cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4275543
title: Dataset related to the article "Human Cardiac Mesenchymal Stromal Cells From Right and Left Ventricles Display Differences in Number, Function, and Transcriptomic Profile"

description: This record contains raw data related to the article "Human Cardiac Mesenchymal Stromal Cells From Right and Left Ventricles Display Differences in Number, Function, and Transcriptomic Profile". <strong>Background:</strong> Left ventricle (LV) and right ventricle (RV) are characterized by well-known physiological differences, mainly related to their different embryological origin, hemodynamic environment, function, structure, and cellular composition. Nevertheless, scarce information is available about cellular peculiarities between left and right ventricular chambers in physiological and pathological contexts. Cardiac mesenchymal stromal cells (C-MSC) are key cells affecting many functions of the heart. Differential features that distinguish LV from RV C-MSC are still underappreciated. <strong>Aim:</strong> To analyze the physiological differential amount, function, and transcriptome of human C-MSC in LV versus (vs.) RV. <strong>Methods:</strong> Human cardiac specimens of LV and RV from healthy donors were used for tissue analysis of C-MSC number, and for C-MSC isolation. Paired LV and RV C-MSC were compared as for surface marker expression, cell proliferation/death ratio, migration, differentiation capabilities, and transcriptome profile. <strong>Results:</strong> Histological analysis showed a greater percentage of C-MSC in RV vs. LV tissue. Moreover, a higher C-MSC amount was obtained from RV than from LV after isolation procedures. LV and RV C-MSC are characterized by a similar proportion of surface markers. Functional studies revealed comparable cell growth curves in cells from both ventricles. Conversely, LV C-MSC displayed a higher apoptosis rate and RV C-MSC were characterized by a higher migration speed and collagen deposition. Consistently, transcriptome analysis showed that genes related to apoptosis regulation or extracellular matrix organization and integrins were over-expressed in LV and RV, respectively. Besides, we revealed additional pathways specifically associated with LV or RV C-MSC, including energy metabolism, inflammatory response, cardiac conduction, and pluripotency. <strong>Conclusion:</strong> Taken together, these results contribute to the functional characterization of RV and LV C-MSC in physiological conditions. This information suggests a possible differential role of the stromal compartment in chamber-specific pathologic scenarios.
description: The project was funded by Italian Ministry of Health (RC2019 EF5C ID: 2754330).
DOI: 10.15454/sqwfn4/4ndldd
title: oak4-45-bru.xyz

description: :unav
DOI: 10.5281/zenodo.4275542
title: Dataset related to the article "Human Cardiac Mesenchymal Stromal Cells From Right and Left Ventricles Display Differences in Number, Function, and Transcriptomic Profile"

description: This record contains raw data related to the article "Human Cardiac Mesenchymal Stromal Cells From Right and Left Ventricles Display Differences in Number, Function, and Transcriptomic Profile". <strong>Background:</strong> Left ventricle (LV) and right ventricle (RV) are characterized by well-known physiological differences, mainly related to their different embryological origin, hemodynamic environment, function, structure, and cellular composition. Nevertheless, scarce information is available about cellular peculiarities between left and right ventricular chambers in physiological and pathological contexts. Cardiac mesenchymal stromal cells (C-MSC) are key cells affecting many functions of the heart. Differential features that distinguish LV from RV C-MSC are still underappreciated. <strong>Aim:</strong> To analyze the physiological differential amount, function, and transcriptome of human C-MSC in LV versus (vs.) RV. <strong>Methods:</strong> Human cardiac specimens of LV and RV from healthy donors were used for tissue analysis of C-MSC number, and for C-MSC isolation. Paired LV and RV C-MSC were compared as for surface marker expression, cell proliferation/death ratio, migration, differentiation capabilities, and transcriptome profile. <strong>Results:</strong> Histological analysis showed a greater percentage of C-MSC in RV vs. LV tissue. Moreover, a higher C-MSC amount was obtained from RV than from LV after isolation procedures. LV and RV C-MSC are characterized by a similar proportion of surface markers. Functional studies revealed comparable cell growth curves in cells from both ventricles. Conversely, LV C-MSC displayed a higher apoptosis rate and RV C-MSC were characterized by a higher migration speed and collagen deposition. Consistently, transcriptome analysis showed that genes related to apoptosis regulation or extracellular matrix organization and integrins were over-expressed in LV and RV, respectively. Besides, we revealed additional pathways specifically associated with LV or RV C-MSC, including energy metabolism, inflammatory response, cardiac conduction, and pluripotency. <strong>Conclusion:</strong> Taken together, these results contribute to the functional characterization of RV and LV C-MSC in physiological conditions. This information suggests a possible differential role of the stromal compartment in chamber-specific pathologic scenarios.
description: The project was funded by Italian Ministry of Health (RC2019 EF5C ID: 2754330).
DOI: 10.15454/sqwfn4/kma4sv
title: radius

description: :unav
DOI: 10.15454/sqwfn4/igvono
title: oak613-1004-ec.xyz

description: :unav
DOI: 10.15454/sqwfn4/lmhgo7
title: beech7-10010-sp.xyz

description: :unav
DOI: 10.15454/sqwfn4/hyr2hr
title: oak0-821-unk.xyz

description: :unav
DOI: 10.15454/sqwfn4/ftujps
title: oak5-104-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/qk5qu4
title: oak8-291-pi.xyz

description: :unav
DOI: 10.15454/sqwfn4/eiymcv
title: beech2-3-am.xyz

description: :unav
DOI: 10.15454/sqwfn4/urhhxe
title: oak8-331-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/g9udzn
title: oak0-69-unk.xyz

description: :unav
DOI: 10.15454/sqwfn4/gs7tbc
title: oak8-251-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/amamdk
title: measure.tab

description: :unav
DOI: 10.15454/sqwfn4/qnhgvr
title: radius

description: :unav
DOI: 10.5281/zenodo.4139777
title: Dataset related to:"Prenylcysteine oxidase 1, a novel player in atherosclerosis "

description: This record contains raw data related to the article " Prenylcysteine oxidase 1, a novel player in atherosclerosis" Abstract The research into the pathophysiology of atherosclerosis has considerably increased our understanding of the disease complexity, but still many questions remain unanswered, both mechanistically and pharmacologically. We found that the pro-oxidant enzyme Prenylcysteine Oxidase 1 (PCYOX1), contributes to the oxidation of the lipoproteins, and it is transported within the subintimal space by proatherogenic lipoproteins accumulating in the arterial wall. PCYOX1 deficiency in apoE<sup>-/-</sup> mice retards atheroprogression, is associated with decreased features of lesion vulnerability and lower levels of lipid peroxidation, improves plasma lipid profile, and reduces inflammation. Collectively, our findings identify a previously undiscovered biological role for PCYOX1 in atherogenesis.
description: This work was supported by the Italian Ministry of Health, Italy (Ricerca Corrente ID 2755301 MPP 1A, and Ricerca Finalizzata RF-2013-02355543), the Swedish Research Council (12660) and the Swedish Heart-Lung Foundation (20180451).
DOI: 10.15454/sqwfn4/ozajx0
title: trunkdatareadme.txt

description: :unav
DOI: 10.15454/sqwfn4/ayb0mj
title: oak8-5-ec.xyz

description: :unav
DOI: 10.15454/sqwfn4/aidari
title: oak0-22-bru.xyz

description: :unav
DOI: 10.15454/sqwfn4/56b26o
title: trunk.off

description: :unav
DOI: 10.15454/sqwfn4/ivlvnc
title: beech6-3-ci.xyz

description: :unav
DOI: 10.15454/sqwfn4/rlhh70
title: centerline.xyz

description: :unav
DOI: 10.15454/sqwfn4/itggzo
title: fir3-15-ci.xyz

description: :unav
DOI: 10.15454/sqwfn4/2kegyb
title: beech1-120-unk.xyz

description: :unav
DOI: 10.15454/sqwfn4/fkvos3
title: beech103-281-ci.xyz

description: :unav
DOI: 10.15454/sqwfn4/nc8h2t
title: oak4-141-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/u9ct1y
title: fir1-12-ci.xyz

description: :unav
DOI: 10.15454/sqwfn4/gjlsew
title: beech2-107-unk.xyz

description: :unav
DOI: 10.15454/sqwfn4/reckdj
title: beech1-16-br2.xyz

description: :unav
DOI: 10.15454/sqwfn4/bmfxig
title: oak0-2-unk.xyz

description: :unav
DOI: 10.15454/sqwfn4/pqyrdf
title: oak613-1-ec.xyz

description: :unav
DOI: 10.15454/sqwfn4/155s7h
title: oak8-18b-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/gbjkr0
title: oak613-1015-ec.xyz

description: :unav
DOI: 10.15454/sqwfn4/9esmvk
title: beech2-9-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/8cxdm4
title: measure.tab

description: :unav
DOI: 10.15454/sqwfn4/rkz3h6
title: beech7-1003-sp.xyz

description: :unav
DOI: 10.15454/sqwfn4/kpiavs
title: oak613-11-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/i3gyeh
title: oak8-45-br.xyz

description: :unav
DOI: 10.5281/zenodo.4269976
title: Dataset related to the article "Clinical and Molecular Data Define a Diagnosis of Arrhythmogenic Cardiomyopathy in a Carrier of a Brugada-Syndrome-Associated PKP2 Mutation"

description: This record contains raw data related to the article “ Molecular Data Define a Diagnosis of Arrhythmogenic Cardiomyopathy in a Carrier of a Brugada-Syndrome-Associated PKP2 Mutation”. Plakophilin-2 (<em>PKP2</em>) is the most frequently mutated desmosomal gene in arrhythmogenic cardiomyopathy (ACM), a disease characterized by structural and electrical alterations predominantly affecting the right ventricular myocardium. Notably, ACM cases without overt structural alterations are frequently reported, mainly in the early phases of the disease. Recently, the <em>PKP2</em> p.S183N mutation was found in a patient affected by Brugada syndrome (BS), an inherited arrhythmic channelopathy most commonly caused by sodium channel gene mutations. We here describe a case of a patient carrier of the same BS-related <em>PKP2</em> p.S183N mutation but with a clear diagnosis of ACM. Specifically, we report how clinical and molecular investigations can be integrated for diagnostic purposes, distinguishing between ACM and BS, which are increasingly recognized as syndromes with clinical and genetic overlaps. This observation is fundamentally relevant in redefining the role of genetics in the approach to the arrhythmic patient, progressing beyond the concept of "one mutation, one disease", and raising concerns about the most appropriate approach to patients affected by structural/electrical cardiomyopathy. The merging of genetics, electroanatomical mapping, and tissue and cell characterization summarized in our patient seems to be the most complete diagnostic algorithm, favoring a reliable diagnosis.
description: The project was funded by the Italian Ministry of Health (RC2019 EF5C ID:2754330).
DOI: 10.15454/sqwfn4/mwophg
title: oak4-1002-ec.xyz

description: :unav
DOI: 10.5281/zenodo.4269975
title: Dataset related to the article "Clinical and Molecular Data Define a Diagnosis of Arrhythmogenic Cardiomyopathy in a Carrier of a Brugada-Syndrome-Associated PKP2 Mutation"

description: This record contains raw data related to the article “ Molecular Data Define a Diagnosis of Arrhythmogenic Cardiomyopathy in a Carrier of a Brugada-Syndrome-Associated PKP2 Mutation”. Plakophilin-2 (<em>PKP2</em>) is the most frequently mutated desmosomal gene in arrhythmogenic cardiomyopathy (ACM), a disease characterized by structural and electrical alterations predominantly affecting the right ventricular myocardium. Notably, ACM cases without overt structural alterations are frequently reported, mainly in the early phases of the disease. Recently, the <em>PKP2</em> p.S183N mutation was found in a patient affected by Brugada syndrome (BS), an inherited arrhythmic channelopathy most commonly caused by sodium channel gene mutations. We here describe a case of a patient carrier of the same BS-related <em>PKP2</em> p.S183N mutation but with a clear diagnosis of ACM. Specifically, we report how clinical and molecular investigations can be integrated for diagnostic purposes, distinguishing between ACM and BS, which are increasingly recognized as syndromes with clinical and genetic overlaps. This observation is fundamentally relevant in redefining the role of genetics in the approach to the arrhythmic patient, progressing beyond the concept of "one mutation, one disease", and raising concerns about the most appropriate approach to patients affected by structural/electrical cardiomyopathy. The merging of genetics, electroanatomical mapping, and tissue and cell characterization summarized in our patient seems to be the most complete diagnostic algorithm, favoring a reliable diagnosis.
description: The project was funded by the Italian Ministry of Health (RC2019 EF5C ID:2754330).
DOI: 10.15454/sqwfn4/dpq2yt
title: beech9-19-gm.xyz

description: :unav
DOI: 10.15454/sqwfn4/uxxbs6
title: oak4-11-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/vyoozk
title: beech1-107b-br2.xyz

description: :unav
DOI: 10.15454/sqwfn4/usdjb4
title: radius

description: :unav
DOI: 10.15454/sqwfn4/9r0jp8
title: oak2-4-pi.xyz

description: :unav
DOI: 10.15454/sqwfn4/jeqlpk
title: oak0-15-pi.xyz

description: :unav
DOI: 10.15454/sqwfn4/lw4brd
title: fir1-7-ci.xyz

description: :unav
DOI: 10.15454/sqwfn4/tr8d01
title: oak8-41-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/p8j1z0
title: oak0-70-unk.xyz

description: :unav
DOI: 10.15454/sqwfn4/wejfd8
title: oak8-9-ec.xyz

description: :unav
DOI: 10.15454/sqwfn4/wpsiag
title: oak8-8-ec.xyz

description: :unav
DOI: 10.15454/sqwfn4/j3uktb
title: beech1-1-br2.xyz

description: :unav
DOI: 10.15454/sqwfn4/ubkn9m
title: beech103-20-ci.xyz

description: :unav
DOI: 10.15454/sqwfn4/f8kdxv
title: centerline.xyz

description: :unav
DOI: 10.15454/sqwfn4/jwffgr
title: oak8-2-ec.xyz

description: :unav
DOI: 10.15454/sqwfn4/skuli8
title: oak8-261-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/grmaqv
title: beech2-11-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/kvmeik
title: oak8-2-br2.xyz

description: :unav
DOI: 10.15454/sqwfn4/qvte7a
title: oak0-16-unk.xyz

description: :unav
DOI: 10.15454/sqwfn4/qqgajv
title: beech1-2-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/stz4ny
title: oak8-57-br.xyz

description: :unav
DOI: 10.21227/958q-rw06
title: Datasets for performance monitoring in the froth flotation

description: There are three datasets, which include the labeled grade by the XRF analyzer and its related visual features and feed grades.It can be used for training and validation the performance monitoring model in the froth flotation.
DOI: 10.15454/sqwfn4/dwiie3
title: oak4-1010-ec.xyz

description: :unav
DOI: 10.15454/sqwfn4/7iuhky
title: oak0-18-bru.xyz

description: :unav
DOI: 10.15454/sqwfn4/6hxnzk
title: beech1-105-br2.xyz

description: :unav
DOI: 10.15454/sqwfn4/9lhkwk
title: oak4-21-br.xyz

description: :unav
DOI: 10.5281/zenodo.3876097
title: Dataset related to the article "Design of novel multiplex MinION sequencing workflow based on the required depth required to analyse human primary cell cDNA"

description: This record contains raw data related to the article “Design of novel multiplex MinION sequencing workflow based on the required depth required to analyse human primary cell cDNA" <strong>Abstract</strong> <strong>Background</strong> Transcript sequencing is a crucial tool for gaining a deep understanding of biological processes in diagnostic and clinical medicine. Given their potential to analyse novel complex eukaryotic transcriptomes, long-read sequencing technologies are able to overcome some limitations of short-read RNA-sequencing approaches. Oxford Nanopore Technologies (ONT) offers the ability to generate long-read sequencing data via portable protein nanopore USB devices at a reasonable cost. The aim of this study was to identify the depth needed to achieve the best trade-off between accuracy and cost-effectiveness by multiplex ONT MinION sequencing of human cell RNA. <strong>Results</strong> We analysed four cDNA libraries from isolated human aortic valve interstitial cells, by an ONT MinION sequencer. Synthetic datasets with different sizes were generated to evaluate the performance as a function of the read number. We were able to detect a high number of genes (&gt;12,500) with ~2 million reads, whose expression measurements were comparable to the full dataset (r<sub>p</sub> = 0.98). These data were further confirmed by the implementation of a new and user-friendly multiplexing method, including of 6 custom designed barcodes integrated in the reverse transcription step. We obtained comparable results between the different barcoded samples, both in terms of the number of identified genes (average value &gt;12,500) and expression levels (r<sub>p</sub>&gt;0.86). <strong>Conclusions</strong> ONT sequencing allows a batch of six different barcoded samples to be efficiently analysed in a unique MinION run. Thus, these data support the use of our sequencing workflow for human cells to further decrease run time and cost per sample
description: This work was supported by the Italian Ministry of Health funds (Ricerca Finalizzata: GR-2018-12366423; ERA-CVD: PICASSO-JTC-2018-042) and by Fondazione Gigi e Pupa Ferrari ONLUS (FPF-14).
DOI: 10.15454/sqwfn4/cc8tvg
title: beech2-12-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/tfhdzd
title: beech1-21-bra.xyz

description: :unav
DOI: 10.15454/sqwfn4/w8reka
title: oak8-46-br.xyz

description: :unav
DOI: 10.15454/sqwfn4/kakpau
title: centerline.xyz

description: :unav
DOI: 10.15454/sqwfn4/40bxrp
title: oak1-1001-ec.xyz

description: :unav
DOI: 10.15454/sqwfn4/fsnyci
title: oak5-1002-ec.xyz

description: :unav
DOI: 10.15454/sqwfn4/43i9bs
title: beech9-131-gm.xyz

description: :unav
DOI: 10.15454/sqwfn4/rxnrdt
title: oak0-681-bru.xyz

description: :unav
DOI: 10.15454/sqwfn4/hofhl3
title: radius

description: :unav
DOI: 10.15454/sqwfn4/jojp9z
title: beech2-21-gm.xyz

description: :unav
DOI: 10.15454/sqwfn4/jxgdht
title: oak613-2-ec.xyz

description: :unav
DOI: 10.15156/bio/sh1705370.08fu
title: SH1705370.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1705371.08fu
title: SH1705371.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1705372.08fu
title: SH1705372.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh341013.07fu
title: SH341013.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh341014.07fu
title: SH341014.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.