cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57903/uj/5wgsjx
title: ZintegrUJ physics samples - Time steps

description: Tools for fixed time methods in the Godot engine Tools for adapted time methods in the Godot engine This content was created as part of a project co-financed by the European Union within the framework of the European Social Fund POWER.03.05.00-00-Z309/17-00.
DOI: 10.5281/zenodo.10149764
title: Prevalence of Hematodinium sp. in Norway lobsters (Nephrops norvegicus) from the Clyde Sea Area (period 2018-2019)

description: Norway lobsters (Nephrops norvegicus) are important representatives of the benthos and support valuable fisheries accross Europe. Nephrops are susceptible to Hematodinium sp., an endoparasitic dinoflagellate that causes morbidity and mortality.  From an epizootiological perspective, the Clyde Sea Area (CSA; west of Scotland) is the best studied Hematodinium-Nephrops pathosystem. This dataset contains prevalence data of Hematodinium sp. in Nephrops collected from the CSA from November 2018 to October 2019. This dataset is linked to the publication 'Infection of Norway lobster (Nephrops norvegicus) by the parasite Hematodinium sp.: Insights from 30 years of field observations'.
Summary on methodology: Trawls were conducted monthly from November 2018 to October 2019 (12 months) aboard the commercial fishing vessel Eilidh Anne GK2. The main capture site was the Largs-Fairly Channel (LFC) in the CSA, Scotland. Nephrops were caught at depths of between 22-74 m, using a commercial net of 86 mm diamond mesh and 3 mm compact twine size. The average trawling time was 84.5 ± 20.5 min. All trawls occurred during crepuscular periods. Nephrops were separated from by-catch on-board, and a random subset of ~150 animals per month (n = 1,739) were retained and transported on ice to the University of Stirling for the individual assessment of sex, carapace length (CL), moulting stage and the level of patent infection (via BCM and PM; see section on pleopod examination) (Field, 1992).
DOI: 10.6084/m9.figshare.24903509
title: Data from Cultural influences on the effects of social norm appeals

description: This study reports on an experimental test of the effects of descriptive and injunctive norm appeals on intentions to prevent food waste in China and the United States (<i>N</i> = 1449), testing the role of cultural context and group orientation in this process. Results showed that the main effects of descriptive and injunctive norm messages on behavioural intentions were mediated by normative perceptions, and cultural context moderated both paths of this mediation. Specifically, with the same message exposure, Chinese participants perceived food waste prevention as more prevalent and socially approved compared to US participants. Normative perceptions interacted with cultural context to influence behavioural intentions, such that both descriptive and injunctive norm perceptions predicted stronger intentions to prevent food waste among Chinese participants compared to Americans. Group orientation yielded a main effect on behavioural intentions, instead of the moderation effects as expected. Findings suggest the need for culturally grounded and contextualized approaches to communication of social norms, as well as building cultural concepts into theories of social norms.This article is part of the theme issue ‘Social Norm Change: From Evolution to Policy Intervention’.
DOI: 10.6084/m9.figshare.24903509.v1
title: Data from Cultural influences on the effects of social norm appeals

description: This study reports on an experimental test of the effects of descriptive and injunctive norm appeals on intentions to prevent food waste in China and the United States (<i>N</i> = 1449), testing the role of cultural context and group orientation in this process. Results showed that the main effects of descriptive and injunctive norm messages on behavioural intentions were mediated by normative perceptions, and cultural context moderated both paths of this mediation. Specifically, with the same message exposure, Chinese participants perceived food waste prevention as more prevalent and socially approved compared to US participants. Normative perceptions interacted with cultural context to influence behavioural intentions, such that both descriptive and injunctive norm perceptions predicted stronger intentions to prevent food waste among Chinese participants compared to Americans. Group orientation yielded a main effect on behavioural intentions, instead of the moderation effects as expected. Findings suggest the need for culturally grounded and contextualized approaches to communication of social norms, as well as building cultural concepts into theories of social norms.This article is part of the theme issue ‘Social Norm Change: From Evolution to Policy Intervention’.
DOI: 10.57770/mxa1nk
title: Connective tissue growth factor decreases mitochondrial metabolism through ubiquitin-mediated degradation of mitochondrial transcription factor A in oral squamous cell carcinoma.

description: Background/Purpose: Deregulation of metabolic pathways is one of the hallmarks of cancer progression. Connective tissue growth factor (CTGF/CCN2) acts as a tumor suppressor in oral squamous cell carcinoma (OSCC). However, the role of CTGF in modulating cancer metabolism is still unclear. Methods: OSCC cells stably overexpressing CTGF (SAS/CTGF) and shRNA against CTGF (TW2.6/ shCTGF) were established. Oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) were examined by the Seahorse XF24 analyzer. The expression of CTGF and mitochondrial biogenesis related genes was measured by real-time polymerase chain reaction or Western blot analysis. Results: CTGF decreased OCR, ECAR, adenosine triphosphate (ATP) generation, mitochondrial DNA (mtDNA), and mitochondrial transcription factor A (mtTFA) protein expression in OSCC cells. Overexpression of mtTFA restored CTGF-decreased OCR, ECAR, mtDNA copy number, migration and invasion of SAS/CTGF cells. Immunoprecipitation assay showed a higher level of ubiquitinated mtTFA protein after CTGF treatment. MG132, an inhibitor of proteasomal degradation, reversed the effect of CTGF on mtTFA protein expression in SAS cells. Conclusion: CTGF can decrease glycolysis, mitochondrial oxidative phosphorylation, ATP generation, and mtDNA copy number by increasing mtTFA protein degradation through ubiquitin
DOI: 10.57770/o6b8te
title: Promoter analysis and transcriptional regulation of human carbonic anhydrase VIII gene in a MERRF disease cell model.

description: Myoclonic epilepsy with ragged-red fibers (MERRF) is a maternally inherited mitochondrial neuromuscular disease. We previously reported a significant decrease of mRNA and protein levels of nuclear DNA-encoded carbonic anhydrase VIII (CA8) in MERRF cybrids harboring A8344G mutation in mitochondrial DNA (mtDNA). In this study, we established a reporter construct of luciferase gene-carrying hCA8 promoter containing several putative transcription factor-binding sites, including GC-box, AP-2 and TATA-binding element in the 5'flanking region of the hCA8 gene. Using a series of mutated hCA8 promoter constructs, we demonstrated that a proximal GC-box, recognized by Sp1 and other Sp family members, may be a key cis-element functioning at the promoter. Additionally, a significant increase of the hCA8 promoter activity was observed in the wild-type and mutant cybrids with over-expression of eGFP-Sp1, but no detectable increase in the CA8 protein expression. In contrast, over-expression of Flag-Sp1 and Flag-Sp4 significantly increased the hCA8 promoter activity as well as endogenous CA8 protein expression in neuron-like HEK-293 T cells. However, down-regulation of Sp1, but not Sp4, in 293 T cells revealed a significant reduction of CA8 expression, suggesting that Sp1 is a predominant transcription factor for regulation of CA8 activity. Furthermore, our data indicate that chromatin structure may be involved in the expression of hCA8 gene in MERRF cybrids. Taken together, these results suggest that Sp1 transactivates hCA8 gene through the proximal GC box element in the promoter region. The key modulator-responsive factor to the mtDNA mutation and how it may affect nuclear hCA8 gene transcription need further investigations.
DOI: 10.57903/uj/suw4bm
title: ZintegrUJ physics samples - SPH

description: A SPH library Application: water with SPH algorithm This content was created as part of a project co-financed by the European Union within the framework of the European Social Fund POWER.03.05.00-00-Z309/17-00.
DOI: 10.5281/zenodo.10526721
title: Metabolic investigations of popular antiasthmatic drugs by an artificial lung consortium

description: Metadata files for the Masterthesis: "Metabolic investigations of popular antiasthmatic drugs by an artificial lung consortium"
DOI: 10.17028/rd.lboro.24614109
title: Data for particle analysis in "Effects of post weld heat treatment on the microstructure and properties of the matching SMAW filler metal for weld joints in MARBN steel"

description: Data set consisting of collected backscattered electron images together with the particle size data produced from the images.These data are discussed in the journal article with the title: Effects of post weld heat treatment on the microstructure and properties of the matching SMAW filler metal for weld joints in MARBN steel<b>Abstract</b>A detailed investigation has been carried out of the matching composition filler metal for welding MARBN steel to explore the influence of welding procedure and post weld heat treatment (PWHT) on the microstructure and properties of the weld metal and a MARBN steel weld joint. The filler metal was in the form of a shielded metal arc welding (SMAW) electrode. With different inter-pass temperatures and PWHT procedures applied, the microstructure and mechanical properties, particularly toughness, of the all-weld metal deposits and welded MARBN alloy joints were examined. The differences in microstructure (grain structure, precipitates, etc.) were evaluated to provide a better understanding of how the PWHTs influence the starting conditions of the matching weld metal and welded MARBN steel joints before service.Current work found that, for a 30 mm thick all-weld metal coupon, reasonable impact toughness was achieved after PWHT of 735°C x 8h; longer heat treatment durations (16 h and 36 h) did not further increase the toughness. For thicker cast blocks, a PWHT of 735°C x 16h was needed for weld toughness comparable to the base metal, hence was considered more appropriate for actual engineering applications. Evenly distributed Laves phase precipitation was observed after 735°C x 8h; the precipitates gradually increased in size and area fraction as the duration of PWHT increased, and appeared to be stable when approaching 36 h. Differences in the precipitation were observed between different weld regions. The weld cap region had a lower density of Laves precipitates compared to the lower weld area. From the current investigation, aspects for further investigation are also identified.© the authors, CC-BY-NC 4.0
DOI: 10.17028/rd.lboro.24614109.v1
title: Data for particle analysis in "Effects of post weld heat treatment on the microstructure and properties of the matching SMAW filler metal for weld joints in MARBN steel"

description: Data set consisting of collected backscattered electron images together with the particle size data produced from the images.These data are discussed in the journal article with the title: Effects of post weld heat treatment on the microstructure and properties of the matching SMAW filler metal for weld joints in MARBN steel<b>Abstract</b>A detailed investigation has been carried out of the matching composition filler metal for welding MARBN steel to explore the influence of welding procedure and post weld heat treatment (PWHT) on the microstructure and properties of the weld metal and a MARBN steel weld joint. The filler metal was in the form of a shielded metal arc welding (SMAW) electrode. With different inter-pass temperatures and PWHT procedures applied, the microstructure and mechanical properties, particularly toughness, of the all-weld metal deposits and welded MARBN alloy joints were examined. The differences in microstructure (grain structure, precipitates, etc.) were evaluated to provide a better understanding of how the PWHTs influence the starting conditions of the matching weld metal and welded MARBN steel joints before service.Current work found that, for a 30 mm thick all-weld metal coupon, reasonable impact toughness was achieved after PWHT of 735°C x 8h; longer heat treatment durations (16 h and 36 h) did not further increase the toughness. For thicker cast blocks, a PWHT of 735°C x 16h was needed for weld toughness comparable to the base metal, hence was considered more appropriate for actual engineering applications. Evenly distributed Laves phase precipitation was observed after 735°C x 8h; the precipitates gradually increased in size and area fraction as the duration of PWHT increased, and appeared to be stable when approaching 36 h. Differences in the precipitation were observed between different weld regions. The weld cap region had a lower density of Laves precipitates compared to the lower weld area. From the current investigation, aspects for further investigation are also identified.© the authors, CC-BY-NC 4.0
DOI: 10.5281/zenodo.10498472
title: Hyperspectral spectroscopic transmittance data collected in-vivo healthy and diseased tomato leaflets in controlled conditions - dataset II

description: Hyperspectral Spectroscopic Transmittance data collected in-vivo tomato leaflets in controlled conditions

Hyperspectral point-of-measurements (HS-POM) were collected in vivo from the adaxial side of healthy and diseased leaflets of nine tomato plants, in a dark room (in detail, three Control plants, three plants inoculated with Pseudomonas syringae pv. tomato, and three plants inoculated with Xanthomonas euvesicatoria). For each plant, spectral assessments were performed randomly on nine points of different leaflets, belonging to the 4th, 5th, and 6th expanded leaves.

Hyperspectral data were acquired using a Hamamatsu Photonics K.K. TM Series C11697MB spectrometer, which covers a wavelength range of 200-1100 nm with a spectral resolution of 0.6 nm. A transmission optical fiber bundle (FCR-7UVIR200-2-45-BX, Avantes, Eerbeek, The Netherlands) with a range of 200-2500 nm was used along with a stainless-steel slitted reflection probe that was positioned 0.5 cm above the sample surface to capture the leaflet's spectral signal and direct it to the spectrometer's entrance lens. A white LED light was placed underneath the leaflet to provide uniform illumination to its entire abaxial surface. The spectral range of the LED emits light from 390 to 800 nm. Therefore, the LED spectra were used as a reference to the spectral range measured by the spectrophotometer and to check measurement and light emission stability. The hyperspectral transmittance data were collected using specialized evaluation software (SpecEvaluationUSB2.exe, Hamamatsu Photonics K.K., Japan).

For more detailed description of the bacterial inoculation protocol please check:

Reis Pereira M, Santos FNd, Tavares F and Cunha M (2023) Enhancing host-pathogen phenotyping dynamics: early detection of tomato bacterial diseases using hyperspectral point measurement and predictive modeling. Front. Plant Sci. 14:1242201. doi: 10.3389/fpls.2023.1242201
DOI: 10.5281/zenodo.10498473
title: Hyperspectral spectroscopic transmittance data collected in-vivo healthy and diseased tomato leaflets in controlled conditions - dataset II

description: Hyperspectral Spectroscopic Transmittance data collected in-vivo tomato leaflets in controlled conditions

Hyperspectral point-of-measurements (HS-POM) were collected in vivo from the adaxial side of healthy and diseased leaflets of nine tomato plants, in a dark room (in detail, three Control plants, three plants inoculated with Pseudomonas syringae pv. tomato, and three plants inoculated with Xanthomonas euvesicatoria). For each plant, spectral assessments were performed randomly on nine points of different leaflets, belonging to the 4th, 5th, and 6th expanded leaves.

Hyperspectral data were acquired using a Hamamatsu Photonics K.K. TM Series C11697MB spectrometer, which covers a wavelength range of 200-1100 nm with a spectral resolution of 0.6 nm. A transmission optical fiber bundle (FCR-7UVIR200-2-45-BX, Avantes, Eerbeek, The Netherlands) with a range of 200-2500 nm was used along with a stainless-steel slitted reflection probe that was positioned 0.5 cm above the sample surface to capture the leaflet's spectral signal and direct it to the spectrometer's entrance lens. A white LED light was placed underneath the leaflet to provide uniform illumination to its entire abaxial surface. The spectral range of the LED emits light from 390 to 800 nm. Therefore, the LED spectra were used as a reference to the spectral range measured by the spectrophotometer and to check measurement and light emission stability. The hyperspectral transmittance data were collected using specialized evaluation software (SpecEvaluationUSB2.exe, Hamamatsu Photonics K.K., Japan).

For more detailed description of the bacterial inoculation protocol please check:

Reis Pereira M, Santos FNd, Tavares F and Cunha M (2023) Enhancing host-pathogen phenotyping dynamics: early detection of tomato bacterial diseases using hyperspectral point measurement and predictive modeling. Front. Plant Sci. 14:1242201. doi: 10.3389/fpls.2023.1242201
DOI: 10.57770/nxzek9
title: Current understanding and future perspectives of the roles of sirtuins in the reprogramming and differentiation of pluripotent stem cells.

description: In mammalian cells, there are seven members of the sirtuin protein family (SIRT1–7). SIRT1, SIRT6, and SIRT7 catalyze posttranslational modification of proteins in the nucleus, SIRT3, SIRT4, and SIRT5 are in the mitochondria and SIRT2 is in the cytosol. SIRT1 can deacetylate the transcription factor SOX2 and regulate induced pluripotent stem cells (iPSCs) reprogramming through the miR-34a–SIRT1–p53 axis. SIRT2 can regulate the function of pluripotent stem cells through GSK3β. SIRT3 can positively regulate PPAR gamma coactivator 1-alpha (PGC-1α) expression during the differentiation of stem cells. SIRT4 has no direct role in regulating reprogramming but may have the potential to prevent senescence of somatic cells and to facilitate the reprogramming of iPSCs. SIRT5 can deacetylate STAT3, which is an important transcription factor in regulating pluripotency and differentiation of stem cells. SIRT6 can enhance the reprogramming efficiency of iPSCs from aged skin fibroblasts through miR-766 and increase the expression levels of the reprogramming genes including Sox2, Oct4, and Nanog through acetylation of histone H3 lysine 56. SIRT7 plays a regulatory role in the process of mesenchymal-to-epithelial transition (MET), which has been suggested to be a crucial process in the generation of iPSCs from fibroblasts. In this review, we summarize recent findings of the roles of sirtuins in the metabolic reprogramming and differentiation of stem cells and discuss the bidirectional changes in the gene expression and activities of sirtuins in the commitment of differentiation of mesenchymal stem cells (MSCs) and reprogramming of somatic cells to iPSCs, respectively. Thus, understanding the molecular basis of the interplay between different sirtuins and mitochondrial function will provide new insights into the regulation of differentiation of stem cells and iPSCs formation, respectively, and may help design effective stem cell therapies for regenerative medicine.
DOI: 10.6084/m9.figshare.25018643
title: CRF01_AE sequences

description: The 1364 CRF01_AE pol sequences
DOI: 10.6084/m9.figshare.25018643.v1
title: CRF01_AE sequences

description: The 1364 CRF01_AE pol sequences
DOI: 10.57770/ko5zhw
title: Essential role of connective tissue growth factor (CTGF) in transforming growth factor-β1 (TGF-β1)-induced myofibroblast transdifferentiation from Graves' orbital fibroblasts.

description: Connective tissue growth factor (CTGF) associated with transforming growth factor-β (TGF-β) play a pivotal role in the pathophysiology of many fibrotic disorders. However, it is not clear whether this interaction also takes place in GO. In this study, we investigated the role of CTGF in TGF-β-induced extracellular matrix production and myofibroblast transdifferentiation in Graves’ orbital fibroblasts. By Western blot analysis, we demonstrated that TGF-β1 induced the expression of CTGF, fibronectin, and alpha-smooth muscle actin (α-SMA) in Graves’ orbital fibroblasts. In addition, the protein levels of fibronectin and α-SMA in Graves’ orbital fibroblasts were also increased after treatment with a recombinant human protein CTGF (rhCTGF). Moreover, we transfected the orbital fibroblasts with a small hairpin RNA of CTGF gene (shCTGF) to knockdown the expression levels of CTGF, which showed that knockdown of CTGF significantly diminished TGF-β1-induced expression of CTGF, fibronectin and α-SMA proteins in Graves’ orbital fibroblasts. Furthermore, the addition of rhCTGF to the shCTGF-transfected orbital fibroblasts could restore TGF-β1-induced expression of fibronectin and α-SMA proteins. Our findings demonstrate that CTGF is an essential downstream mediator for TGF-β1-induced extracellular matrix production and myofibroblast transdifferentiation in Graves’ orbital fibroblasts and thus may provide with a potential therapeutic target for treatment of GO.
DOI: 10.57770/l29krd
title: ATOH1/RFX1/RFX3 transcription factors facilitate the differentiation and characterisation of inner ear hair cell-like cells from patient-specific induced pluripotent stem cells harbouring A8344G mutation of mitochondrial DNA.

description: Degeneration or loss of inner ear hair cells (HCs) is irreversible and results in sensorineural hearing loss (SHL). Human-induced pluripotent stem cells (hiPSCs) have been employed in disease modelling and cell therapy. Here, we propose a transcription factor (TF)-driven approach using ATOH1 and regulatory factor of x-box (RFX) genes to generate HC-like cells from hiPSCs. Our results suggest that ATOH1/RFX1/RFX3 could significantly increase the differentiation capacity of iPSCs into MYO7AmCherry-positive cells, upregulate the mRNA expression levels of HC-related genes and promote the differentiation of HCs with more mature stereociliary bundles. To model the molecular and stereociliary structural changes involved in HC dysfunction in SHL, we further used ATOH1/RFX1/RFX3 to differentiate HC-like cells from the iPSCs from patients with myoclonus epilepsy associated with ragged-red fibres (MERRF) syndrome, which is caused by A8344G mutation of mitochondrial DNA (mtDNA), and characterised by myoclonus epilepsy, ataxia and SHL. Compared with isogenic iPSCs, MERRF-iPSCs possessed ~42–44% mtDNA with A8344G mutation and exhibited significantly elevated reactive oxygen species (ROS) production and CAT gene expression. Furthermore, MERRF-iPSC-differentiated HC-like cells exhibited significantly elevated ROS levels and MnSOD and CAT gene expression. These MERRF-HCs that had more single cilia with a shorter length could be observed only by using a non-TF method, but those with fewer stereociliary bundle-like protrusions than isogenic iPSCs-differentiated-HC-like cells could be further observed using ATOH1/RFX1/RFX3 TFs. We further analysed and compared the whole transcriptome of M1ctrl-HCs and M1-HCs after treatment with ATOH1 or ATOH1/RFX1/RFX3. We revealed that the HC-related gene transcripts in M1ctrl-iPSCs had a significantly higher tendency to be activated by ATOH1/RFX1/RFX3 than M1-iPSCs. The ATOH1/RFX1/RFX3 TF-driven approach for the differentiation of HC-like cells from iPSCs is an efficient and promising strategy for the disease modelling of SHL and can be employed in future therapeutic strategies to treat SHL patients.