cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26208/fp6n-xb08
title: Supplementary data, code, and information for ‘The likelihood of recent warmth’ (Nature Scientific Reports, Mann et al. 2016)

description: 2014 was nominally the warmest year on record for both the globe and northern hemisphere based on historical records spanning the past one and a half centuries. It was the latest in a recent run of record temperatures spanning the past decade and a half. Press accounts reported odds as low as one-in-650 million that the observed run of global temperature records would be expected to occur in the absence of human-caused global warming. Press reports notwithstanding, the question of how likely observed temperature records may have have been both with and without human influence is interesting in its own right. Here we attempt to address that question using a semi-empirical approach that combines the latest (CMIP5) climate model simulations with observations of global and hemispheric mean temperature. We find that individual record years and the observed runs of record-setting temperatures were extremely unlikely to have occurred in the absence of human-caused climate change, though not nearly as unlikely as press reports have suggested. These same record temperatures were, by contrast, quite likely to have occurred in the presence of anthropogenic climate forcing.
DOI: 10.25345/c50b9c
title: MassIVE MSV000087311 - Transgenerational metabolomic signature of coral bleaching history
title: The increase in frequency and severity of coral bleaching has generated a necessity to identify attributes associated with thermal tolerance in both the coral animal and their intracellular algal symbionts. Recent advances in the field of metabolomics have allowed for the identification and investigation of such attributes through chemical profiling; however, this has yet to be investigated in gametic or zygotic life-history stages, thus limiting the understanding of how biochemical signatures are passed across generations. Here, we use mass spectrometry-based metabolomics to analyze the biochemicals associated with coral sperm, eggs, and embryos. We show a strong signal of the parent colony in all cell types and demonstrate evidence for imprinting of past bleaching events on the metabolome at both the gametic and zygotic life-history stages. Overall this work provides evidence of the transgenerational effects of thermal stress on corals, which has potentially profound implications for coral reef restoration and management.
DOI: 10.5281/zenodo.4723299
title: Synthetic data used in Cho et al. (2021)

description: Archive of the synthetic data used to verify equations formulated in Cho et al. (2021). Cho, I., Yoshida, K., & Uebayashi, H., 2021, Microtremor surveys base on rotational seismology: theoretical analysis with focus on separation of Rayleigh and Love waves in general wavefield of microtremors, submitted to Geophysical Journal International.
DOI: 10.5281/zenodo.4723298
title: Synthetic data used in Cho et al. (2021)

description: Archive of the synthetic data used to verify equations formulated in Cho et al. (2021). Cho, I., Yoshida, K., & Uebayashi, H., 2021, Microtremor surveys base on rotational seismology: theoretical analysis with focus on separation of Rayleigh and Love waves in general wavefield of microtremors, submitted to Geophysical Journal International.
DOI: 10.17894/ucph.0d7524f2-b6ad-4a69-a718-5ed7cdfbe4b0
title: Sanger Sequencing data of attP of Sa3int phages
DOI: 10.5281/zenodo.4722066
title: Data repository of the paper "An optical neural network using less than 1 photon per multiplication".

description: This repository contains the data and code necessary to derive the main results of the paper “An optical neural network using less than 1 photon per multiplication”. It includes the datasets generated during the characterization of dot-product accuracy (Figure 2) and the execution of the ONN using different photon budgets (Figure 3), along with the code used to analyze them. Besides, the codes for training the neural network model and collecting data in the experimental setup are also included. The scripts and data in "Figure 2.zip" ("Figure 3.zip") were used to generate Figure 2 (Figure 3) in the main manuscript. "ONN-device-control.zip" contains the device control codes in the experiments for data collection, available at https://github.com/mcmahon-lab/ONN-device-control. "ONN-QAT-SQL.zip" contains the trained model and training scripts (Python 3.8.3, PyTorch version 1.7.0, torchvision version 0.8.1) for the neural network executed in the experiment, available at https://github.com/mcmahon-lab/ONN-QAT-SQL. For more details, please refer to the README files in the root directory and each separate folder.
DOI: 10.5281/zenodo.4722065
title: Data repository of the paper "An optical neural network using less than 1 photon per multiplication".

description: This repository contains the data and code necessary to derive the main results of the paper “An optical neural network using less than 1 photon per multiplication”. It includes the datasets generated during the characterization of dot-product accuracy (Figure 2) and the execution of the ONN using different photon budgets (Figure 3), along with the code used to analyze them. Besides, the codes for training the neural network model and collecting data in the experimental setup are also included. The scripts and data in "Figure 2.zip" ("Figure 3.zip") were used to generate Figure 2 (Figure 3) in the main manuscript. "ONN-device-control.zip" contains the device control codes in the experiments for data collection, available at https://github.com/mcmahon-lab/ONN-device-control. "ONN-QAT-SQL.zip" contains the trained model and training scripts (Python 3.8.3, PyTorch version 1.7.0, torchvision version 0.8.1) for the neural network executed in the experiment, available at https://github.com/mcmahon-lab/ONN-QAT-SQL. For more details, please refer to the README files in the root directory and each separate folder.
DOI: 10.5281/zenodo.4650995
title: MS data of Increase of SARS-CoV-2 RNA load in faecal samples prompts for rethinking of SARS-CoV-2 biology and COVID-19 epidemiology

description: Mass spectrometry dataset, as described in Petrillo, M. et al. Increase of SARS-CoV-2 RNA load in faecal samples prompts for rethinking of SARS-CoV-2 biology and COVID-19 epidemiology. It consists of one file in format .mgf
DOI: 10.17894/ucph.d6a30dc3-54bb-430e-a90c-c4e5baefd3ca
title: Source data for Manuscript entiled Bacteriophages encoding human immune evasion factors adapt to livestock-associated strains of Staphylococcus aureus through rounds of integration and excision
DOI: 10.34740/kaggle/dsv/2166390
title: multilevel causality relations deaths age sex
DOI: 10.34740/kaggle/dsv/2166397
title: multilevel causality relations deaths age sex
DOI: 10.5281/zenodo.4562345
title: ViquiQuAD: an extractive QA dataset from Catalan Wikipedia

description: <em>Dataset de QA extractiu amb 6282 parells de pregunta-resposta desenvolupats a partir d'articles de la Viquipèdia (https://</em>ca.wikipedia.org<em>) </em><em>utilitzats sota la llicència Creative Commons Reconeixement i Compartir-Igual.</em> <em>“ViquiQuAD: an extractive QA dataset from Catalan Wikipedia” es distribueix sota la llicència CC-BY-SA per Carlos Rodríguez y Carme Armentano de la Unitat de Text Mining del BSC - CNS.</em> From a set of high quality original articles in the Catalan Wikipedia (the Viquipedia), 597 were randomly chosen, and from them 3111, 5 to 8 sentence contexts were extracted. Creation of between 1 and 5 questions for each context was commissioned, following an adaptation of the guidelines from SQUAD 1.0 (Rajpurkar, Pranav et al. “SQuAD: 100, 000+ Questions for Machine Comprehension of Text.” EMNLP (2016)), http://arxiv.org/abs/1606.05250. In total, 15153 pairs of a question and an context fragment that contains the answer were annotated. Funded by the Generalitat de Catalunya, Departament de Polítiques Digitals i Administració Pública (AINA), MT4ALL and Plan de Impulso de las Tecnologías del Lenguaje (Plan TL).
DOI: 10.5281/zenodo.4605496
title: MICCAI 2016 challenge dataset demographics data

description: This dataset contains supplementary material for the 2016 MS segmentation challenge data article. It contains the full demographic data for the datasets opened to the public.
DOI: 10.6084/m9.figshare.12951861
title: Sequential Multiple Assignment Randomized Trials for COMparing Personalized Antibiotic StrategieS (SMART COMPASS): Design Considerations

description: Clinical patient management is dynamic. It is not based on a single decision but on a sequence of decisions, with adjustments of therapy overtime, where adjustment are personalized to individual patients. However, strategies allowing for such adjustments are infrequently studied. In the treatment of serious bacterial infections, there are two therapeutic decision points: empirical therapy when the patient is first seen by the clinician, and definitive therapy when drug susceptibility results are available to help guide therapeutic choices. COMparing Personalized Antibiotic StrategieS (COMPASS) is a trial design that compares strategies consistent with clinical practice rather than specific treatments. A strategy is a decision-rule guiding treatments of bacterial infections both at the empirical and at the definitive stages. Sequential multiple assignment randomized (SMART) COMPASS allows evaluation of strategies when there are multiple definitive therapy choices. SMART COMPASS is a pragmatic design, mirroring antibiotic treatment decision-making as they unfold in clinical practice and addressing the most relevant question for treating patients: identification of the patient-management strategy that optimizes ultimate patient outcomes. Complex statistical challenges are encountered during the design of SMART COMPASS including how to: appropriately estimate effects and associated standard errors within the context of sequential randomization, identify the best of several strategies while controlling trial-wise error, and calculate sample size and power when trying to identify the optimal strategy. Design considerations for SMART COMPASS are discussed.
DOI: 10.6084/m9.figshare.13187434
title: Type I Error Inflation of Blinded Sample Size Re-Estimation in Equivalence Testing

description: Biosimilar products are a relative newcomer in the pharmaceutical industry. It was only in 2006 that the first biosimilar product, Omnitrope[textregistered] (somatropin), a human growth hormone produced by Sandoz was approved by the European Medicine Agency, followed later the same year by the US Food & Drug Administration, and in 2009 by Pharmaceuticals and Medical Devices Agency in Japan. The clinical component of a biosimilar development borrows extensively from traditional drug development. However, when it comes to clinical study designs, this may not always be applicable. This article investigates Type I error violations that occur when blinded sample size reviews are applied in equivalence testing as used in biosimilar drug development. We give a derivation which explains why such violations are more pronounced in equivalence testing than in the case of superiority testing. In addition, the amount of Type I error inflation is quantified by simulation as well as by some theoretical considerations. Nonnegligible Type I error violations arise when blinded interim reassessments of sample sizes are performed particularly if sample sizes are small, but within the range of what is practically relevant.
DOI: 10.6084/m9.figshare.12951861.v1
title: Sequential Multiple Assignment Randomized Trials for COMparing Personalized Antibiotic StrategieS (SMART COMPASS): Design Considerations

description: Clinical patient management is dynamic. It is not based on a single decision but on a sequence of decisions, with adjustments of therapy overtime, where adjustment are personalized to individual patients. However, strategies allowing for such adjustments are infrequently studied. In the treatment of serious bacterial infections, there are two therapeutic decision points: empirical therapy when the patient is first seen by the clinician, and definitive therapy when drug susceptibility results are available to help guide therapeutic choices. COMparing Personalized Antibiotic StrategieS (COMPASS) is a trial design that compares strategies consistent with clinical practice rather than specific treatments. A strategy is a decision-rule guiding treatments of bacterial infections both at the empirical and at the definitive stages. Sequential multiple assignment randomized (SMART) COMPASS allows evaluation of strategies when there are multiple definitive therapy choices. SMART COMPASS is a pragmatic design, mirroring antibiotic treatment decision-making as they unfold in clinical practice and addressing the most relevant question for treating patients: identification of the patient-management strategy that optimizes ultimate patient outcomes. Complex statistical challenges are encountered during the design of SMART COMPASS including how to: appropriately estimate effects and associated standard errors within the context of sequential randomization, identify the best of several strategies while controlling trial-wise error, and calculate sample size and power when trying to identify the optimal strategy. Design considerations for SMART COMPASS are discussed.
DOI: 10.6084/m9.figshare.13187434.v2
title: Type I Error Inflation of Blinded Sample Size Re-Estimation in Equivalence Testing

description: Biosimilar products are a relative newcomer in the pharmaceutical industry. It was only in 2006 that the first biosimilar product, Omnitrope[textregistered] (somatropin), a human growth hormone produced by Sandoz was approved by the European Medicine Agency, followed later the same year by the US Food & Drug Administration, and in 2009 by Pharmaceuticals and Medical Devices Agency in Japan. The clinical component of a biosimilar development borrows extensively from traditional drug development. However, when it comes to clinical study designs, this may not always be applicable. This article investigates Type I error violations that occur when blinded sample size reviews are applied in equivalence testing as used in biosimilar drug development. We give a derivation which explains why such violations are more pronounced in equivalence testing than in the case of superiority testing. In addition, the amount of Type I error inflation is quantified by simulation as well as by some theoretical considerations. Nonnegligible Type I error violations arise when blinded interim reassessments of sample sizes are performed particularly if sample sizes are small, but within the range of what is practically relevant.
DOI: 10.6084/m9.figshare.13187434.v1
title: Type I error inflation of blinded sample size re-estimation in equivalence testing

description: Biosimilar products are a relative newcomer in the pharmaceutical industry. It was only in 2006 that the first biosimilar product, Omnitrope<sup>®</sup> (somatropin), a human growth hormone produced by Sandoz was approved by the European Medicine Agency (EMA), followed later the same year by the US Food & Drug Administration (FDA) [1], and in 2009 by Pharmaceuticals and Medical Devices Agency (PMDA) in Japan. The clinical component of a biosimilar development borrows extensively from traditional drug development. However, when it comes to clinical study designs, this may not always be applicable. This paper investigates type I error violations that occur when blinded sample size reviews are applied in equivalence testing as used in biosimilar drug development. We give a derivation which explains why such violations are more pronounced in equivalence testing than in the case of superiority testing. In addition, the amount of type I error inflation is quantified by simulation as well as by some theoretical considerations. Non-negligible type I error violations arise when blinded interim re-assessments of sample sizes are performed particularly if sample sizes are small, but within the range of what is practically relevant.
DOI: 10.6084/m9.figshare.13187437.v2
title: Assessment of Overall Treatment Effect in the Presence of Inconsistent Regional Effects in Multiregional Clinical Trials

description: The use of multiregional clinical trials (MRCTs) in clinical developments increased to accelerate patients’ access to new drugs globally. MRCTs inherently assume that the treatment effect is consistent across regions; therefore, we generally estimate the overall treatment effect using a weighted mean of regional estimates with the proportions of enrolled patients as a weight. However, recent MRCTs occasionally encountered an inconsistency in treatment effect among regions. This study was motivated by two actual MRCTs showing the inconsistency of the treatment effects. In these trials, inconsistent treatment effects were observed in a few regions and the estimates in these regions impacted the overall treatment effect estimate. In this study, we propose an exploratory analysis to estimate the overall treatment effect based on robust estimation. The proposed estimator adaptively changes the weights for each region by minimizing the weighted jackknife-based mean squared error of the proposed estimator. We examined the utility of the proposed method through simulation studies. We found that the proposed estimators were less biased and more statistically powerful compared with other ordinary estimators when inconsistent regions existed. We also illustrated estimation of the overall treatment effect by applying the proposed estimators to the two MRCTs.
DOI: 10.6084/m9.figshare.13187437.v1
title: Assessment of overall treatment effect in the presence of inconsistent regional effects in multi-regional clinical trials

description: The use of multi-regional clinical trials (MRCTs) in clinical developments increased to accelerate patients’ access to new drugs globally. MRCTs inherently assume that the treatment effect is consistent across regions; therefore, we generally estimate the overall treatment effect using a weighted mean of regional estimates with the proportions of enrolled patients as a weight. However, recent MRCTs occasionally encountered an inconsistency in treatment effect among regions. This study was motivated by two actual MRCTs showing the inconsistency of the treatment effects. In these trials, inconsistent treatment effects were observed in a few regions and the estimates in these regions impacted the overall treatment effect estimate. In this study, we propose an exploratory analysis to estimate the overall treatment effect based on robust estimation. The proposed estimator adaptively changes the weights for each region by minimizing the weighted jackknife-based mean squared error of the proposed estimator. We examined the utility of the proposed method through simulation studies. We found that the proposed estimators were less biased and more statistically powerful compared with other ordinary estimators when inconsistent regions existed. We also illustrated estimation of the overall treatment effect by applying the proposed estimators to the two MRCTs.
DOI: 10.6084/m9.figshare.13093092.v1
title: Blinded Sample Size Re-estimation in Comparative Clinical Trials With Overdispersed Count Data: Incorporation of Misspecification of the Variance Function

description: In randomized clinical trials to compare overdispersed count data between treatment groups, blinded sample size re-estimation (BSSR) is an effective approach to ensure power control even under possible misspecifications of the variance function on overdispersion specified at the design stage. Based on interim clinical trial data, the existing BSSR methods try to find a more appropriate value of the dispersion parameter for a “fixed” variance function specified at the design stage. In this paper, we develop a new BSSR method that allows for modification of the variance function itself. Simulation studies demonstrated a stable power control of the proposed method. An application to a phase III clinical trial in chronic obstructive pulmonary disease also demonstrated effectiveness of the proposed method.
DOI: 10.6084/m9.figshare.13187437
title: Assessment of Overall Treatment Effect in the Presence of Inconsistent Regional Effects in Multiregional Clinical Trials

description: The use of multiregional clinical trials (MRCTs) in clinical developments increased to accelerate patients’ access to new drugs globally. MRCTs inherently assume that the treatment effect is consistent across regions; therefore, we generally estimate the overall treatment effect using a weighted mean of regional estimates with the proportions of enrolled patients as a weight. However, recent MRCTs occasionally encountered an inconsistency in treatment effect among regions. This study was motivated by two actual MRCTs showing the inconsistency of the treatment effects. In these trials, inconsistent treatment effects were observed in a few regions and the estimates in these regions impacted the overall treatment effect estimate. In this study, we propose an exploratory analysis to estimate the overall treatment effect based on robust estimation. The proposed estimator adaptively changes the weights for each region by minimizing the weighted jackknife-based mean squared error of the proposed estimator. We examined the utility of the proposed method through simulation studies. We found that the proposed estimators were less biased and more statistically powerful compared with other ordinary estimators when inconsistent regions existed. We also illustrated estimation of the overall treatment effect by applying the proposed estimators to the two MRCTs.
DOI: 10.18112/openneuro.ds003642.v1.0.0
title: CEREBRUM-7T: Fast and Fully-volumetric Brain Segmentation of 7 Tesla MR Volumes
DOI: 10.6084/m9.figshare.12472634
title: Data set containing process execution log data with time sequence information for conference proceeding 2020 paper: Analyzing Process Concept Drifts Based on Sensor Event Streams During Runtime

description: A data set containing 37 instances of a manufacturing process. It describes the production of a part and the measurement of the produced parts dimensions as a time sequence
DOI: 10.6084/m9.figshare.12472634.v1
title: Data set containing process execution log data with time sequence information for conference proceeding 2020 paper: Analyzing Process Concept Drifts Based on Sensor Event Streams During Runtime

description: A data set containing 37 instances of a manufacturing process. It describes the production of a part and the measurement of the produced parts dimensions as a time sequence
DOI: 10.6084/m9.figshare.13655975.v7
title: Characteristics of volunteers

description: Description of the volunteers including age, sex, height and others anthropometric data.<br><strong>CC BY-NC-SA licence<br></strong>
DOI: 10.6084/m9.figshare.12130155
title: D'Ario_et_al_2021_Imaging_data_CDT1-CFP_time_course_replicate_2_38h_to_46h

description: This dataset contains images of Arabidopsis shoot apical meristems expressing cell cycle reporters. These images have been used to study how cell cycle progression is coordinated with cell growth in plants. The images have been segmented in three dimensions and tracked in time course experiments; cell volumes, position in the meristem and expression level of reporter genes have been measured. The details of genotypes and reporter genes used, imaging methods and processing steps are described in the associated manuscript.
DOI: 10.6084/m9.figshare.12130155.v2
title: D'Ario_et_al_2021_Imaging_data_CDT1-CFP_time_course_replicate_2_38h_to_46h

description: This dataset contains images of Arabidopsis shoot apical meristems expressing cell cycle reporters. These images have been used to study how cell cycle progression is coordinated with cell growth in plants. The images have been segmented in three dimensions and tracked in time course experiments; cell volumes, position in the meristem and expression level of reporter genes have been measured. The details of genotypes and reporter genes used, imaging methods and processing steps are described in the associated manuscript.