cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13811888.v1
title: A phase 1b clinical trial optimizing regulatory T cell depletion in combination with platinum-based chemotherapy in thoracic cancers

description: <b>Background</b>: Single-agent cyclophosphamide can deplete regulatory T-cells (Treg). We aimed to determine optimal dosing and scheduling of oral cyclophosphamide, alongside pemetrexed-based chemotherapy, to deplete Treg in mesothelioma or non-small-cell lung cancer patients. <b>Methods</b>: 31 Patients received pemetrexed ± cisplatin or carboplatin on day 1 of a 21-day cycle (maximum 6 cycles). From cycle two, patients received cyclophosphamide, 50 mg/day, with intrapatient escalation to maximum 100/150 mg/day alternately. Immunological changes were examined by flow cytometry. Primary endpoint was Treg proportion of CD4<sup>+</sup> T-cells, with doses tailored to target Treg nadir &lt;4%. <b>Results</b>: Reduction in Treg proportion was observed on day 8 of all cycles, and was not augmented by cyclophosphamide. Few patients achieved the &lt;4% Treg target. Treg proliferation reached nadir one week after chemotherapy, and peaked on day 1 of the subsequent cycle. Efficacy parameters were similar to chemotherapy alone. Seventeen percent of patients ceased cyclophosphamide due to toxicity. <b>Conclusions</b>: Specific Treg depletion to the degree seen with single-agent cyclophosphamide was not observed during pemetrexed-based chemotherapy. This study highlights the poor evidence basis for use of cyclophosphamide as an immunotherapeutic in combination with chemotherapy, and the importance of detailed flow cytometry studies. <b>Trial registration</b>: Clinical trial registration: www.anzctr.org.au identifier is ACTRN12609000260224.
DOI: 10.6084/m9.figshare.13574839
title: Predicting pathological response to chemoradiotherapy for rectal cancer: a systematic review

description: <b>Introduction</b>: Pathological complete response (pCR) rates of approximately 20% following neoadjuvant long-course chemoradiotherapy for rectal cancer have given rise to non-operative or watch-and-wait (W&W) management. To improve outcomes there has been significant research into predictors of response. The goal is to optimize selection for W&W, avoid chemoradiotherapy in those who won’t benefit and improve treatment to maximize the clinical complete response (cCR) rate and the number of patients who can be considered for W&W. <b>Areas covered</b>: A systematic review of articles published 2008–2018 and indexed in PubMed, Embase or Medline was performed to identify predictors of pathological response (including pCR and recognized tumor regression grades) to fluoropyrimidine-based chemoradiotherapy in patients who underwent total mesorectal excision for rectal cancer. Evidence for clinical, biomarker and radiological predictors is discussed as well as potential future directions. <b>Expert opinion</b>: Our current ability to predict the response to chemoradiotherapy for rectal cancer is very limited. cCR of 40% has been achieved with total neoadjuvant therapy. If neoadjuvant treatment for rectal cancer continues to improve it is possible that the treatment for rectal cancer may eventually parallel that of anal squamous cell carcinoma, with surgery reserved for the minority of patients who don’t respond to chemoradiotherapy.
DOI: 10.6084/m9.figshare.13574839.v1
title: Predicting pathological response to chemoradiotherapy for rectal cancer: a systematic review

description: <b>Introduction</b>: Pathological complete response (pCR) rates of approximately 20% following neoadjuvant long-course chemoradiotherapy for rectal cancer have given rise to non-operative or watch-and-wait (W&W) management. To improve outcomes there has been significant research into predictors of response. The goal is to optimize selection for W&W, avoid chemoradiotherapy in those who won’t benefit and improve treatment to maximize the clinical complete response (cCR) rate and the number of patients who can be considered for W&W. <b>Areas covered</b>: A systematic review of articles published 2008–2018 and indexed in PubMed, Embase or Medline was performed to identify predictors of pathological response (including pCR and recognized tumor regression grades) to fluoropyrimidine-based chemoradiotherapy in patients who underwent total mesorectal excision for rectal cancer. Evidence for clinical, biomarker and radiological predictors is discussed as well as potential future directions. <b>Expert opinion</b>: Our current ability to predict the response to chemoradiotherapy for rectal cancer is very limited. cCR of 40% has been achieved with total neoadjuvant therapy. If neoadjuvant treatment for rectal cancer continues to improve it is possible that the treatment for rectal cancer may eventually parallel that of anal squamous cell carcinoma, with surgery reserved for the minority of patients who don’t respond to chemoradiotherapy.
DOI: 10.6084/m9.figshare.14562231
title: barcodedata.zip

description: Supporting data and code for my re-analysis of Thompson & Newmaster 2014 Biodiversity & Conservation.
DOI: 10.6084/m9.figshare.14562231.v1
title: barcodedata.zip

description: Supporting data and code for my re-analysis of Thompson & Newmaster 2014 Biodiversity & Conservation.
DOI: 10.6084/m9.figshare.12029685.v1
title: Characterization of the Paint from “The Lord’s Transfiguration” Icon by Grigore Ranite

description: “The Lord’s Transfiguration” icon painted by Grigore Ranite belongs to a collection of altarpiece icons from the Ethnographic Museum of Transylvania. The aim of this paper is to present the results obtained from the scientific investigations carried out to establish the materials and methods used by the painter for the accomplishment of the religious art work, both for conservation and restoration purposes, as well as to enrich the knowledge about the work of this particular author and about the Transylvanian iconography in general. The analyses were performed by means of X-ray fluorescence (XRF) spectroscopy and destructive and nondestructive Fourier transform infrared (FTIR) spectroscopy.
DOI: 10.6084/m9.figshare.12115161.v1
title: Characterization of the Paint Used by Dumitru Ispas in the Wooden Straja Church, Cluj County, Romania

description: The wooden Straja Church represents an interesting historical monument from Transylvania that still retains the original popular religious paintings with various degrees of degradation. This paper aims to present the scientific investigation results about the materials and methods used by the painter and his son for both restoration and conservation purposes, and also to enrich the knowledge regarding the work of this author in particular and Transylvanian historical religious art in general. The investigations were performed by means of X-ray fluorescence (XRF) spectroscopy, destructive and nondestructive Fourier transform infrared (FTIR) spectroscopy, and differential scanning calorimetry (DSC).
DOI: 10.6084/m9.figshare.13379084.v3
title: Data and R codes from: Testing the underlying assumptions of dilution effect mechanisms through quantifying the long-term dynamics of a pathogen in multiple host species.

description: Data and R codes from: <i>Garrido et al. 2021. </i><i>Testing the underlying assumptions of dilution effect mechanisms through quantifying the long-term dynamics of a pathogen in multiple host species.</i>
DOI: 10.21942/uva.14216294
title: Data set belonging to Verbeij et al. (2021). The Accuracy and Validity of Social Media Use Measures Among Adolescents.csv

description: These data sets belongs to:<br>Verbeij, T., Pouwels, J. L., Beyens, I., & Valkenburg, P. M. (2021). The accuracy and validity of self-reported social media use measures among adolescents. <i>Computers in Human Behavior Reports</i>, <i>3</i>, 100090. https://doi.org/10.1016/j.chbr.2021.100090<br>The preregistration of the design, sampling and analysis plan of the study, as well as all syntax files and online supplemental materials are available on the Open Science Framework (OSF) at https://osf.io/sp3wf/.<br><br>For more information, please contact the authors at t.verbeij@uva.nl or info@project-awesome.nl.
DOI: 10.21942/uva.14216294.v1
title: Data set belonging to Verbeij et al. (2021). The Accuracy and Validity of Social Media Use Measures Among Adolescents.csv

description: These data sets belongs to:<br>Verbeij, T., Pouwels, J. L., Beyens, I., & Valkenburg, P. M. (2021). The accuracy and validity of self-reported social media use measures among adolescents. <i>Computers in Human Behavior Reports</i>, <i>3</i>, 100090. https://doi.org/10.1016/j.chbr.2021.100090<br>The preregistration of the design, sampling and analysis plan of the study, as well as all syntax files and online supplemental materials are available on the Open Science Framework (OSF) at https://osf.io/sp3wf/.<br><br>For more information, please contact the authors at t.verbeij@uva.nl or info@project-awesome.nl.
DOI: 10.6084/m9.figshare.13379084.v4
title: Data and R codes from: Testing the underlying assumptions of dilution effect mechanisms through quantifying the long-term dynamics of a pathogen in multiple host species.

description: Data and R codes from: <i>Garrido et al. 2021. </i><i>Testing the underlying assumptions of dilution effect mechanisms through quantifying the long-term dynamics of a pathogen in multiple host species.</i>
DOI: 10.6084/m9.figshare.10297793
title: A causal modelling framework for reference-based imputation and tipping point analysis in clinical trials with quantitative outcome

description: We consider estimation in a randomised placebo-controlled or standard-of-care-controlled drug trial with quantitative outcome, where participants who discontinue an investigational treatment are not followed up thereafter, and the estimand follows a treatment policy strategy for handling treatment discontinuation. Our approach is also useful in situations where participants take rescue medication or a subsequent line of therapy and the estimand follows a hypothetical strategy to estimate the effect of initially randomised treatment in the absence of rescue or other active treatment. Carpenter et al proposed reference-based imputation methods which use a reference arm to inform the distribution of post-discontinuation outcomes and hence to inform an imputation model. However, the reference-based imputation methods were not formally justified. We present a causal model which makes an explicit assumption in a potential outcomes framework about the maintained causal effect of treatment after discontinuation. We use mathematical argument and a simulation study to show that the “jump to reference”, “copy reference” and “copy increments in reference” reference-based imputation methods, with the control arm as the reference arm, are special cases of the causal model with specific assumptions about the causal treatment effect. We also show that the causal model provides a flexible and transparent framework for a tipping point sensitivity analysis in which we vary the assumptions made about the causal effect of discontinued treatment. We illustrate the approach with data from two longitudinal clinical trials.
DOI: 10.6084/m9.figshare.10297793.v2
title: A causal modelling framework for reference-based imputation and tipping point analysis in clinical trials with quantitative outcome

description: We consider estimation in a randomised placebo-controlled or standard-of-care-controlled drug trial with quantitative outcome, where participants who discontinue an investigational treatment are not followed up thereafter, and the estimand follows a treatment policy strategy for handling treatment discontinuation. Our approach is also useful in situations where participants take rescue medication or a subsequent line of therapy and the estimand follows a hypothetical strategy to estimate the effect of initially randomised treatment in the absence of rescue or other active treatment. Carpenter et al proposed reference-based imputation methods which use a reference arm to inform the distribution of post-discontinuation outcomes and hence to inform an imputation model. However, the reference-based imputation methods were not formally justified. We present a causal model which makes an explicit assumption in a potential outcomes framework about the maintained causal effect of treatment after discontinuation. We use mathematical argument and a simulation study to show that the “jump to reference”, “copy reference” and “copy increments in reference” reference-based imputation methods, with the control arm as the reference arm, are special cases of the causal model with specific assumptions about the causal treatment effect. We also show that the causal model provides a flexible and transparent framework for a tipping point sensitivity analysis in which we vary the assumptions made about the causal effect of discontinued treatment. We illustrate the approach with data from two longitudinal clinical trials.
DOI: 10.6084/m9.figshare.10297793.v1
title: A causal modelling framework for reference-based imputation and tipping point analysis in clinical trials with quantitative outcome

description: We consider estimation in a randomised placebo-controlled or standard-of-care-controlled drug trial with quantitative outcome, where participants who discontinue an investigational treatment are not followed up thereafter, and the estimand follows a treatment policy strategy for handling treatment discontinuation. Our approach is also useful in situations where participants take rescue medication or a subsequent line of therapy and the estimand follows a hypothetical strategy to estimate the effect of initially randomised treatment in the absence of rescue or other active treatment. Carpenter et al proposed reference-based imputation methods which use a reference arm to inform the distribution of post-discontinuation outcomes and hence to inform an imputation model. However, the reference-based imputation methods were not formally justified. We present a causal model which makes an explicit assumption in a potential outcomes framework about the maintained causal effect of treatment after discontinuation. We use mathematical argument and a simulation study to show that the “jump to reference”, “copy reference” and “copy increments in reference” reference-based imputation methods, with the control arm as the reference arm, are special cases of the causal model with specific assumptions about the causal treatment effect. We also show that the causal model provides a flexible and transparent framework for a tipping point sensitivity analysis in which we vary the assumptions made about the causal effect of discontinued treatment. We illustrate the approach with data from two longitudinal clinical trials.
DOI: 10.5281/zenodo.4743764
title: SILVER - Subj B data

description: pre-processed (using `read_and_save_TURBINE.m`) k-space TURBINE data in a healthy volunteer, B, acquired on 3T Siemens Prisma 16.3.2021. Angles with which data was acquired (a, and b are repeats of the same acquisition method): GR (111.24610) UNIFORM 1/46 (3.9130) UNIFORM 1/55 (3.2727) UNIFORM 1/10 (18.0000) UNIFORM 1/8 (22.5000) SILVER {8,55} electrostatic_potential (157.1022) SILVER {10,46} electrostatic_potential (53.6145) Resting state (rs) and task fMRI data was also acquired. The task was a 30 s on 30 s off flashing checkerboard. Sensitivity maps derived from the GR are also included along with noise covariances. Separate maps are derived for the fMRI experiments (from GR rs) and for the noise measurements (from GRa). The covariances are derived from the same GR scans' pre-scan noise measurement.
DOI: 10.5281/zenodo.4743763
title: SILVER - Subj B data

description: pre-processed (using `read_and_save_TURBINE.m`) k-space TURBINE data in a healthy volunteer, B, acquired on 3T Siemens Prisma 16.3.2021. Angles with which data was acquired (a, and b are repeats of the same acquisition method): GR (111.24610) UNIFORM 1/46 (3.9130) UNIFORM 1/55 (3.2727) UNIFORM 1/10 (18.0000) UNIFORM 1/8 (22.5000) SILVER {8,55} electrostatic_potential (157.1022) SILVER {10,46} electrostatic_potential (53.6145) Resting state (rs) and task fMRI data was also acquired. The task was a 30 s on 30 s off flashing checkerboard. Sensitivity maps derived from the GR are also included along with noise covariances. Separate maps are derived for the fMRI experiments (from GR rs) and for the noise measurements (from GRa). The covariances are derived from the same GR scans' pre-scan noise measurement.
DOI: 10.5281/zenodo.4744695
title: Halcyon badia SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744694
title: Halcyon badia SPAdes preassembly

description: .
DOI: 10.6084/m9.figshare.14562273
title: NEUROLOGY/2021/170855 Supplemental References

description: Supplemental References
DOI: 10.6084/m9.figshare.13227464
title: 16S rRNA sequences from deadwood studies

description: 16S rRNA representative sequence of bacterial genus Sodalis extracted from deadwood amplicon studies. <br><br>Selected as most abundant sequence within OTUs at 97% similarity threshold.
DOI: 10.6084/m9.figshare.14562279
title: nifH phylogenetic tree Proteobacteria

description: Phylogenetic tree of nifH genes from Proteobacteria.<br>
DOI: 10.6084/m9.figshare.13221074
title: Sodalis deadwood metagenome mapping

description: Anvio database files with occurrence of Sodalis strain in deadwood metagenome.<br>
DOI: 10.6084/m9.figshare.13221074.v1
title: Sodalis deadwood metagenome mapping

description: Anvio database files with occurrence of Sodalis strain in deadwood metagenome.<br>
DOI: 10.6084/m9.figshare.13227464.v1
title: 16S rRNA sequences from deadwood studies

description: 16S rRNA representative sequence of bacterial genus Sodalis extracted from deadwood amplicon studies. <br><br>Selected as most abundant sequence within OTUs at 97% similarity threshold.
DOI: 10.6084/m9.figshare.13221065
title: Anvio Sodalis pangenome databases

description: Anvio database files for pangenome analysis of bacterial genus Sodalis.Sodalis_only-GENOMES is a collection of available Sodalis genomes.<br>Sodalis-PAN pangenome database.<br>
DOI: 10.6084/m9.figshare.14562279.v1
title: nifH phylogenetic tree Proteobacteria

description: Phylogenetic tree of nifH genes from Proteobacteria.<br>
DOI: 10.6084/m9.figshare.13221065.v1
title: Anvio Sodalis pangenome databases

description: Anvio database files for pangenome analysis of bacterial genus Sodalis.Sodalis_only-GENOMES is a collection of available Sodalis genomes.<br>Sodalis-PAN pangenome database.<br>
DOI: 10.6084/m9.figshare.14562291
title: Supplementary Table 1

description: Outlet temperature (in °C) and chemical composition of the fumarolic discharge from Calbuco volcano PDC. All compounds are reported in umol/mol as gas dry fraction, except H2O which is reported in mol%.
DOI: 10.21227/4ma4-3z49
title: AI-Based and Mobility-aware Energy Efficient Resource Allocation and Trajectory Design for NFV enabled Aerial Networks

description: This repository includes the DDPG, MADDPG, HHCDA, and MAHHCDA based on the paper "AI-Based and Mobility-aware Energy Efficient Resource Allocation and Trajectory Design for NFV enabled Aerial Networks".
DOI: 10.5281/zenodo.4744741
title: Heteractis magnifica SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744740
title: Heteractis magnifica SPAdes preassembly

description: .
DOI: 10.6084/m9.figshare.13489728
title: Progression of potential etiologies of the chronic kidney disease of unknown etiology in Sri Lanka

description: Chronic kidney disease of unknown etiology (CKDu) is a major health issue in agricultural areas in Sri Lanka. Despite many attempts to identifying causative factors of CKDu, the real cause/s remain/s elusive to date. Understanding the progression of potential etiologies may provide valuable insight into this quest. Literature relevant to CKDu addresses several etiologies, including quality of drinking water in the affected areas including hardness, fluoride, ionicity, agrochemical and heavy metal contaminations, consumption of contaminated food, and the genetic makeup of vulnerable populations. Progression of the etiologies revealed persistent interest in heavy metals of multiple origins: waterborne, foodborne, or soilborne. Secondary factors, such as water hardness, fluoride, and ionicity appear to act synergistically, aggravating the role of heavy metals on the onset, and the progression of CKDu. Demographical factors, such as male sex, over 50 years of age, agriculture-related occupation, and the consumption of contaminated water and food are intricately related with the disease progression while other minor risk factors such as smoking, alcohol consumption, etc. exasperate the disease condition. Since, none of these etiologies are examined adequately, conducting laboratory exposure studies under <i>in-vivo</i> and <i>in-vitro</i> settings to understand their role in CKDu is crucial.
DOI: 10.6084/m9.figshare.13489728.v1
title: Progression of potential etiologies of the chronic kidney disease of unknown etiology in Sri Lanka

description: Chronic kidney disease of unknown etiology (CKDu) is a major health issue in agricultural areas in Sri Lanka. Despite many attempts to identifying causative factors of CKDu, the real cause/s remain/s elusive to date. Understanding the progression of potential etiologies may provide valuable insight into this quest. Literature relevant to CKDu addresses several etiologies, including quality of drinking water in the affected areas including hardness, fluoride, ionicity, agrochemical and heavy metal contaminations, consumption of contaminated food, and the genetic makeup of vulnerable populations. Progression of the etiologies revealed persistent interest in heavy metals of multiple origins: waterborne, foodborne, or soilborne. Secondary factors, such as water hardness, fluoride, and ionicity appear to act synergistically, aggravating the role of heavy metals on the onset, and the progression of CKDu. Demographical factors, such as male sex, over 50 years of age, agriculture-related occupation, and the consumption of contaminated water and food are intricately related with the disease progression while other minor risk factors such as smoking, alcohol consumption, etc. exasperate the disease condition. Since, none of these etiologies are examined adequately, conducting laboratory exposure studies under <i>in-vivo</i> and <i>in-vitro</i> settings to understand their role in CKDu is crucial.
DOI: 10.5281/zenodo.4744756
title: Supplementary material for Khaldy et al. 2021; Compass cue integration and its relation to the visual ecology of three tribes of ball-rolling dung beetles

description: <strong>Supplementary Materials:</strong> The following are available online at [link]; Table S1: Absolute angular difference in exit bearing of each manipulation (<em>test: </em>first and second exit bearing; <em>control: </em>first and third exit bearing) for each individual beetle, in each paradigm; Table S2: Exit angles (0-359°) of ten exit rolls of ten individuals of <em>K. nigroaeneus</em>, <em>G. unicolor </em>and <em>S. fasciculatus, </em>respectively,<em> </em>and the corresponding calculated mean vector length (R); Table S3: Eye area and step size for <em>K. nigroaeneus, G. unicolor </em>and <em>S. fasciculatus. </em>
DOI: 10.5281/zenodo.4744768
title: Crosswalks among metadata schemas for data cube descriptions in RELIANCE

description: This Excel file contains crosswalks among different metadata schemas that can be used for the description of data cubes in the areas of Marine Science, Earth Sciences and Climate Research. These data cubes common contain observations of some variables in some feature of interest, taken by Earth Observation systems (e.g., satellites) or as in-situ observations.