cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5522/04/24236101
title: Child labour prevalence in the cocoa industry in Cote d'Ivoire

description:  
The data set is the one used in the paper "Estimating the prevalence of child labour in the cocoa industry via indirect elicitation methods: A mixed-methods study" by Lepine et al. It contains data collected from 1,741 cocoa producers working in Côte d’Ivoire to estimate whether child labour prevalence could be elicited from parents using indirect elicitation methods. The data set includes child labour prevalence capturing hazardous child labour levels elicited via direct questioning versus using a list experiment and a newly developed nonverbal method called ‘colorbox’.
DOI: 10.6084/m9.figshare.22040554
title: Joint Analysis of Longitudinal Data and Zero-Inflated Recurrent Events

description: Longitudinal data together with recurrent events are commonly encountered in clinical trials. In many applications, these two processes are highly correlated. When there exist a large portion of subjects not experiencing recurrent events of interest, it is possible that some of these subjects are unsusceptible to the events. Therefore, we assume the underlying population is composed of two subpopulations: one subpopulation susceptible to the recurrent events, and the other unsusceptible. In this article, we propose a joint model of longitudinal outcomes and zero-inflated recurrent event data. Our model consists of three submodels: (1) a generalized linear mixed model for the longitudinal process; (2) a proportional intensities model for the recurrent event process in the susceptible subpopulation; and (3) a logistic regression model for the probability such that a subject belongs to the unsusceptible subpopulation. We consider associations (1) between longitudinal outcomes and the zero-inflation rate; and (2) between longitudinal outcomes and the intensity rate of recurrent events in the susceptible subpopulation. Estimation is carried out by maximizing the log-likelihood function using Gaussian quadrature techniques, which can be conveniently implemented in SAS Proc NLMIXED. Simulation studies demonstrate that the proposed method performs well. We apply the method to a clinical trial.
DOI: 10.6084/m9.figshare.22040554.v1
title: Joint Analysis of Longitudinal Data and Zero-Inflated Recurrent Events

description: Longitudinal data together with recurrent events are commonly encountered in clinical trials. In many applications, these two processes are highly correlated. When there exist a large portion of subjects not experiencing recurrent events of interest, it is possible that some of these subjects are unsusceptible to the events. Therefore, we assume the underlying population is composed of two subpopulations: one subpopulation susceptible to the recurrent events, and the other unsusceptible. In this article, we propose a joint model of longitudinal outcomes and zero-inflated recurrent event data. Our model consists of three submodels: (1) a generalized linear mixed model for the longitudinal process; (2) a proportional intensities model for the recurrent event process in the susceptible subpopulation; and (3) a logistic regression model for the probability such that a subject belongs to the unsusceptible subpopulation. We consider associations (1) between longitudinal outcomes and the zero-inflation rate; and (2) between longitudinal outcomes and the intensity rate of recurrent events in the susceptible subpopulation. Estimation is carried out by maximizing the log-likelihood function using Gaussian quadrature techniques, which can be conveniently implemented in SAS Proc NLMIXED. Simulation studies demonstrate that the proposed method performs well. We apply the method to a clinical trial.
DOI: 10.6084/m9.figshare.22137797
title: Targeted Learning: Toward a Future Informed by Real-World Evidence

description: The 21st Century Cures Act of 2016 includes a provision for the U.S. Food and Drug Administration10.13039/100000038 (FDA) to evaluate the potential use of Real-World Evidence (RWE) to support new indications for use for previously approved drugs, and to satisfy post-approval study requirements. Extracting reliable evidence from Real-World Data (RWD) is often complicated by a lack of treatment randomization, potential intercurrent events, and informative loss to follow-up. Targeted Learning (TL) is a sub-field of statistics that provides a rigorous framework to help address these challenges. The TL Roadmap offers a step-by-step guide to generating valid evidence and assessing its reliability. Following these steps produces an extensive amount of information for assessing whether the study provides reliable scientific evidence, including in support of regulatory decision-making. This article presents two case studies that illustrate the utility of following the roadmap. We used targeted minimum loss-based estimation combined with super learning to estimate causal effects. We also compared these findings with those obtained from an unadjusted analysis, propensity score matching, and inverse probability weighting. Nonparametric sensitivity analyses illuminate how departures from (untestable) causal assumptions affect point estimates and confidence interval bounds that would impact the substantive conclusion drawn from the study. TL’s thorough approach to learning from data provides transparency, allowing trust in RWE to be earned whenever it is warranted.
DOI: 10.6084/m9.figshare.22137797.v1
title: Targeted learning: Towards a future informed by real-world evidence

description: The 21st Century Cures Act of 2016 includes a provision for the U.S. Food and Drug Administration (FDA) to evaluate the potential use of real-world evidence (RWE) to support new indications for use for previously approved drugs, and to satisfy post-approval study requirements. Extracting reliable evidence from real-world data (RWD) is often complicated by a lack of treatment randomization, potential intercurrent events, and informative loss to follow-up. Targeted Learning (TL) is a sub-field of statistics that provides a rigorous framework to help address these challenges. The TL Roadmap offers a step-by-step guide to generating valid evidence and assessing its reliability. Following these steps produces an extensive amount of information for assessing whether the study provides reliable scientific evidence, including in support of regulatory decision making. This paper presents two case studies that illustrate the utility of following the roadmap. We used targeted minimum loss-based estimation combined with super learning to estimate causal effects. We also compared these findings with those obtained from an unadjusted analysis, propensity score matching, and inverse probability weighting. Non-parametric sensitivity analyses illuminate how departures from (untestable) causal assumptions affect point estimates and confidence interval bounds that would impact the substantive conclusion drawn from the study. TL's thorough approach to learning from data provides transparency, allowing trust in RWE to be earned whenever it is warranted.
DOI: 10.3886/e197701v1
title: Veterans’ Grandchildren Mortality Plus: Vital Records, Census and Draft Cards Across Three Generations

description: The Veterans’ Grandchildren Mortality Plus sample consists of the records of more than 35,700 total grandchildren<br>both male and female in nearly equal numbers,about 28,000 of which survived to age 45,who were born after the war to 16,791 children of 2,825 veterans,and contains an oversample of ex-POW veterans.The primary purpose of the project was to explore how grandfathers’ trauma affects the longevity and overweight of descendants. <br>The dataset contains birth and death dates of grandchildren, census information on their parents' household, select socioeconomic and education information from the 1930 and 1940 census, and height and weight information from WWII draft cards for the grandsons. This multigenerational dataset can be used for researching the intergenerational transmission of longevity, overweight and socioeconomic status and the sex-specific pathways of this transmission and for testing mechanical linkage algorithms. <br>Researchers built on a previously collected NIA-funded project containing census and death information of children of ex-POW and non-POW veterans (“Early Indicators, Intergenerational Processes, and Aging,” NIA grant P01AG10120, PI: Costa). The Veterans’ Grandchildren Mortality Plus data set contains the newly collected records of the veterans’ grandchildren, as well as the previously collected data of the veterans and their children.
description: The data are available as csv, Stata, Excel, SAS, and SPSS file types. <br><br>The data set has been divided into two parts. To use the entire data set, append part 1 and part 2. For example, using Stata: use grandchildren_pt1_stata.dta , clear<br>append using grandchildren_pt2_stata.dta<br>
DOI: 10.3886/e197701
title: Veterans’ Grandchildren Mortality Plus: Vital Records, Census and Draft Cards Across Three Generations

description: The Veterans’ Grandchildren Mortality Plus sample consists of the records of more than 35,700 total grandchildren<br>both male and female in nearly equal numbers,about 28,000 of which survived to age 45,who were born after the war to 16,791 children of 2,825 veterans,and contains an oversample of ex-POW veterans.The primary purpose of the project was to explore how grandfathers’ trauma affects the longevity and overweight of descendants. <br>The dataset contains birth and death dates of grandchildren, census information on their parents' household, select socioeconomic and education information from the 1930 and 1940 census, and height and weight information from WWII draft cards for the grandsons. This multigenerational dataset can be used for researching the intergenerational transmission of longevity, overweight and socioeconomic status and the sex-specific pathways of this transmission and for testing mechanical linkage algorithms. <br>Researchers built on a previously collected NIA-funded project containing census and death information of children of ex-POW and non-POW veterans (“Early Indicators, Intergenerational Processes, and Aging,” NIA grant P01AG10120, PI: Costa). The Veterans’ Grandchildren Mortality Plus data set contains the newly collected records of the veterans’ grandchildren, as well as the previously collected data of the veterans and their children.
description: The data are available as csv, Stata, Excel, SAS, and SPSS file types. <br><br>The data set has been divided into two parts. To use the entire data set, append part 1 and part 2. For example, using Stata: use grandchildren_pt1_stata.dta , clear<br>append using grandchildren_pt2_stata.dta<br>
DOI: 10.3886/e197701v2
title: Veterans’ Grandchildren Mortality Plus: Vital Records, Census and Draft Cards Across Three Generations

description: The Veterans’ Grandchildren Mortality Plus sample consists of the records of more than 35,700 total grandchildren<br>both male and female in nearly equal numbers,about 28,000 of which survived to age 45,who were born after the war to 16,791 children of 2,825 veterans,and contains an oversample of ex-POW veterans.The primary purpose of the project was to explore how grandfathers’ trauma affects the longevity and overweight of descendants. <br>The dataset contains birth and death dates of grandchildren, census information on their parents' household, select socioeconomic and education information from the 1930 and 1940 census, and height and weight information from WWII draft cards for the grandsons. This multigenerational dataset can be used for researching the intergenerational transmission of longevity, overweight and socioeconomic status and the sex-specific pathways of this transmission and for testing mechanical linkage algorithms. <br>Researchers built on a previously collected NIA-funded project containing census and death information of children of ex-POW and non-POW veterans (“Early Indicators, Intergenerational Processes, and Aging,” NIA grant P01AG10120, PI: Costa). The Veterans’ Grandchildren Mortality Plus data set contains the newly collected records of the veterans’ grandchildren, as well as the previously collected data of the veterans and their children.
description: The data are available as csv, Stata, Excel, SAS, and SPSS file types. <br><br>The data set has been divided into two parts. To use the entire data set, append part 1 and part 2. For example, using Stata: use grandchildren_pt1_stata.dta , clear<br>append using grandchildren_pt2_stata.dta<br>
DOI: 10.25919/zbem-w249
title: Parkes observations for project P1211 semester 2023OCTS_05

description: Traditional pulsar searching techniques are not sensitive enough to extreme pulsars such as millisecond pulsars (MSPs) in compact binaries (e.g., Pulsar-Blackhole binary systems), extremely fast spinning pulsars (e.g., sub-MSPs), and high dispersion measure (DM) pulsars (e.g., pulsars in Galactic Centre and Galactic Plane). Such a situation is now changed thanks to the development of next generation radio telescope arrays such as Australian Square Kilometer Array Pathfinder (ASKAP). ASKAP is capable of conducting highly sensitive radio continuum surveys with wide sky coverage (e.g, Evolutionary Map of The Universe survey). One of the solutions is to find pulsar candidates in radio continuum surveys such as EMU and then carry out targeted searches. This technique allows us to search over the wide bandwidth with full field of view while avoiding the need for expensive pixel-by-pixel high time resolution searches. 
 
 In this proposal, we propose to observe 16 MSP candidates identified in the Galactic plane using new ASKAP EMU images. We found 23 candidates by selecting sources with spectral index steeper than -1.90 and compactness less than 1.2. Among them 7 are known pulsars giving us high fraction of pulsars (~33%) and a reasonable number of candidates to follow up (16 sources). Because of the dense ionised medium in the Galactic Plane, MSPs are likely to be missed by previous pulsar surveys carried out at 1.4 GHz. Here, we propose a targeted pulsar search with the Parkes UWL which allow us to search pulsation at higher frequencies and therefore avoid strong DM smearing and scattering effects.
DOI: 10.25919/dvet-9317
title: Parkes observations for project P595 semester 2023OCTS_09

description: We propose to continue the PULSE@Parkes project in which high school students from Australia and around the World use the Parkes radio telescope in a remote observing model to observe and analyse pulsar data. The data from some PULSE@Parkes observations are used to support the space missions, other observations supplement the P456 Pulsar Timing Array project and the remainder were chosen in order to make a detailed analysis of pulsar timing irregularities and intermittency.
DOI: 10.6084/m9.figshare.25145891
title: Labeled_action_object_data_anonymous.xlsx

description: The file contains labeled data used for the quantitative evaluation of an NLP-based approach for the automatic inference of physical actions and any linked objects mentioned in textual descriptions of a worker's job.
DOI: 10.6084/m9.figshare.25145891.v1
title: Labeled_action_object_data_anonymous.xlsx

description: The file contains labeled data used for the quantitative evaluation of an NLP-based approach for the automatic inference of physical actions and any linked objects mentioned in textual descriptions of a worker's job.
DOI: 10.3886/e198145v1
title: Data and code: Nominal wage patterns, monopsony, and labour market power in early modern England

description: Records of long-eighteenth-century English wage rates exhibit almost absolute nominal rigidity over many decades, alongside significant dispersion between the wages paid by different organisations for the same type of work in the same location. These features of preindustrial wages have been obscured by data aggregation and the construction of real wage series, which introduce variation. In this paper we argue that the standard explanations for wage rigidity in economic history are insufficient. We show econometric evidence for monopsony power in one major organisation and argue that the main historical wage series are also affected by employer power. Eighteenth-century England had an imperfectly competitive labour market with large frictions. This gave large organisations the power to set wage policies. We discuss the implications for the eighteenth-century British economy and research into long-run wages more generally. <br><br>
DOI: 10.5519/qd.o2lfrz86
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.25345/c5028pq6t
title: MassIVE MSV000094011 - XLMS Analysis of the DSSO-crosslinked proteins affinity-purified from HEK293T cells stably expressing Halo-FAM60A
title: Protein crosslinking | Briefly, cell lysates expressing Halo-Fam60A were mixed with Magne HaloTag Beads, using 100 ul of bead slurry, and incubated overnight at 4C. The beads were then separated with a magnetic concentrator and washed four times using a buffer composed of 10 mM HEPES (pH 7.5), 1.5 mM MgCl2, 0.3 M NaCl, 10 mM KCl, and 0.2% Triton X-100. To elute bound proteins, the beads were treated with 200 ul of a buffer containing 50 mM HEPES (pH 7.5), 0.5 mM EDTA, 1 mM DTT, and 30 units of AcTEV, and incubated for a minimum of 2 h at 4C. The eluate was collected, and proteins were cross-linked using 5 mM disuccinimidylsulfoxide (DSSO; Sigma-Aldrich) for 40 minutes at room temperature. The cross-linking process was quenched by adding 50 mM NH4HCO3 and incubating for 15 minutes at room temperature. LC-MS3 XLMS data acquisition | Crosslinked peptides were analyzed on an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific) coupled to a Dionex UltiMate 3000 RSCLnano System. Peptides were loaded on an Acclaim PepMap 100 C18 0.3-mm-i.d., 5-mm-long trap cartridge (Thermo Fisher Scientific), then eluted to an analytical column (50 um i.d., 150 mm long) packed in-house with ReproSil-Pur C18-AQ 1.9-um resin (Dr. Masch GmbH). Full MS scans were performed at 60,000-m/z resolution in the orbitrap with a 1.6-m/z isolation window and a scan range from 375 to 1,500 m/z. The top three peptides with charge states from +4 to +8 were selected for MS2 fragmentation with 20% CID energy. MS2 scans were detected in the Orbitrap with 30,000-m/z resolution and a dynamic exclusion time of 40 s. Among MS2 fragments, if two peptides with an exact mass difference of 31.9720 with 20 ppm mass tolerance were present, both were selected for MS3 fragmentation at CID energy of 35%. MS3 scans were performed in the ion trap at rapid scan with an isolation window of 3 m/z and a maximum ion injection time of 200 ms. Each MS2 scan was followed by four MS3 scans. XLMS data analysis | The XlinkX node of Proteome Discoverer 3.0 (Thermo Fisher Scientific) was used to search for crosslinked peptides in the XLMS dataset by identifying MS2 scans with reporter ions characteristic of DSSO-modified lysine residues, with mass shifts of 158.00376 Da (monoisotopic mass), 54.01056 Da (alkene fragment), and 85.98264 Da (thiol fragment). In addition, the Sequest HT node searched the dataset with the following settings: 10 ppm precursor ion mass tolerance; 0.6 Da fragment ion mass tolerance; fixed modification: Cys carbamidomethylation; variable modifications: Met oxidation, N-terminal acetylation, Lys with amidated DSSO (279.07766 Da), and Lys with hydrolyzed DSSO (176.01433 Da); 3 maximum number of dynamic modifications. The data was searched against a non-redundant protein sequence database assembled from NCBI RefSeq GRCh38.p14 and T2T-CHM13v2.0 (2022-04-12 release), complemented with contaminants. The protein false discovery rate was set at 0.01.
DOI: 10.5281/zenodo.10620446
title: graphLambda: Fusion Graph Neural Networks For Binding Affinity Prediction

description: This archive contains materials to reproduce results in paper: graphLambda: Fusion Graph Neural Networks For Binding Affinity Prediction

The source code can be found here: https://github.com/i-Molecule/graphLambda
DOI: 10.5281/zenodo.10620447
title: graphLambda: Fusion Graph Neural Networks For Binding Affinity Prediction

description: This archive contains materials to reproduce results in paper: graphLambda: Fusion Graph Neural Networks For Binding Affinity Prediction

The source code can be found here: https://github.com/i-Molecule/graphLambda
DOI: 10.25345/c5v980317
title: MassIVE MSV000094012 - Application of Predictive Modeling Tools for the Identification of Ocimum spp. Herbal Products
title: LC-MS files for three species of Ocimum, to evaluate the potential of controlled growth studies to predict classification of consumer-based samples.
DOI: 10.5281/zenodo.8167711
title: Dataset for the high-resolution NEMO4 model of Cumberland Bay, South Georgia

description: This data-set consist of the required model set up files to reproduce a NEMO4 high-resolution model of Cumberland Bay, South Georgia, for the years 2001 to 2010 as described in the thesis 'Oceanographic Variability in Cumberland Bay, South Georgia: Implications for Glacier Retreat and Fisheries Management' Joanna Zanker. Files required to reproduce the process tests detailed in the thesis are also provided with the relevant names and the scripts for running the individual-based model with the model flow fields parameterised for mackerel icefish.
DOI: 10.5281/zenodo.8167710
title: Dataset for the high-resolution NEMO4 model of Cumberland Bay, South Georgia

description: This data-set consist of the required model set up files to reproduce a NEMO4 high-resolution model of Cumberland Bay, South Georgia, for the years 2001 to 2010 as described in the thesis 'Oceanographic Variability in Cumberland Bay, South Georgia: Implications for Glacier Retreat and Fisheries Management' Joanna Zanker. Files required to reproduce the process tests detailed in the thesis are also provided with the relevant names and the scripts for running the individual-based model with the model flow fields parameterised for mackerel icefish.
DOI: 10.5281/zenodo.10462597
title: MARS DSLF estimates over the MSG domain between 2004 and 2022

description: Estimates of downward longwave radiation at surface using the multivariate adaptive regression splines algorithm developed by the IPMA, Portugal. Datasets comprise hourly and monthly values (generated from instantaneous 30-minutes values) for performance evaluation at the nearest points to BSRN and FLUXNET2015 networks. Processed monthly data for the whole Meteosat second generation satellite domain is also made available. The provided datasets were used in the creation of the JGR manuscript Lopes et al. 2023 (under review).

 

DSLF_MARS_BSRN_FLUXNET_2004_2019.rar file includes:

MARS (0.05º) hourly nearest to bsrn stations: mars_hour_dslf_nearest_brsn_20040119-20191231.csv; 18.4 Mb

MARS (0.05º) hourly nearest to fluxnet stations: mars_hour_dslf_nearest_fluxnet_20040119-20141231.csv; 42.3 Mb

MARS (0.25º) monthly nearest to bsrn stations: mars_month_dslf_nearest_brsn_20040119-20191231 .csv; 56.2 KB

MARS (0.25º) monthly nearest to fluxnet stations: mars_month_dslf_nearest_fluxnet_20040119-20141231.csv; 60.1 KB

 

MARS_processed_data_2004_2022.rar file includes:

MARS (0.05º) monthly means MSG Disc: NETCDF4_LSASAF_MSG_DSLF_MSG-Disk_2004-2022.nc (1.7 Gb)

MARS (0.25º) monthly means MSG Disc: NETCDF4_LSASAF_MSG_DSLF_MSG-Disk-025_2004-2022.nc (71 Mb)

MARS (0.05º) 30-minutes MSG Disc 15th July 2021: NETCDF4_LSASAF_MSG_DSLF_MSG-Disk_20210715.nc (152 Mb)