cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10623388
title: Clinical investigations to evaluate high-risk orthopaedic devices: a systematic review of the peer-reviewed medical literature

description: CORE-MD undertook systematic reviews of methodologies used in clinical trials to evaluate high-risk medical devices. It compared guidance for clinical trial designs, review statistical methods for device trials, and assess the utility of patient-reported outcomes for regulatory decisions. This dataset was used for the work package 1, task 1.1 of the CORE-MD project and lists the characteristics of the reviewed publications of orthopedic devices.

Purpose: The objective of this systematic review was to give an overview of clinical investigations regarding hip and knee arthroplasty implants published in peer-reviewed scientific medical journals before entry into force of the EU Medical Device Regulation in May 2021.

Methods: We systematically reviewed the medical literature for a random selection of hip and knee implants, to identify all peer-reviewed clinical investigations published within 10years before and up to 20years after regulatory approval. We report study characteristics, methodologies, outcomes, measures to prevent bias, and timing of clinical investigations, of 30 current implants. The review process was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.

Results: We identified 2912 publications and finally included 151 papers published between 1995 and 2021 (63 on hip stems, 34 on hip cups, 54 on knee systems). We identified no clinical studies published before CE-marking for any selected device, and no studies even up to 20 years after CE-marking in one quarter of devices. There were very few randomized controlled trials, and registry-based studies generally had larger sample sizes and better methodology.

Conclusions: The peer-reviewed literature alone is insufficient as source of clinical investigations of these high-risk devices intended for life-long use. A more systematic, efficient and faster way to evaluating safety and performance is necessary. Using a phased introduction approach, nesting comparative studies of observational and experimental design in existing registries, increasing use of benefit measures, and accelerating surrogate outcomes research, will help to minimise risks and maximise benefits.
DOI: 10.5281/zenodo.10623389
title: Clinical investigations to evaluate high-risk orthopaedic devices: a systematic review of the peer-reviewed medical literature

description: CORE-MD undertook systematic reviews of methodologies used in clinical trials to evaluate high-risk medical devices. It compared guidance for clinical trial designs, review statistical methods for device trials, and assess the utility of patient-reported outcomes for regulatory decisions. This dataset was used for the work package 1, task 1.1 of the CORE-MD project and lists the characteristics of the reviewed publications of orthopedic devices.

Purpose: The objective of this systematic review was to give an overview of clinical investigations regarding hip and knee arthroplasty implants published in peer-reviewed scientific medical journals before entry into force of the EU Medical Device Regulation in May 2021.

Methods: We systematically reviewed the medical literature for a random selection of hip and knee implants, to identify all peer-reviewed clinical investigations published within 10years before and up to 20years after regulatory approval. We report study characteristics, methodologies, outcomes, measures to prevent bias, and timing of clinical investigations, of 30 current implants. The review process was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.

Results: We identified 2912 publications and finally included 151 papers published between 1995 and 2021 (63 on hip stems, 34 on hip cups, 54 on knee systems). We identified no clinical studies published before CE-marking for any selected device, and no studies even up to 20 years after CE-marking in one quarter of devices. There were very few randomized controlled trials, and registry-based studies generally had larger sample sizes and better methodology.

Conclusions: The peer-reviewed literature alone is insufficient as source of clinical investigations of these high-risk devices intended for life-long use. A more systematic, efficient and faster way to evaluating safety and performance is necessary. Using a phased introduction approach, nesting comparative studies of observational and experimental design in existing registries, increasing use of benefit measures, and accelerating surrogate outcomes research, will help to minimise risks and maximise benefits.
DOI: 10.5281/zenodo.10558835
title: Alterations in Zonal Distribution and Plasma Membrane Localization of Hepatocyte Bile Acid Transporters in NAFLD Patients

description: This dataset includes R code and the accompanying Microsoft Excel raw data files used for data analysis and Bayesian modeling of the zonal abundance, plasma membrane localization, and membrane-localized zonal abundance phenotypes reported in "Alterations in Zonal Distribution and Plasma Membrane Localization of Hepatocyte Bile Acid Transporters in NAFLD Patients" (published in Hepatology Communications, 2024). Raw data and R code files used to evaluate the hepatic acinus size phenotype as reported in the Supplement Digital Content of this publication are also included with this upload. Please reference the following document for more detailed information: Murphyetal_DataRepositoryGuide.docx.
DOI: 10.5281/zenodo.10558834
title: Alterations in Zonal Distribution and Plasma Membrane Localization of Hepatocyte Bile Acid Transporters in NAFLD Patients

description: This dataset includes R code and the accompanying Microsoft Excel raw data files used for data analysis and Bayesian modeling of the zonal abundance, plasma membrane localization, and membrane-localized zonal abundance phenotypes reported in "Alterations in Zonal Distribution and Plasma Membrane Localization of Hepatocyte Bile Acid Transporters in NAFLD Patients" (published in Hepatology Communications, 2024). Raw data and R code files used to evaluate the hepatic acinus size phenotype as reported in the Supplement Digital Content of this publication are also included with this upload. Please reference the following document for more detailed information: Murphyetal_DataRepositoryGuide.docx.
DOI: 10.25934/pr00008850
title: The impact of malnutrition on the Efficacy and Safety of empagliflozin for people with heart failure

description: Heart failure is a syndrome of impaired cardiac circulation due to impaired systolic (when the heart contracts to pump blood around the body) and/or diastolic (when the heart relaxes and refills with blood) function of the heart and is the end stage of heart disease, with an estimated prevalence of >37.7 million individuals globally. Malnutrition is common in heart failure (HF), affecting up to 62% of patients with heart failure, and is associated with mortality.

Treatment with empagliflozin, a sodium-glucose cotransporter 2 (SGLT2) inhibitor, reduces the risk of adverse events in patients with heart failure. Empagliflozin works by reducing the amount of glucose being reabsorbed into the blood from the kidneys so that the glucose is passed out in the urine, and hence blood glucose levels are lowered. SGLT2 inhibitors have been seen to cause weight loss in heart failure patients as sugar is a very important nutrient. However, whether empagliflozin benefits patients with malnutrition in the same way it does in other patients is unclear. This analysis of individual participant data (IPD) from two clinical trials of patients with chronic heart failure may provide guidance on whether empagliflozin is recommended in clinical practice in patients with malnutrition and heart failure.

This subanalysis  from EMPEROR-Reduced trial may provide guidance on whether empagliflozin is recommended in clinical practice in patients with malnutrition and heart failure with reduced ejection fraction (HFrEF - when one of the chambers on the left side of the heart loses its ability to contract normally. The heart can't pump with enough force to push enough blood into circulation).
DOI: 10.5066/p9f0vw9l
title: Late Holocene and Living Coral Composition of Pompano Ridge, FL

description: Pompano Ridge is a coral reef located on the southeast Florida nearshore ridge complex, ~500 meters off the coast of northern Broward County in southeast Florida. This data release compiles data collected on the late Holocene and living coral composition of Pompano Ridge. The data are described in detail in Modys and others (in prep). The samples were collected under Scientific Activity Licenses (SAL) from the Florida Fish and Wildlife Conservation Commission (SAL-18-1650(A)-SRP) and with permission from Broward County Environmental Protection and Growth Management.

Modys, A.B., Toth, L.T, Oleinik, A.E., Precht, W.F., and Mortlock, R.A., in prep, Modern coral range expansion off southeast Florida falls short of late Holocene baseline: Nature Communications Earth and Environment.
DOI: 10.5281/zenodo.10628848
title: Full BaCoN-II data sets and production pipelines needed to create the data sets using ReACT, HMCode2020 and EuclidEmulator2.

description: The zips:



data: The full Bayesian Cosmological Network (BaCoN) non-linear cosmological matter power spectrum data sets (training and test sets) used in the second version of the network. This includes EuclidEmulator based data sets and HMCode2020 based data sets, with and without massive neutrinos and baryonic effects. It also includes the algorithms used to generate the random filters and theory error curves as described in the associated publication. 

data_production_pipelines: Bash scripts and code that were used to create the data sets using the publicly available ReACT, HMCode2020 and EuclidEmulator codes. 

notebooks: Notebooks to check cosmological parameter distributions, generate new cosmological parameter files and to plot spectra. 

binning: Bash scripts and code used to bin power spectra data according to the values of a specific cosmological/gravitational parameter. 


Please contact Ben Bose via ben.bose@ed.ac.uk if you have any questions.
DOI: 10.5281/zenodo.10628849
title: Full BaCoN data sets with all files needed to create the data sets using ReACT, HMCode2020 and EuclidEmulator2.

description: The zip includes:



The full Bayesian Cosmological Network (BaCoN) nonlinear cosmological matter power spectrum data sets (training and test sets) used in the second version of the network. This includes EuclidEmulator based data sets and HMCode2020 based data sets, with and without massive neutrinos and baryonic effects. 

Bash scripts and code edits that were used to create the data sets using the publicly available ReACT, HMCode2020 and EuclidEmulator  codes. 

Notebooks to check cosmological parameter distributions, generate new cosmology files and to plot spectra. 


Please contact Ben Bose via ben.bose@ed.ac.uk if you have any questions.
DOI: 10.5281/zenodo.10688282
title: Full BaCoN-II data sets and production pipelines needed to create the data sets using ReACT, HMCode2020 and EuclidEmulator2.

description: The zips:



data: The full Bayesian Cosmological Network (BaCoN) non-linear cosmological matter power spectrum data sets (training and test sets) used in the second version of the network. This includes EuclidEmulator based data sets and HMCode2020 based data sets, with and without massive neutrinos and baryonic effects. It also includes the algorithms used to generate the random filters and theory error curves as described in the associated publication. 

data_production_pipelines: Bash scripts and code that were used to create the data sets using the publicly available ReACT, HMCode2020 and EuclidEmulator codes. 

notebooks: Notebooks to check cosmological parameter distributions, generate new cosmological parameter files and to plot spectra. 

binning: Bash scripts and code used to bin power spectra data according to the values of a specific cosmological/gravitational parameter. 


Please contact Ben Bose via ben.bose@ed.ac.uk if you have any questions.
DOI: 10.5285/efa039d8-e411-724c-e053-6c86abc0317e
title: Measurements of intraspecific variability in functional trait expression obtained from laboratory experiments conducted, between June 2021 and April 2022, on marine bioturbating benthic invertebrate macrofauna, collected between May 2021 and February 2022.

description: This dataset contains species mass, respiration, burial times, sediment particle analysis, redox potential depths, and water nutrient concentrations (ammonium, nitrate+nitrite, nitrite, and phosphate) data obtained from two separate laboratory experiments involving the following macroinvertebrate species held at different densities: <em>Amphiura filiformis</em>, <em>Amphiura chiajei</em>, <em>Turritellinella tricarinata</em>, <em>Edwardsia claparedii</em>, <em>Sternaspsis scutata</em>, <em>Paraleptopentacta elongata</em>, <em>Hediste diversicolor</em>, and <em>Nephtys hombergii</em>. The macroinvertebrates were collected from various locations around the UK (Plymouth, Oban, and Newcastle) on 6 occasions between May 2021 and February 2022. Subtidal species were collected using a Van Veen grab or Agassiz trawl (depths 10-42 m) whilst intertidal species were collected at low tide in mud flats by bucket and spade. The experiments were conducted at the National Oceanography Centre in Southampton from June 2021 - April 2022. One experiment tested the effects of season and geographic locality on body size, burial traits, bioirrigation, sediment oxygen penetration depth and respiration, and nutrient release with all measurements taken at the end of the 1.5-month experiment. The second experiment focused on how individual density and climate conditions impact burial traits, bioirrigation, sediment nutrient release and sediment redox discontinuity depth with all measurements being taken at the end of the 2-month experiment. Body size was measured using digital weighing scales, burial traits were measured using fluorescent sediment profile imaging and video analysis, sediment respiration was measured using optical oxygen probes and oxygen penetration depth was measured using a motorised sediment depth profiler, and nutrient release measured using a flow injection auto-analyser. Bioirrigation was measured at the end of both experiments by taking water samples at 0, 4 and 8 hours and analysed using a flow injection auto-analyser. Sediment redox discontinuity was measured using sediment profile imaging. These data were collected to investigate intraspecific variability in functional trait expression in marine bioturbating benthic invertebrate fauna. Data were generated under NERC Discovery Science project 'Implications of intraspecific trait variability across different environmental conditions for projections of marine ecosystem futures' (grant reference NE/T001577/1).
DOI: 10.5281/zenodo.10684155
title: AOD selected datasets from GAWPFR network  for aerosol properties retrievals using GRASP-AOD

description: A sample of Aerosol Optical Depth (AOD) measurements from 3 stations of GAW-PFR network (Davos, Izana and Hohenpeissenberg).

Each folder corresponds to a station identifier (DAV for Davos, HPB for Hohenpeissenberg and IZO for Izaña). The file names include the identifier for each station, the name of the instrument, the year, month and day of the measurements. The first 4 lines of the file include information about the station. The following columns are included in every text file: date(1-3), time UTC (4), air mass (5), AOD at 368, 412, 500 and 862 nm (6-9) and Angström Exponent (10).

The dataset includes 10 days per station of at least 200 cloud screened measurements per day of PFR AOD. 7 days correspond to AOD>0.2 and 3 days to AOD<0.1 at 500 nm. For all days and stations there was a CIMEL sun photometer from AERONET measuring in parallel. For Davos and Izana there were one or more PFRs measuring in parallel apart from the one present in the dataset.
DOI: 10.5281/zenodo.10684156
title: AOD selected datasets from GAWPFR network  for aerosol properties retrievals using GRASP-AOD

description: A sample of Aerosol Optical Depth (AOD) measurements from 3 stations of GAW-PFR network (Davos, Izana and Hohenpeissenberg).

Each folder corresponds to a station identifier (DAV for Davos, HPB for Hohenpeissenberg and IZO for Izaña). The file names include the identifier for each station, the name of the instrument, the year, month and day of the measurements. The first 4 lines of the file include information about the station. The following columns are included in every text file: date(1-3), time UTC (4), air mass (5), AOD at 368, 412, 500 and 862 nm (6-9) and Angström Exponent (10).

The dataset includes 10 days per station of at least 200 cloud screened measurements per day of PFR AOD. 7 days correspond to AOD>0.2 and 3 days to AOD<0.1 at 500 nm. For all days and stations there was a CIMEL sun photometer from AERONET measuring in parallel. For Davos and Izana there were one or more PFRs measuring in parallel apart from the one present in the dataset.
DOI: 10.6084/m9.figshare.12452072
title: Additional file 5 of Systematic identification and comparative analysis of lysine succinylation between the green and white parts of chimeric leaves of Ananas comosus var. bracteatus

description: Additional file 5: Table S2. Proteins with opposing changes of protein and succinylation levels in the white (Wh) parts. Gr: green parts.
DOI: 10.6084/m9.figshare.12452072.v1
title: Additional file 5 of Systematic identification and comparative analysis of lysine succinylation between the green and white parts of chimeric leaves of Ananas comosus var. bracteatus

description: Additional file 5: Table S2. Proteins with opposing changes of protein and succinylation levels in the white (Wh) parts. Gr: green parts.
DOI: 10.6084/m9.figshare.25260177.v1
title: Magma mixing between rhyolite and pseudotachylite as the origin for the Glencoe 'Flinty Crush Rock'

description: The compositions of matrix regions of flinty crush rock from Stob Mic Mhartuin.
DOI: 10.6084/m9.figshare.25260177
title: Magma mixing between rhyolite and pseudotachylite as the origin for the Glencoe 'Flinty Crush Rock'

description: The compositions of matrix regions of flinty crush rock from Stob Mic Mhartuin.
DOI: 10.6084/m9.figshare.25260180.v1
title: Magma mixing between rhyolite and pseudotachylite as the origin for the Glencoe 'Flinty Crush Rock'

description: Examples of power-law distributions modified by removing a constant radius from each clast.
DOI: 10.6084/m9.figshare.25260180
title: Magma mixing between rhyolite and pseudotachylite as the origin for the Glencoe 'Flinty Crush Rock'

description: Examples of power-law distributions modified by removing a constant radius from each clast.
DOI: 10.5281/zenodo.10657314
title: EXAFS spectra during formation of palladium oxides in alumina supported palladium nanoparticles

description: This dataset contain extended X-ray absorption fine structure (EXAFS) spectra for 5%Pd/Al2O3 (named TO326) and 2%Pd/P4VP (named TO203) samples, measrured in situ with high time resolution during exposre of the samples to hydrogen and oxygen flows at different temperatures. The file Parameters.txt contain sample names, temperatures and times together with structural parameters obtained from EXAFS fitting. File Spectra.txt contain normalized EXAFS spectra (as rows) for each energy point (energies shown in the first row). Each row in Parameters.txt correspond to a row (spectrum) in Spectra.txt
DOI: 10.6084/m9.figshare.24641244.v1
title: ENCFF095QTA Homo sapiens excitatory neuron.bigWig

description: xwdjdfgf
DOI: 10.34740/kaggle/dsv/7672219
title: Mahanagar Yatayat Transport Dataset
DOI: 10.6084/m9.figshare.25260184
title: Supplementary Material for: The use of Anemia Control Model is Associated with Improved Hemoglobin Target Achievement, Lower Rates of Inappropriate Erythropoietin Stimulating Agents and Severe Anemia Among Dialysis Patients

description: INTRODUCTION
The Anemia Control Model (ACM) is a certified medical device suggesting the optimal ESA and iron dosage for patients on hemodialysis. We sought to assess the effectiveness and safety of ACM in a large cohort of hemodialysis patients.
METHODS
This is a retrospective study of dialysis patients treated in Nephrocare centers between 01-06-2013 and 31-12-2019. We compared patients treated according to ACM suggestions and patients treated in clinics where ACM was not activated. We stratified patients belonging to the reference group by historical target achievement rates in their referral centers (tier 1: &lt;70%; tier 2: 70%-80%; tier 3: &gt;80%). Groups were matched by propensity score. 
RESULTS
After matching, we obtained four groups with 85512 patient-months each. ACM had 18% higher target achievement rate, 63% smaller inappropriate ESA administration rate, and 59% smaller severe anemia risk compared to Tier 1 centers (all p&lt;0.01). The corresponding risk ratios for ACM compared to Tier 2 centers were 1.08 (95% CI: 1.08 - 1.09), 0.49 (95% CI: 0.47 - 0.51), and 0.64 (95% CI: 0.61 - 0.68); for ACM compared to Tier 3 centers, 1.01 (95% CI: 1.01 - 1.02), 0.66 (95% CI: 0.63 - 0.69), and 0.94 (95% CI: 0.88 - 1.00), respectively. ACM was associated with statistically significant reductions in ESA dose administration.
CONCLUSION
ACM was associated with increased hemoglobin target achievement rate, decreased inappropriate ESA usage and a decreased incidence of severe anemia among patients treated according to ACM suggestion.
DOI: 10.25345/c5610w357
title: MassIVE MSV000094141 - Identification of NKG7-proximal proteins by TurboID
title: NKG7 is a lysosomal membrane protein whose expression is restricted to cytotoxic lymphocytes. Although the importance of NKG7 in anti-tumor immunity has been shown, little is known about the molecular function and regulation of NKG7. To elucidate NKG7 molecular function, we performed NKG7-proximity labeling using TurboID system in 293T cells, followed by mass-spectrometry. We identified vacuolar H+ ATPase (v-ATPase; lysosomal proton pump) subunit ATP6AP2 as a potential NKG7-interacting protein, and validated the interaction via exogenous coimmunoprecipitation. We further showed that NKG7 inhibits v-ATPase activity, thereby impacting lysosomal homeostasis and mTORC1 regulation at lysosomes.
DOI: 10.25934/pr00007751.3
title: Available IPD datapackage for study 'A Phase 3, Randomized, Double-blind, Placebo-controlled, Parallel-group, Multicenter Protocol to Evaluate the Safety and Efficacy of Ustekinumab Induction and Maintenance Therapy in Subjects With Moderately to Severely Active Ulcerative Colitis'

description: The purpose of this study is to evaluate the efficacy and safety of ustekinumab as intravenous (IV: into the vein) infusion in induction study in participants with moderately to severely active Ulcerative Colitis (UC) and as subcutaneous (SC) administration in maintenance study in participants with moderately to severely active Ulcerative Colitis (UC) who have demonstrated a clinical response to Induction treatment with IV ustekinumab.
DOI: 10.5281/zenodo.8435685
title: Dataset for: Longitudinal Observations of the Effects of Ischemic Stroke on Binaural Perception, Frontiers in Neuroscience, 2023

description: This dataset contains the psychoacoustic results (tone in noise detection and lateralization) of stroke patients from measurements in the acute, subacute, and chronic phase of stroke.
DOI: 10.5281/zenodo.8435686
title: Dataset for: Longitudinal Observations of the Effects of Ischemic Stroke on Binaural Perception, Frontiers in Neuroscience, 2023

description: This dataset contains the psychoacoustic results (tone in noise detection and lateralization) of stroke patients from measurements in the acute, subacute, and chronic phase of stroke.