cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7674791
title: Non - invasive identification of individuals of Atlantic salmon (aquarium data)

description: Non - invasive identification of individuals of Atlantic salmon (aquarium data). There are four datasets. First dataset is a 330 fish individuals of atlantic Salmon, they are separated ito 6 part. Then, other Three datsets are tagged 30 fish out of those 330 fish. There are original data and processed data. data were collected in aquarium with water.
DOI: 10.5281/zenodo.7690930
title: Non-invasive identification of individuals of Atlantic salmon (tent data)

description: Non-invasive identification of individuals of Atlantic salmon (tent data). 328 fish were sampled. 30 fish were tagged for next data collection. totally 4 data collection were done. The fish were photographed in tent out of water. The fish were photographed on the green background for simple fish localization. Each image was processed separately. First the green background was detected based on the defined value of the green in HSV color space. The backgound was used as the area of fish appearance. In the secodn step the fish was segmented on the background using the specific color of the fish in HSV color space. The fish was detected as the largest object. Some morphological operations were used to correct fish shape. The object was rotated to the horizontal position. The fish tail was removed by the algorithm because it was detected on some images and not detected on the rest. Therefore the algorithm detects the begining of back tail as the most narrow place at back part of the fish. The lenght of the fish and the height of the fish was used for the localization of the ROI. The ROI is shown on the image bellow. The ROI was selected to cover the fish body with most visible patter. Uploaded files - original and processd files for all data collections.
DOI: 10.1285/i20356609v10i1p169
title: Back to Solidarity-Based Living? The Economic Crisis and the Development of Alternative Projects in Portugal

description: The socio-economic crisis in 2011 caused a decrease in living standards for a large part of the Portuguese population, especially after the implementation of a new austerity programme. At the same time the country saw an increase in alternative projects such as: self-organised cultural centres; urban gardening groups; and solidarity-based exchange networks. The main aim of this contribution is to analyse how the crisis impacted these projects in Portugal in cities and also rural areas. The argument that the crisis had an adverse effect on resilience projects is strengthened by the results of case studies in other countries affected by the crisis and by empirical observations regarding the case of Portugal. After having reviewed the scarce literature on social resilience and alternative projects I present data from an analysis of internet pages and a questionnaire on the impact of the socio-economic crisis on the projects of Rede Convergir in 2015.
DOI: 10.14768/f8c46735-e6c3-45e2-8f6f-26c6d67c4723
title: PTR-MS measurements in 2020-2021

description: This dataset presents the first two-years of long-term atmospheric measurements of Volatile Organic Compounds (VOCs) at the peri-urban SIRTA-ACTRIS site (Paris region). VOCs are involved in atmospheric chemistry, by modifying the oxidation capacity of the atmosphere, and acting as precursors of secondary pollutants (ozone, aerosols). Online measurements using a Proton-Transfer-Reaction Mass Spectrometer (PTR-MS) were implemented in January 2020. 5-min (2020) and 10-min (2021) measurements of 31 mass-to-charge ratios (m/z) were performed at 15 m above ground level. Raw data were treated to obtain volume mixing ratios (ppb), averaged to hourly resolution, and a thorough quality assessment was carried out on all m/z, of which 12 were further quality checked by ACTRIS. The measured m/z correspond to compounds including aromatics (benzene, toluene, …), oxygenated (methanol, acetone, …), and biogenic (isoprene, monoterpenes, …). The presentation and analysis of this dataset is available in a paper submitted to Earth System Science Data (Simon et al, in prep). reference article: Simon et al (in prep); Two years of Volatile Organic Compounds online in-situ measurements at SIRTA (Paris region, France) using Proton-Transfer-Reaction Mass Spectrometry; Earth System Science Data
DOI: 10.21227/zp7a-0683
title: BVI-LOWLIGHT

description: One of the weak points of most of denoising algoritms (deep learning based ones) is the training data. Due to no or very limited amount of groundtruth data available, these algorithms are often evaluated using synthetic noise models such as Additive Zero-Mean Gaussian noise. The downside of this approach is that these simple model do not represent noise present in natural imagery. For evaluation of denoising algorithms’ performance in poor light conditions, we need either representative models or real noisy images paired with those we can consider as groundtruth.
DOI: 10.6084/m9.figshare.20678612
title: Phenylboronic acid catalyzed synthesis of polysubstituted 1,4-dihydropyridine derivatives as promising antioxidant agents correlated with molecular docking

description: Supporting data for research article.
DOI: 10.18462/iir.icr.2015.0092
title: Design, development and testing of a compressive thermoelastic cooling system.

description: Thermoelastic cooling was recently proposed as a candidate to substitute the vapor compression cooling. In order to prove its feasibility, a thermoelastic cooling prototype system using the compression drive mechanism and nitinol tubes working as functioning material has been designed, constructed, and tested in this study. The prototype consisted of two beds filled with nitinol tubes, a linear actuator as the compressing machine, and a sophisticated water circulation system to transfer heat and improve the system’s efficiency. The entire system was operated under the reverse Brayton cycle, which was developed in a previous numerical study. As the first endeavour in this field, the measured maximum system temperature lift reached 1.5 K as a baseline for this prototype. We also achieved maximum of 38 W net cooling from the prototype. Although current research proved the thermoelastic cooling concept, new designs are in progress as following studies.
DOI: 10.5281/zenodo.5556801
title: evotext/ielex-data-and-tree: IELex data and tree (2021/11/08)

description: Data and scripts for producing a Baysian phylogenetic tree sample of for the Indo-European family which is "good enough", using data from IELex (Dunn et al. 2011). This repository contains data and scripts for producing a Baysian phylogenetic tree sample of for the Indo-European family which is <em>good enough</em> for use in phylogenetic comparative methods. It should be considered as the current version of the "Indo-European Lexical Cognacy Database" from Dunn et al. (2011), popularly known as "IELex". The "Indo-European Cognate Relationships" (IE-CoR) database project, now based at the Max Planck Institute for Evolutionary Anthropology, has been working on a much improved database originally based on this data, but has not had any public data release so far. In the meantime, this is the best we can offer, as an alternative to the original website (http://ielex.mpi.nl) which is now offline. The <code>data/</code> directory holds the files most researchers will be interested in: <code>ielex.csv</code> is a single table in long format containing the essential database information, given one entry per row, each with the associated language, concept, and cognate set. It also carries the glottocode (Hammarström et al., 2021) corresponding to each language; concept glosses are given via the corresponding Concepticon (List et al., 2021) cognate set. It is the file most people will want when searching for "IELex data". <code>concepts.csv</code> is a list mapping all concepts used in IELex to their corresponding concept set in Concepticon (List et al., 2021), giving both the gloss and the id. <code>ielex.nex</code> is a NEXUS file with the information from the table above, with ascertainment correction columns, charstate labels, and assumptions. The file is built with <code>build/build_nexus.py</code>. <code>ielex.nn.pdf</code> and <code>ielex.nn.png</code> are a PDF and a high-resolution PNG from the NEXUS file above, generated with SplitsTree (Huson & Bryant, 2006). <code>ielex.mcc.tre</code> is the Maximum Clade Credibility ("consensus") tree from our latest analysis (currently <code>IE-tree-v1</code>). The first 50% of the sample was removed as burn-in. <code>ielex.mcc.pdf</code> is a graphic rendering of the tree above, generated with FigTree. The <code>build/</code> directory holds the files used for preparing the phylogenetic reconstruction. The <code>IE-trees-v1/</code> directory holds the files related to the phylogenetic reconstruction, including model, logs, and state. As stated above, a summary of the main output, as <code>ielex.mcc.tre</code>, is found in the <code>data/</code> directory. For statistical purposes researchers are likely to want the entire (unsummarised) tree sample, <code>IE-trees-v1/ie-v1.nex</code>.
DOI: 10.5258/soton/d2638
title: Dataset supporting the publication: Effects of surfactant head group modification on vertically oriented mesoporous silica produced by the electrochemically assisted surfactant assembly method

description: This dataset supports the publication by N. A. N. Mohamed et al, "Effects of surfactant head group modification on vertically oriented mesoporous silica produced by the electrochemically assisted surfactant assembly method", published in Nanoscale Advances. PAPER DOI: 10.1039/D3NA00031A This dataset contains: The original data associated with each figure in the manuscript, in text files with the column header denoting the parameter in each case.
DOI: 10.4121/1fbd5ecd-d0af-4b77-a28a-0aca7b38f45f
title: Code and datasets of the dissertation 'Behaviour and Stability of Interconnected Systems: From Biological Applications to Opinion Dynamics'

description: This .zip file contains the code and data necessary to reproduce the results presented in the PhD dissertation 'Behaviour and Stability of Interconnected Systems: From Biological Applications to Opinion Dynamics'. The code is divided in five directories. Each directory has instructions on how to reproduce the corresponding results. The README also provides information on how to run the code.There is also a Excel file that explains the contents and origin of the most relevant datasets. The broad research objective is to undercover the mechanisms of opinion formation in large-scale populations. To do this, different opinion formation models are simulated, the resulting data gathered and analysed. All the code is in .m Matlab scripts, and the data is in .mat Matlab files.
DOI: 10.4121/1fbd5ecd-d0af-4b77-a28a-0aca7b38f45f.v2
title: Code and datasets of the dissertation 'Behaviour and Stability of Interconnected Systems: From Biological Applications to Opinion Dynamics'

description: This .zip file contains the code and data necessary to reproduce the results presented in the PhD dissertation 'Behaviour and Stability of Interconnected Systems: From Biological Applications to Opinion Dynamics'. The code is divided in five directories. Each directory has instructions on how to reproduce the corresponding results. The README also provides information on how to run the code.There is also a Excel file that explains the contents and origin of the most relevant datasets. The broad research objective is to undercover the mechanisms of opinion formation in large-scale populations. To do this, different opinion formation models are simulated, the resulting data gathered and analysed. All the code is in .m Matlab scripts, and the data is in .mat Matlab files.
DOI: 10.17632/8jch3rtcb2.1
title: Mitochondrial bioenergetics of TFP/LCHAD deficiency human fibroblasts evaluated by Seahorse XFe96 Extracellular Flux Analyzer 

description: Evaluation of mitochondrial bioenergetics of cultured fibroblasts from TFP/LCHAD deficiency patients in a Seahorse XFe96 Extracellular Flux Analyzer
DOI: 10.5519/qd.jx7klepf
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (477 records)
DOI: 10.17632/z46cyfd8tz.1
title: Parkin_mediated_mitophagy_is_induced_by_the_probiotics_Saccharomyces_boulardii_and_Lactococcus_lactis

description: Dysfunctional mitochondria are a hallmark feature of neurodegenerative disorders, such as Parkinson’s
disease, and upregulation of Parkin-mediated mitophagy pathways serve to remove unhealthy
mitochondria from cells. Probiotics have been used to alleviate symptoms of Parkinson’s disease and
there is evidence to suggest that they modulate mitochondrial pathways. In this study, we conducted a
screen of 49 probiotics and tested various stages of mitophagy to determine whether any of the
probiotics can upregulate mitophagy in cells sustaining mitochondrial damage. We found that two
probiotics, Saccharomyces boulardii and Lactococcus lactis upregulate mitochondrial Parkin recruitment,
phospho-ubiquitination, and mitofusin degradation. Further, these strains increase lysosomal
degradation of dysfunctional mitochondria in the brain of Drosophila that were subjected to the
mitochondrial toxin paraquat, and also improve longevity and motor function in this Drosophila model of
Parkinson’s disease. These effects occur due to exogenous soluble factors that are released by probiotics
under laboratory conditions. We identified methyl-isoquinoline-6-carboxylate as one such molecule,
which upregulates mitochondrial parkin recruitment, phospho-ubiquitination, mitofusin degradation, and
lysosomal degradation, while restoring motor function in paraquat-treated flies. These data suggest a
novel mechanism that probiotics use to stimulate mitophagy through a Parkin-dependent pathway that
could potentially be utilized to treat neurological diseases at an early stage.
DOI: 10.17632/j3vbb6yfdv.1
title: Chemical modification of human decellularized extracellular matrix for incorporation into phototunable hybrid-hydrogel models of tissue fibrosis

description: Tissue fibrosis remains a serious health condition with high morbidity and mortality rates. There is a critical need to engineer model systems that better recapitulate the spatial and temporal changes in the fibrotic extracellular microenvironment and enable study of the cellular and molecular alterations that occur during pathogenesis. Here, we present a process for chemically modifying human decellularized extracellular matrix (dECM) and incorporating it into a dynamically tunable hybrid-hydrogel system containing a poly(ethylene glycol)-alpha methacrylate (PEGαMA) backbone. Following modification and characterization, an off-stoichiometry thiol-ene Michael addition reaction resulted in hybrid-hydrogels with mechanical properties that could be tuned to recapitulate many healthy tissue types. Next, photoinitiated, free-radical homopolymerization of excess α-methacrylates increased crosslinking density and hybrid-hydrogel elastic modulus to mimic a fibrotic microenvironment. The incorporation of dECM into the PEGαMAhydrogel decreased the elastic modulus and, relative to fully synthetic hydrogels, increased the swelling ratio, the average molecular weight between crosslinks, and the mesh size of hybrid-hydrogel networks. These changes were proportional to the amount of dECM incorporated into the network. Dynamic stiffening increased the elastic modulus and decreased the swelling ratio, average molecular weight between crosslinks, and the mesh size of hybrid-hydrogels, as expected. Stiffening also activated human fibroblasts, as measured by increases in average cellular aspect ratio (1.59 ± 0.02 to 2.98 ± 0.20) and expression of α-smooth muscle actin (αSMA). Fibroblasts expressing αSMA increased from 24.4% to 51.8% upon dynamic stiffening, demonstrating that hybrid-hydrogels containing human dECM support investigation of dynamic mechanosensing. These results improve our understanding of the biomolecular networks formed within hybrid-hydrogels: this fully human phototunable hybrid-hydrogel system will enable researchers to control and decouple the biochemical changes that occur during fibrotic pathogenesis from the resulting increases in stiffness to study the dynamic cell-matrix interactions that perpetuate fibrotic diseases.
DOI: 10.17632/j3vbb6yfdv.2
title: Chemical modification of human decellularized extracellular matrix for incorporation into phototunable hybrid-hydrogel models of tissue fibrosis

description: Tissue fibrosis remains a serious health condition with high morbidity and mortality rates. There is a critical need to engineer model systems that better recapitulate the spatial and temporal changes in the fibrotic extracellular microenvironment and enable study of the cellular and molecular alterations that occur during pathogenesis. Here, we present a process for chemically modifying human decellularized extracellular matrix (dECM) and incorporating it into a dynamically tunable hybrid-hydrogel system containing a poly(ethylene glycol)-alpha methacrylate (PEGαMA) backbone. Following modification and characterization, an off-stoichiometry thiol-ene Michael addition reaction resulted in hybrid-hydrogels with mechanical properties that could be tuned to recapitulate many healthy tissue types. Next, photoinitiated, free-radical homopolymerization of excess α-methacrylates increased crosslinking density and hybrid-hydrogel elastic modulus to mimic a fibrotic microenvironment. The incorporation of dECM into the PEGαMAhydrogel decreased the elastic modulus and, relative to fully synthetic hydrogels, increased the swelling ratio, the average molecular weight between crosslinks, and the mesh size of hybrid-hydrogel networks. These changes were proportional to the amount of dECM incorporated into the network. Dynamic stiffening increased the elastic modulus and decreased the swelling ratio, average molecular weight between crosslinks, and the mesh size of hybrid-hydrogels, as expected. Stiffening also activated human fibroblasts, as measured by increases in average cellular aspect ratio (1.59 ± 0.02 to 2.98 ± 0.20) and expression of α-smooth muscle actin (αSMA). Fibroblasts expressing αSMA increased from 24.4% to 51.8% upon dynamic stiffening, demonstrating that hybrid-hydrogels containing human dECM support investigation of dynamic mechanosensing. These results improve our understanding of the biomolecular networks formed within hybrid-hydrogels: this fully human phototunable hybrid-hydrogel system will enable researchers to control and decouple the biochemical changes that occur during fibrotic pathogenesis from the resulting increases in stiffness to study the dynamic cell-matrix interactions that perpetuate fibrotic diseases.
DOI: 10.17632/j3vbb6yfdv.3
title: Chemical modification of human decellularized extracellular matrix for incorporation into phototunable hybrid-hydrogel models of tissue fibrosis

description: Tissue fibrosis remains a serious health condition with high morbidity and mortality rates. There is a critical need to engineer model systems that better recapitulate the spatial and temporal changes in the fibrotic extracellular microenvironment and enable study of the cellular and molecular alterations that occur during pathogenesis. Here, we present a process for chemically modifying human decellularized extracellular matrix (dECM) and incorporating it into a dynamically tunable hybrid-hydrogel system containing a poly(ethylene glycol)-alpha methacrylate (PEGαMA) backbone. Following modification and characterization, an off-stoichiometry thiol-ene Michael addition reaction resulted in hybrid-hydrogels with mechanical properties that could be tuned to recapitulate many healthy tissue types. Next, photoinitiated, free-radical homopolymerization of excess α-methacrylates increased crosslinking density and hybrid-hydrogel elastic modulus to mimic a fibrotic microenvironment. The incorporation of dECM into the PEGαMAhydrogel decreased the elastic modulus and, relative to fully synthetic hydrogels, increased the swelling ratio, the average molecular weight between crosslinks, and the mesh size of hybrid-hydrogel networks. These changes were proportional to the amount of dECM incorporated into the network. Dynamic stiffening increased the elastic modulus and decreased the swelling ratio, average molecular weight between crosslinks, and the mesh size of hybrid-hydrogels, as expected. Stiffening also activated human fibroblasts, as measured by increases in average cellular aspect ratio (1.59 ± 0.02 to 2.98 ± 0.20) and expression of α-smooth muscle actin (αSMA). Fibroblasts expressing αSMA increased from 24.4% to 51.8% upon dynamic stiffening, demonstrating that hybrid-hydrogels containing human dECM support investigation of dynamic mechanosensing. These results improve our understanding of the biomolecular networks formed within hybrid-hydrogels: this fully human phototunable hybrid-hydrogel system will enable researchers to control and decouple the biochemical changes that occur during fibrotic pathogenesis from the resulting increases in stiffness to study the dynamic cell-matrix interactions that perpetuate fibrotic diseases.
DOI: 10.6084/m9.figshare.22731560
title: Alteration of the gut microbiota composition

description: rawdata. Alteration of the gut microbiota composition after P.g injection of health and diabetes rats.
DOI: 10.5281/zenodo.7965617
title: Dataset associated to the publication NATASTRON-22125961A arXiv:2212.10924

description: # Dataset description 1. Single stellar model grids at Zsun All single stellar model grids are labeled as "single_star_grid_Zsun_*.h5".<br> To access the dataset you should use the POSYDON v1 code and refer to the<br> code documentation, see https://github.com/POSYDON-code/POSYDON/releases/tag/v1.0.0.<br> The data can be accessed, e.g., with POSYDON as ```py<br> from posydon.grids.psygrid import PSyGrid<br> grid = PSyGrid()<br> grid.load(path_to_grid)<br> print(grid.initial_values)<br> print(grid.final_values)<br> print(grid[0].history1['log_L'])<br> print(grid[0].history1['log_Teff'])<br> ``` 2. Binary black hole population at Zsun We provide the binary black hole population in the file labeled<br> "BBH_population_Zsun.h5". This file contains all binary systems forming<br> binary black holes as simulated from a population synthesis model of 50 million<br> binaries generated with POSYDON v1 at solar metallicity. The data can be<br> accessed, e.g., with Pandas as ```py<br> import pandas as pd<br> df = pd.read_hdf('./data_release/source_data/BBH_population_Zsun.h5',<br> key='history')<br> df.head(10)<br> ``` For convenience we also provide a dataset labeled "arXiv_2212.10924.csv.gz"<br> that contains the subset of merging binary black holes obtained from<br> "BBH_population_Zsun.h5" at the time of double compact object formation used to<br> generate the Figure 4 of the main manuscript and compute the binary black hole<br> rates using the software released on https://github.com/ssbvr/BBH_merging_rates.<br> The data can be accessed, e.g., with Pandas as ```py<br> import pandas as pd<br> df = pd.read_csv('./data_release/source_data/arXiv_2212.10924.csv.gz',<br> compression='gzip')<br> df.head(10)<br> ``` Please refer to the following notebook on how use the data to compute the<br> detectable and intrinsic merging population as well as rates, see<br> https://github.com/ssbvr/BBH_merging_rates/blob/main/arXiv_221210924_POSYDON_BBH_Zsun.ipynb
DOI: 10.6084/m9.figshare.23131421
title: Gene database of Fructilactobacillus sanfranciscensis

description: This work describes the gene database of <em>Fructilactobacillus sanfranciscensis</em>. Original annotated genome file of the species was obtained from Genbank, and processed by an in-house MATLAB gene database analysis software to reveal gene name, gene function and gene sequence for each gene across the genome of the species. It is hoped that the data encapsulated herein will help inform future research seeking to understand the physiology of this microorganism.