality of the data and wrote to disk an XPIP (i2MassChroq project file) file for the four replicates of both sample sets all taken together. Then we did this likewise for the "heavy-only" X!Tandem-generated XML files (at this time we configured i2MassChroQ to look for heavy-isotope-labelled peptides). We finally open the two XPIP files (light-only and heavy-only) and save the combination of the data to a new XPIP file (light-and-heavy). The quantitative analysis was performed inside the i2MassChroq's MassChroQ module which is then directed to write a spreadsheet file with all the identification/quantification data of the peptides. That spreadsheet file was then used within GNU-R to perform data reformatting and peptide quantification work (comparison of the amount of selected peptides belonging to known ribosome subunits between the two data sets).