cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22249263
title: Stimuli-sensitive nano-drug delivery with programmable size changes to enhance accumulation of therapeutic agents in tumors

description: Nano-based drug delivery systems hold significant promise for cancer therapies. Presently, the poor accumulation of drug-carrying nanoparticles in tumors has limited their success. In this study, based on a combination of the paradigms of intravascular and extravascular drug release, an efficient nanosized drug delivery system with programmable size changes is introduced. Drug-loaded smaller nanoparticles (secondary nanoparticles), which are loaded inside larger nanoparticles (primary nanoparticles), are released within the microvascular network due to temperature field resulting from focused ultrasound. This leads to the scale of the drug delivery system decreasing by 7.5 to 150 times. Subsequently, smaller nanoparticles enter the tissue at high transvascular rates and achieve higher accumulation, leading to higher penetration depths. In response to the acidic pH of tumor microenvironment (according to the distribution of oxygen), they begin to release the drug doxorubicin at very slow rates (i.e., sustained release). To predict the performance and distribution of therapeutic agents, a semi-realistic microvascular network is first generated based on a sprouting angiogenesis model and the transport of therapeutic agents is then investigated based on a developed multi-compartment model. The results show that reducing the size of the primary and secondary nanoparticles can lead to higher cell death rate. In addition, tumor growth can be inhibited for a longer time by enhancing the bioavailability of the drug in the extracellular space. The proposed drug delivery system can be very promising in clinical applications. Furthermore, the proposed mathematical model is applicable to broader applications to predict the performance of drug delivery systems.
DOI: 10.6084/m9.figshare.22249263.v1
title: Stimuli-sensitive nano-drug delivery with programmable size changes to enhance accumulation of therapeutic agents in tumors

description: Nano-based drug delivery systems hold significant promise for cancer therapies. Presently, the poor accumulation of drug-carrying nanoparticles in tumors has limited their success. In this study, based on a combination of the paradigms of intravascular and extravascular drug release, an efficient nanosized drug delivery system with programmable size changes is introduced. Drug-loaded smaller nanoparticles (secondary nanoparticles), which are loaded inside larger nanoparticles (primary nanoparticles), are released within the microvascular network due to temperature field resulting from focused ultrasound. This leads to the scale of the drug delivery system decreasing by 7.5 to 150 times. Subsequently, smaller nanoparticles enter the tissue at high transvascular rates and achieve higher accumulation, leading to higher penetration depths. In response to the acidic pH of tumor microenvironment (according to the distribution of oxygen), they begin to release the drug doxorubicin at very slow rates (i.e., sustained release). To predict the performance and distribution of therapeutic agents, a semi-realistic microvascular network is first generated based on a sprouting angiogenesis model and the transport of therapeutic agents is then investigated based on a developed multi-compartment model. The results show that reducing the size of the primary and secondary nanoparticles can lead to higher cell death rate. In addition, tumor growth can be inhibited for a longer time by enhancing the bioavailability of the drug in the extracellular space. The proposed drug delivery system can be very promising in clinical applications. Furthermore, the proposed mathematical model is applicable to broader applications to predict the performance of drug delivery systems.
DOI: 10.6084/m9.figshare.24885540.v1
title: Datasets for the reproduction of the experiments presented in the LoCoHD article

description: Use the LoCoHD Rust implementation along with the Python scripts in the linked GitHub repository. Datasets provided here can be used to test and reproduce the same experiments described in the article (peer review pending).
DOI: 10.5519/qd.sucbqggk
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (68 records)
DOI: 10.5281/zenodo.3608349
title: Tephra fall hazard curves in Japan

description: This is the dataset of tephra fall hazard curves at 47 prefecural offices. These were created usng the database of TephraDB_Prototype_ver1 at 10.5281/zenodo.3608346 and the scripts at https://github.com/s-uesawa/Prototype-TephraDB-Japan. Related paper is now availavle online at https://dx.doi.org/10.21203/rs.2.23106/v1.
DOI: 10.5281/zenodo.3608350
title: Tephra fall hazard curves in Japan

description: This is the dataset of tephra fall hazard curves at 47 prefecural offices. These were created usng the database of TephraDB_Prototype_ver1 at 10.5281/zenodo.3608346 and the scripts at https://github.com/s-uesawa/Prototype-TephraDB-Japan. Related paper is now availavle online at https://dx.doi.org/10.21203/rs.2.23106/v1.
DOI: 10.6084/m9.figshare.25450765
title: <b>Emergence of SXT/R391 family integrative conjugative elements carrying tigecycline resistance genes </b><b><i>tet</i></b><b>(X4) and </b><b>tmexCD2-toprJ2 </b><b>in </b><b>Shewanella</b><b> spp. i</b><b>so</b><b>lated from seafood</b>

description: Genomes for review.
DOI: 10.6084/m9.figshare.25450765.v1
title: <b>Emergence of SXT/R391 family integrative conjugative elements carrying tigecycline resistance genes </b><b><i>tet</i></b><b>(X4) and </b><b>tmexCD2-toprJ2 </b><b>in </b><b>Shewanella</b><b> spp. i</b><b>so</b><b>lated from seafood</b>

description: Genomes for review.
DOI: 10.5519/qd.ypa6cl0r
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (5 records)
DOI: 10.6084/m9.figshare.25234900
title: <i>Laminaria ochroleuca</i>

description: Transcriptome assembly and annotation files of <i>Laminaria ochroleuca</i>
DOI: 10.6084/m9.figshare.25234900.v1
title: <i>Laminaria ochroleuca</i>

description: Transcriptome assembly and annotation files of <i>Laminaria ochroleuca</i>
DOI: 10.5519/qd.gpq8g5nv
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (20 records)
DOI: 10.5281/zenodo.10036578
title: A detectable change in the air-sea CO2 flux estimate from sailboat measurements

description: This repository contains files and scripts used to generate figures for the paper titled "A detectable change in the air-sea CO2 flux estimate from sailboat measurements". The study quantifies the impact of pCO2 observations measured by the sailboat "Seaexplorer" on the air-sea CO2 flux estimate.
 Overview:
We used pCO2 measurements sourced from SOCAT (www.socat.info), along with other environmental variables. We applied the 2-step neural network method SOM-FFN (Landschützer et al., 2013) to reconstruct air-sea CO2 flux estimates.
Four sets of air-sea CO2 flux estimates were reconstructed, each with 40 ensemble members to account for random errors in the neural network. These are the four sets:
E1) fluxesA - Based on SOCATv2022 including Seaexplorer data
E2) fluxesB - Based on SOCATv2022 excluding Seaexplorer data.
E3) fluxesC - Based on SOCATv2022 data, including Seaexplorer data, but introducing a random uncertainty of ± 5 μatm to the Seaexplorer data.
E4) fluxesD - Based on SOCATv2022 data, including Seaexplorer data, but introducing a constant measurement offset of 5 μatm to the Seaexplorer data.
These air-sea CO2 flux density estimates are 4-dimensional, represented in mol C m-2 yr-1, with the following dimensions:
- Ensemble size of flux reconstructions (40)
- Time (months from 1982 to 2021, totaling 480 months)
- Latitude (1-degree intervals, totaling 180 latitudes)
- Longitude (1-degree intervals, totaling 360 longitudes)
DOI: 10.5281/zenodo.10036579
title: A detectable change in the air-sea CO2 flux estimate from sailboat measurements

description: This repository contains files and scripts used to generate figures for the paper titled "A detectable change in the air-sea CO2 flux estimate from sailboat measurements". The study quantifies the impact of pCO2 observations measured by the sailboat "Seaexplorer" on the air-sea CO2 flux estimate.
 Overview:
We used pCO2 measurements sourced from SOCAT (www.socat.info), along with other environmental variables. We applied the 2-step neural network method SOM-FFN (Landschützer et al., 2013) to reconstruct air-sea CO2 flux estimates.
Four sets of air-sea CO2 flux estimates were reconstructed, each with 40 ensemble members to account for random errors in the neural network. These are the four sets:
E1) fluxesA - Based on SOCATv2022 including Seaexplorer data
E2) fluxesB - Based on SOCATv2022 excluding Seaexplorer data.
E3) fluxesC - Based on SOCATv2022 data, including Seaexplorer data, but introducing a random uncertainty of ± 5 μatm to the Seaexplorer data.
E4) fluxesD - Based on SOCATv2022 data, including Seaexplorer data, but introducing a constant measurement offset of 5 μatm to the Seaexplorer data.
These air-sea CO2 flux density estimates are 4-dimensional, represented in mol C m-2 yr-1, with the following dimensions:
- Ensemble size of flux reconstructions (40)
- Time (months from 1982 to 2021, totaling 480 months)
- Latitude (1-degree intervals, totaling 180 latitudes)
- Longitude (1-degree intervals, totaling 360 longitudes)
DOI: 10.5281/zenodo.10803884
title: A detectable change in the air-sea CO2 flux estimate from sailboat measurements

description: This repository contains files and scripts used to generate figures for the paper titled "A detectable change in the air-sea CO2 flux estimate from sailboat measurements". The study quantifies the impact of pCO2 observations measured by the sailboat "Seaexplorer" on the air-sea CO2 flux estimate.
 Overview:
We used pCO2 measurements sourced from SOCAT (www.socat.info), along with other environmental variables. We applied the 2-step neural network method SOM-FFN (Landschützer et al., 2013) to reconstruct air-sea CO2 flux estimates.
Four sets of air-sea CO2 flux estimates were reconstructed, each with 40 ensemble members to account for random errors in the neural network. These are the four sets:
E1) fluxesA - Based on SOCATv2022 including Seaexplorer data
E2) fluxesB - Based on SOCATv2022 excluding Seaexplorer data.
E3) fluxesC - Based on SOCATv2022 data, including Seaexplorer data, but introducing a random uncertainty of ± 5 μatm to the Seaexplorer data.
E4) fluxesD - Based on SOCATv2022 data, including Seaexplorer data, but introducing a constant measurement offset of 5 μatm to the Seaexplorer data.
These air-sea CO2 flux density estimates are 4-dimensional, represented in mol C m-2 yr-1, with the following dimensions:
- Ensemble size of flux reconstructions (40)
- Time (months from 1982 to 2021, totaling 480 months)
- Latitude (1-degree intervals, totaling 180 latitudes)
- Longitude (1-degree intervals, totaling 360 longitudes)
DOI: 10.5281/zenodo.10848217
title: MOTL: enhancing multi-omics matrix factorization with transfer learning

description: The Lrn_5000D_Fctrzn_100k_001TH.zip file contains the results of a MOFA factorization of the TGCA learning dataset, to be downloaded and used for transfer learning factorization of a target dataset with MOTL. The MOFA output is in the Model.hdf5 file, and intercepts for the factorization are in the EstimatedIntercepts.rds file.  The FctrMeta.json file contains metadata related to the MOFA factorization. The nohup.out file is the log of the factorization.

The expdat_meta.rds file contains metadata from the preprocessing of the TCGA multi-omics learning dataset that was factorized. This should also to be downloaded as it is an input to MOTL
DOI: 10.5281/zenodo.10847986
title: MOTL: enhancing multi-omics matrix factorization with transfer learning

description: The Lrn_5000D_Fctrzn_100k_001TH.zip file contains the results of a MOFA factorization of the TGCA learning dataset, to be downloaded and used for transfer learning factorization of a target dataset with MOTL. The MOFA output is in the Model.hdf5 file, and intercepts for the factorization are in the EstimatedIntercepts.rds file.  The FctrMeta.json file contains metadata related to the MOFA factorization. The nohup.out file is the log of the factorization.

The expdat_meta.rds file contains metadata from the preprocessing of the TCGA multi-omics learning dataset that was factorized. This should also to be downloaded as it is an input to MOTL
DOI: 10.5281/zenodo.10847987
title: TCGA Learning dataset factorization for MOTL

description: The Lrn_5000D_Fctrzn_100k_001TH.zip file contains the results of a MOFA factorization of the TGCA learning dataset, to be downloaded and used for transfer learning factorization of a target dataset with MOTL. The MOFA output is in the Model.hdf5 file, and intercepts for the factorization are in the EstimatedIntercepts.rds file.  The FcrMeta.json file contains metadata related to the MOFA factorization. The nohup.out file is the log of the factorization.

The expdat_meta.rds file contains metadata form the preprocessing of the TCGA multi-omics learning dataset that was factorized.
DOI: 10.18712/nsd-nsd3162-v1
title: The Families with Children Panel, round 1

description: The Families with Children Panel is a longitudinal survey created and administered by the City of Bergen that provides knowledge about the leisure activities of children and their parents. In 2019, all families with children (3-15 years old) registered as living in the municipality of Bergen were invited to participate, and around 20 percent of the families responded. The survey was repeated in 2020 and 2021 with the same respondents. In 2022, the survey was extended to the whole of Vestland county where all families with children (3-17 years old) were invited to participate. New rounds of the survey are in planning.

In the survey, parents are asked to answer on behalf of themselves and one of their children. The survey covers culture, sports, and other leisure activities, as well as background information on the parents' level of education and income.

For more detailed variable description, refer to the code book. 

The City of Bergen is the owner of the Children's Family Panel. Vestland County Council has shared data control for data from 2022. Ideas2evidence is responsible for the technical implementation of the survey. Data is stored and distributed by Sikt - the Knowledge Sector's service provider.
DOI: 10.5281/zenodo.10809740
title: Atmospheric Rivers Antacrtica IPSL-CM6

description: Netcdf file of detected Atmospheric Rivers (AR) in Antarctica using an vIVT based algorithm.

Two time periods:



"hist":  1995 to 2015, calculated from historical simulations from IPSL-CM6. r*i1p1f1 represent the diferente ensemble members

"ssp245": calculated from scenarioMIP simulations from IPSL-CM6 with the ssp245 scenariop. 2015 to 2055 for folowing ensemble members: r2i1p1f1, r3i1p1f1, r4i1p1f1,  r6i1p1f1, r14i1p1f1 r22i1p1f1 and 2015 to 2100 for r1i1p1f1, r5i1p1f1, r10i1p1f1,  r11i1p1f1.


Two threshods used during the detection:



"hist_thr": Threshold based on the 98th percentile of Historical vIVT values (it is a fixed threshold).

"adp_thr": Adaptive threshold scaled on the increase of humidity in the southern hemisphere.
DOI: 10.5281/zenodo.10809741
title: Atmospheric Rivers Antacrtica IPSL-CM6

description: Netcdf file of detected Atmospheric Rivers (AR) in Antarctica using an vIVT based algorithm.

Two time periods:



"hist":  1995 to 2015, calculated from historical simulations from IPSL-CM6. r*i1p1f1 represent the diferente ensemble members

"ssp245": calculated from scenarioMIP simulations from IPSL-CM6 with the ssp245 scenariop. 2015 to 2055 for folowing ensemble members: r2i1p1f1, r3i1p1f1, r4i1p1f1,  r6i1p1f1, r14i1p1f1 r22i1p1f1 and 2015 to 2100 for r1i1p1f1, r5i1p1f1, r10i1p1f1,  r11i1p1f1.


Two threshods used during the detection:



"hist_thr": Threshold based on the 98th percentile of Historical vIVT values (it is a fixed threshold).

"adp_thr": Adaptive threshold scaled on the increase of humidity in the southern hemisphere.
DOI: 10.5281/zenodo.10848882
title: Atmospheric Rivers Antacrtica IPSL-CM6

description: Netcdf file of detected Atmospheric Rivers (AR) in Antarctica using an vIVT based algorithm.

Two time periods:



"hist":  1995 to 2015, calculated from historical simulations from IPSL-CM6. r*i1p1f1 represent the diferente ensemble members

"ssp245": calculated from scenarioMIP simulations from IPSL-CM6 with the ssp245 scenariop. 2015 to 2055 for folowing ensemble members: r2i1p1f1, r3i1p1f1, r4i1p1f1,  r6i1p1f1, r14i1p1f1 r22i1p1f1 and 2015 to 2100 for r1i1p1f1, r5i1p1f1, r10i1p1f1,  r11i1p1f1.


Two threshods used during the detection:



"hist_thr": Threshold based on the 98th percentile of Historical vIVT values (it is a fixed threshold).

"adp_thr": Adaptive threshold scaled on the increase of humidity in the southern hemisphere.
DOI: 10.6084/m9.figshare.25163684
title: BTR dataset

description: This spreadsheet contains a portion of the PRECISE and MAS datasets utilized in our article "Exploring the Link between Brain Topological Resilience and Cognitive Performance in the Context of Aging and Vascular Risk Factors: A Cross-Ethnicity Population-Based Study." The data include the sample IDs used and the BTR values after our processing. Data of models are also included here. Due to data ethical restrictions, the full datasets can only be accessed via the following link:PRECISE dataset: http://paper.ncrcnd.ttctrc.com/default/project-detail?id=297&lang=enMAS dataset: https://cheba.unsw.edu.au/research-projects/sydney-memory-and-ageing-study
DOI: 10.6084/m9.figshare.25163684.v4
title: BTR dataset

description: This spreadsheet contains a portion of the PRECISE and MAS datasets utilized in our article "Exploring the Link between Brain Topological Resilience and Cognitive Performance in the Context of Aging and Vascular Risk Factors: A Cross-Ethnicity Population-Based Study." The data include the sample IDs used and the BTR values after our processing. Data of models are also included here. Due to data ethical restrictions, the full datasets can only be accessed via the following link:PRECISE dataset: http://paper.ncrcnd.ttctrc.com/default/project-detail?id=297&lang=enMAS dataset: https://cheba.unsw.edu.au/research-projects/sydney-memory-and-ageing-study
DOI: 10.48597/ug2b-nx7j
title: Measurement of POPs (persistent organic pollutants) at Råö

description: Measurement of POPs (persistent organic pollutants) at Råö
DOI: 10.5287/ora-qqd05nv46
title: Electroencephalogram (EEG) and behavioural data concerning the Go/NoGo/Conflict task

description: Electroencephalogram (EEG) and behavioural data (joystick) was collected from 15 healthy participants who completed a modified version of a Go/No-go task. This dataset consists of raw data, pre-processed EEG and behavioural data, along with impulsivity scores in a .csv file. The pre-processed data is in MATLAB .mat format. 

Raw Data 

The EEG and behavioural data (Joystick) along with trigger data was collected using a TMSi Porti amplifier with a sampling rate of 2,048Hz and is in .een format. The raw EEG files contain brain activity recorded in the first 16 channels and last 2 channels (channels 17 and 18) correspond to Joystick and Trigger information (used to identify the type of event – Go/Conflict/NoGo) respectively. 

The Raw data is segregated into 2 folders- Active and Sham which is further divided into baseline and after stimulation conditions. 

The main behavioural outcome is the change in NoGo errors (pre-processed folder- Figure 1C in from the article ‘Tuning the brakes – Modulatory role of transcranial random noise stimulation on inhibition,’ Brain Stimulation, 2024), comparing baseline and after-stimulation in sham and active conditions. Metadata corresponding to impulsivity scores and the change in NoGo behaviour are provided in ‘UPPS_nogo.csv’ (used for Figure 1D). The EEG data was recorded while the participants completed the task during baseline and after stimulation, and was used to calculate the spectral power (Figure 1E). The study also presents intermittent bursts from the EEG data, comparing the average burst durations at baseline and after-stimulation (Figure 1F) in sham and active stimulation conditions. 

 

Code 

All data were analysed in MATLAB (2018b) using a combination of EEGLAB, ERP LAB and FieldTrip packages. 

Installation guides can be found on 
https://sccn.ucsd.edu/eeglab/index.php 
https://matlab.mathworks.com/ 
https://erpinfo.org/erplab  
https://www.fieldtriptoolbox.org/download/

The behavioural data plots use the software IOSR toolbox :
https://github.com/IoSR-Surrey/MatlabToolbox 

Code_figure_IC.m: This script plots the NoGo error rates in baseline and after stimulation in sham and active conditions. This script uses the mat file ‘Nogo_behav_pre_post.mat’ 

Code_figure_1E.m: This script plots the spectral power and grand average of the after-stimulation EEG data with clusters obtained from a non-parametric analysis. This script uses the mat file ‘data_psd_trns_pre_post.mat’. 

Code_figure_1F.m: This script plots the intermittent burst durations during sham and active conditions and uses the file ‘Nogo_bursts_pre_post.mat’
DOI: 10.5281/zenodo.10436721
title: Data from: Immune Transcriptional Response in Head Kidney Primary Cell Cultures Isolated from the Three Most Important Species in Chilean Salmonids Aquaculture.

description: Data from  Immune Transcriptional Response in Head Kidney Primary Cell Cultures Isolated from the Three Most Important Species in Chilean Salmonids Aquaculture. Files in .JBN and .xlsx format
description: Fish cell culture is a common in vitro tool for studies in different fields such as virology, toxicology, pathology and immunology of fish. Fish cell cultures are a promising help to study how to diagnose and control relevant viral and intracellular bacterial infections in aquaculture. They can also be used for developing vaccines and immunostimulants, especially with the ethical demand aiming to reduce and replace the number of fish used in research. This study aimed to isolate head kidney primary cell cultures from three Chilean salmonids: Salmo salar, Oncorhynchus kisutch, and Oncorhynchus mykiss, and characterize the response to bacterial and viral stimuli by evaluating various markers of the innate and adaptive immune response. Specifically, the primary cell cultures of the head kidney from the three salmonids studied were cultured and exposed to two substances that mimic molecular patterns of different pathogens, i.e., Lipopolysaccharide (LPS) (bacterial) and Polyinosinic: polycytidylic acid (POLY I:C). Subsequently, we determined the mRNA expression profiles of the TLR-1, TLR-8, IgM, TLR-5, and MHC II genes. Head kidney primary cell cultures from the three species grown in vitro responded differently to POLY I:C and LPS. This is the first study to demonstrate and characterize the expression of immune genes in head kidney primary cell culture isolated from three salmonid species. It also indicates their potential role in developing immune responses as defense response agents and targets of immunoregulatory factors.
description: This work was supported by Fondecyt Regular (1160877) and (1180957), Fondap-Ideal 15150003, ANID-Millennium Science Initiative Program-Center code “ICN2021_002”. D. Nualart awarded the scholarship ANID-Millennium Science Initiative Program-Center code “ICN2021_002”.