cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5507360
title: SynActJ: Easy-to-use automated analysis of synaptic activity

description: Neuronal synapses are highly dynamic communication hubs that mediate chemical neurotransmission via the exocytic fusion and subsequent endocytic recycling of neurotransmitter-containing synaptic vesicles (SVs). Functional imaging tools allow for the direct visualization of synaptic activity by detecting action potentials, pre- or postsynaptic calcium influx, SV exo- and endocytosis, and glutamate release. Fluorescent organic dyes or synapse-targeted genetic molecular reporters, such as calcium, voltage or neurotransmitter sensors and synapto-pHluorins reveal synaptic activity by undergoing rapid changes in their fluorescence intensity upon neuronal activity on timescales of milliseconds to seconds, which typically are recorded by fast and sensitive widefield live cell microscopy. The analysis of the resulting time-lapse movies in the past has been performed by either manually picking individual structures, custom scripts that have not been made widely available to the scientific community, or advanced software toolboxes that are complicated to use. For the precise, unbiased and reproducible measurement of synaptic activity, it is key that the research community has access to bio-image analysis tools that are easy-to-apply and allow the automated detection of fluorescent intensity changes in active synapses. Here we present SynActJ (<strong>Syn</strong>aptic <strong>Act</strong>ivity in Image<strong>J</strong>), an easy-to-use fully open-source workflow that enables automated image and data analysis of synaptic activity. The workflow consists of a Fiji plugin performing the automated image analysis of active synapses in time-lapse movies via an interactive seeded watershed segmentation that can be easily adjusted and applied to a dataset in batch mode. The extracted intensity traces of each synaptic bouton are automatically processed, analyzed, and plotted using a R Shiny workflow. We validate the workflow on time-lapse images of stimulated synapses expressing the presynaptic pH reporter Synaptophysin-pHluorin or a synapse-targeted calcium sensor, Synaptophysin-RGECO. We compare the automatic workflow to manual analysis and compute calcium-influx and SV exo-/ endocytosis kinetics and other parameters for synaptic vesicle recycling under different conditions. We predict SynActJ to become an important tool for the analysis of synaptic activity and synapse properties.
DOI: 10.5281/zenodo.5510478
title: Suggested Taxonomy: Tracking Technologies to Effectively Capture and Input Key Data on the Blockchain

description: Within the paper titled "Transparency with Blockchain and Physical Tracking Technologies: Enabling Traceability in Raw Material Supply Chains" (Mater. Proc. 2021, 5(1), 1; https://doi.org/10.3390/materproc2021005001), we consider the majority of tracking technologies to be part of the IoT ecosystem and suggest a taxonomy with their key features, benefits and use cases in the mining industry. Although technologies such as markers and QR/Barcodes are not necessarily electronic devices, they can integrate with other IoT objects and provide or qualify a digital identity. The common element connecting all these technologies is that they include functionalities that can capture and communicate granular, timely, relevant and accurate data, which can be automatically or manually entered into the blockchain. We have analysed the following most common physical tracking methods which will be described and exemplified in more detail below: Video monitoring (Table 1) Bar and QR codes (Table 2) Markers and taggants (Table 3) Cellular, near range and low power network tracking tools (Table 4) Satellite network tracking tools (Table 5)
DOI: 10.5281/zenodo.5510477
title: Suggested Taxonomy: Tracking Technologies to Effectively Capture and Input Key Data on the Blockchain

description: Within the paper titled "Transparency with Blockchain and Physical Tracking Technologies: Enabling Traceability in Raw Material Supply Chains" (Mater. Proc. 2021, 5(1), 1; https://doi.org/10.3390/materproc2021005001), we consider the majority of tracking technologies to be part of the IoT ecosystem and suggest a taxonomy with their key features, benefits and use cases in the mining industry. Although technologies such as markers and QR/Barcodes are not necessarily electronic devices, they can integrate with other IoT objects and provide or qualify a digital identity. The common element connecting all these technologies is that they include functionalities that can capture and communicate granular, timely, relevant and accurate data, which can be automatically or manually entered into the blockchain. We have analysed the following most common physical tracking methods which will be described and exemplified in more detail below: Video monitoring (Table 1) Bar and QR codes (Table 2) Markers and taggants (Table 3) Cellular, near range and low power network tracking tools (Table 4) Satellite network tracking tools (Table 5)
DOI: 10.5519/qd.3brbe8t6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (347 records)
DOI: 10.6084/m9.figshare.16624207.v1
title: Original Data of COVID-19 study.xlsx

description: An online investigation studying self-reported injury incidence , aetiology and cause was conducted (September to November 2020) involving Chinese full-time dance students, which covered two 6-month periods just before and during the first COVID-19 lockdown.
DOI: 10.18434/mds2-2462
title: 2021 MML Accolades Program
DOI: 10.6084/m9.figshare.16620583.v1
title: hs_rat_adipose_gene_expression_analysis.zip

description: Analysis of adipose gene expression in heterogeneous stock rats, its relationship to body weight, and comparison with human adipose gene expression.
DOI: 10.6084/m9.figshare.14679480
title: Multispectral grape images dataset

description: 1283 multispectral images with 37 reflectance bands in numpy array format (.npy) of 5 different grape varieties originating from the province of Murcia, Spain. Ready to be used in any supervised learning pipeline to fit classification or regression models.<br>Ground truth is provided together with the images in a tab separated text file with the information of each grape type, weight, Brix index and anthocyanines content
DOI: 10.5517/ccdc.csd.cc23yqsl
title: CCDC 1964990: Experimental Crystal Structure Determination

description: Related Article: Zhixiang Lu, Shuang Bai, Yesi Shi, Dazhuang Xu, Chengchao Chu, Gang Liu|2021|Chem.Eng.Journal|426|131891|doi:10.1016/j.cej.2021.131891
DOI: 10.5517/ccdc.csd.cc271mpm
title: CCDC 2057150: Experimental Crystal Structure Determination

description: Related Article: Jinfang Zhang, Qingxia Qiu, Qian Xiang, Wenjing Li, Zhuo Lin, Chi Zhang|2021|Dyes Pigm.|196|109760|doi:10.1016/j.dyepig.2021.109760
DOI: 10.5517/ccdc.csd.cc271mqn
title: CCDC 2057151: Experimental Crystal Structure Determination

description: Related Article: Jinfang Zhang, Qingxia Qiu, Qian Xiang, Wenjing Li, Zhuo Lin, Chi Zhang|2021|Dyes Pigm.|196|109760|doi:10.1016/j.dyepig.2021.109760
DOI: 10.5517/ccdc.csd.cc278t3g
title: CCDC 2064045: Experimental Crystal Structure Determination

description: Related Article: Mei-Li Guo, Hong-Tao Xu, Jun-Jie Yang, Gui-Xin Chou|2021|Bioorg.Chem.|116|105312|doi:10.1016/j.bioorg.2021.105312
DOI: 10.5517/ccdc.csd.cc279tzc
title: CCDC 2065033: Experimental Crystal Structure Determination

description: Related Article: Takumi Takeuchi, Ryosuke Shishido, Koji Kubota, Hajime Ito|2021|Chemical Science|12|11799|doi:10.1039/D1SC01440D
DOI: 10.6084/m9.figshare.22622864
title: Additional file 7 of Differential expression of pyroptosis-related genes in the hippocampus of patients with Alzheimer’s disease

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.10566770
title: MOESM1 of Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

description: Additional file 1. All of the proteins identified in the present study with annotations.
DOI: 10.6084/m9.figshare.10566770.v1
title: MOESM1 of Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

description: Additional file 1. All of the proteins identified in the present study with annotations.
DOI: 10.6084/m9.figshare.10566785
title: Additional file 3: of Long noncoding RNA 00976 promotes pancreatic cancer progression through OTUD7B by sponging miR-137 involving EGFR/MAPK pathway

description: Table S1. Different proteins in Linc00976 knockdown and NC PANC-1 based on the iTRAQ results. (XLSX 1041 kb)
DOI: 10.6084/m9.figshare.10566785.v1
title: Additional file 3: of Long noncoding RNA 00976 promotes pancreatic cancer progression through OTUD7B by sponging miR-137 involving EGFR/MAPK pathway

description: Table S1. Different proteins in Linc00976 knockdown and NC PANC-1 based on the iTRAQ results. (XLSX 1041 kb)
DOI: 10.6084/m9.figshare.10566788
title: MOESM8 of A single factor dominates the behavior of rhythmic genes in mouse organs

description: Additional file 8: Figure S7. PC1 from the principle component analysis of energetic cost (5′ UTR, 3′ UTR, and coding regions) is strongly correlated with amplitude.
DOI: 10.6084/m9.figshare.10566788.v1
title: MOESM8 of A single factor dominates the behavior of rhythmic genes in mouse organs

description: Additional file 8: Figure S7. PC1 from the principle component analysis of energetic cost (5′ UTR, 3′ UTR, and coding regions) is strongly correlated with amplitude.
DOI: 10.6084/m9.figshare.10566791
title: MOESM3 of Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

description: Additional file 3. Differentially expressed proteins at different time points.
DOI: 10.6084/m9.figshare.10566791.v1
title: MOESM3 of Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

description: Additional file 3. Differentially expressed proteins at different time points.
DOI: 10.6084/m9.figshare.22622864.v1
title: Additional file 7 of Differential expression of pyroptosis-related genes in the hippocampus of patients with Alzheimer’s disease

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.10566803
title: MOESM5 of Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

description: Additional file 5. GO and pathway enrichment analysis of differentially expressed proteins.
DOI: 10.6084/m9.figshare.10566803.v1
title: MOESM5 of Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

description: Additional file 5. GO and pathway enrichment analysis of differentially expressed proteins.
DOI: 10.6084/m9.figshare.22622870
title: Additional file 9 of Differential expression of pyroptosis-related genes in the hippocampus of patients with Alzheimer’s disease

description: Supplementary Material 9
DOI: 10.6084/m9.figshare.22622869.v1
title: Additional file 2 of Functional identification of two novel carbohydrate-binding modules of glucuronoxylanase CrXyl30 and their contribution to the lignocellulose saccharification

description: Additional file 2: Predicted structures of CrCBM13.
DOI: 10.6084/m9.figshare.10566809
title: MOESM6 of Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

description: Additional file 6. Protein-protein interaction networks of DEPs in 4D/0D.
DOI: 10.6084/m9.figshare.10566809.v1
title: MOESM6 of Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

description: Additional file 6. Protein-protein interaction networks of DEPs in 4D/0D.
DOI: 10.6084/m9.figshare.12133827.v1
title: Additional file 1 of KIF15 facilitates gastric cancer via enhancing proliferation, inhibiting apoptosis, and predict poor prognosis

description: Additional file 1: Table S1. The green boxes showed seven positive anti-apoptotic proteins which were detected by the Human Apoptosis Antibody Array kit (ab134001).
DOI: 10.6084/m9.figshare.10566821
title: MOESM8 of Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

description: Additional file 8. Details of the dynamic MRM results.
DOI: 10.6084/m9.figshare.10566821.v1
title: MOESM8 of Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

description: Additional file 8. Details of the dynamic MRM results.
DOI: 10.6084/m9.figshare.7945463
title: The influence of glycemic status on the performance of cystatin C for acute kidney injury detection in the critically ill

description: <b>Objective:</b> Serum cystatin C (sCysC) used clinically for detecting early acute kidney injury (AKI) was reported to be independently associated with hemoglobin (HbA1c) levels, diabetes, and prediabetes. We aimed to assess the influence of HbA1c levels, diabetes, or prediabetes on the performance of sCysC for AKI detection in critically ill adults. <b>Methods:</b> A prospective observational study was conducted in a mixed medical-surgical intensive care unit (ICU). Patients were divided into four quartiles based on levels of HbA1c or serum glucose at ICU admission, respectively. Additionally, patients were stratified into four subgroups according to HbA1c levels and history of diabetes, namely recognized diabetes (previous diagnosis of diabetes), unrecognized diabetes, prediabetes, and normal glycemic status. Comparisons were made using the area under the receiver operator characteristic curve (AUC) for AKI detection, and reassessed after patient stratification by above-mentioned glycemic status. <b>Results:</b> Multivariable linear regression revealed that HbA1c levels and history of diabetes were positively related with sCysC (all <i>p</i> &lt; .05). Although stratification for above-mentioned glycemic status displayed no significant difference between AUC of sCysC (all <i>p</i> &gt; .05), sCysC yielded the highest AUCs for detecting AKI in diabetic patients. Moreover, higher optimal cutoff values of sCysC to detect AKI were observed in patients with versus without diabetes. <b>Conclusion:</b> Glycemic status has no significant impact on the accuracy of sCysC for AKI detection in critically ill adults and a higher optimal cutoff value of sCysC for AKI detection should be considered in diabetic patients.
DOI: 10.6084/m9.figshare.7945463.v1
title: The influence of glycemic status on the performance of cystatin C for acute kidney injury detection in the critically ill

description: <b>Objective:</b> Serum cystatin C (sCysC) used clinically for detecting early acute kidney injury (AKI) was reported to be independently associated with hemoglobin (HbA1c) levels, diabetes, and prediabetes. We aimed to assess the influence of HbA1c levels, diabetes, or prediabetes on the performance of sCysC for AKI detection in critically ill adults. <b>Methods:</b> A prospective observational study was conducted in a mixed medical-surgical intensive care unit (ICU). Patients were divided into four quartiles based on levels of HbA1c or serum glucose at ICU admission, respectively. Additionally, patients were stratified into four subgroups according to HbA1c levels and history of diabetes, namely recognized diabetes (previous diagnosis of diabetes), unrecognized diabetes, prediabetes, and normal glycemic status. Comparisons were made using the area under the receiver operator characteristic curve (AUC) for AKI detection, and reassessed after patient stratification by above-mentioned glycemic status. <b>Results:</b> Multivariable linear regression revealed that HbA1c levels and history of diabetes were positively related with sCysC (all <i>p</i> &lt; .05). Although stratification for above-mentioned glycemic status displayed no significant difference between AUC of sCysC (all <i>p</i> &gt; .05), sCysC yielded the highest AUCs for detecting AKI in diabetic patients. Moreover, higher optimal cutoff values of sCysC to detect AKI were observed in patients with versus without diabetes. <b>Conclusion:</b> Glycemic status has no significant impact on the accuracy of sCysC for AKI detection in critically ill adults and a higher optimal cutoff value of sCysC for AKI detection should be considered in diabetic patients.
DOI: 10.5281/zenodo.10629782
title: Controlled deficit irrigation as a water-saving strategy for processing tomato

description: In a complex scenario characterized by climate change and increasing population demand, it is necessary to adopt production strategies involving a lower use of water. For this purpose, controlled deficit irrigation, CDI, strategies with an initial full irrigation covering 100% crop evapotranspiration (ETc) followed by mild (50%ETc) and moderate (75%ETc) irrigation restrictions after the fruit set stage were evaluated. The study was performed during two years in two growing areas of processing tomato in Spain, using conventional and high-lycopene cultivars. With moderate levels of CDI an average saving of water of 26.1% was achieved, but productivity was reduced on average by 10.7%. It should be considered though, that the effect was dependent on the environment and genotype, and high-yield cultivars seemed to be more sensitive to the negative effects of moderate CDI on productivity. In contrast, mild CDI levels did not affect productivity and still entailed a water saving of 13%. Moderate CDI levels increased soluble solids content, but this increase was not due to a higher accumulation of taste-related compounds, such as sugars and acids. Indeed, irrigation dose had no significant effect on the levels of fructose, glucose, citric and glutamic acid nor on derived variables related to tomato acceptability and CDI decreased the levels of malic acid. Considering previous results, mild CDI strategies would be preferred to continuous deficit irrigation strategies as the former contribute to reduce the use of water, an increasingly scarce resource, avoiding negative impacts on productivity, a key parameter to promote farmer adoption of CDI strategies. 

For more detailed data contact the authors

Acknowledgments This research was funded by Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria with the project RTA2011-00062 and GRU 15112 and AGROS financed by Gobierno de Extremadura. These projects were co-funded by the Fondo Europeo de Desarrollo Regional (FEDER, EU).

  


Valcárcel, M., Lahoz, I., Campillo, C., Martí, R., Leiva-Brondo, M., Rosello, S. and Cebolla-Cornejo, J., 2020. Controlled deficit irrigation as a water-saving strategy for processing tomato. Scientia Horticulturae, 261, p.108972.


Link to publication:
https://www.sciencedirect.com/science/article/pii/S0304423819308581


Link to repository:
https://riunet.upv.es/handle/10251/171697
DOI: 10.5281/zenodo.10629783
title: Controlled deficit irrigation as a water-saving strategy for processing tomato

description: In a complex scenario characterized by climate change and increasing population demand, it is necessary to adopt production strategies involving a lower use of water. For this purpose, controlled deficit irrigation, CDI, strategies with an initial full irrigation covering 100% crop evapotranspiration (ETc) followed by mild (50%ETc) and moderate (75%ETc) irrigation restrictions after the fruit set stage were evaluated. The study was performed during two years in two growing areas of processing tomato in Spain, using conventional and high-lycopene cultivars. With moderate levels of CDI an average saving of water of 26.1% was achieved, but productivity was reduced on average by 10.7%. It should be considered though, that the effect was dependent on the environment and genotype, and high-yield cultivars seemed to be more sensitive to the negative effects of moderate CDI on productivity. In contrast, mild CDI levels did not affect productivity and still entailed a water saving of 13%. Moderate CDI levels increased soluble solids content, but this increase was not due to a higher accumulation of taste-related compounds, such as sugars and acids. Indeed, irrigation dose had no significant effect on the levels of fructose, glucose, citric and glutamic acid nor on derived variables related to tomato acceptability and CDI decreased the levels of malic acid. Considering previous results, mild CDI strategies would be preferred to continuous deficit irrigation strategies as the former contribute to reduce the use of water, an increasingly scarce resource, avoiding negative impacts on productivity, a key parameter to promote farmer adoption of CDI strategies. 

For more detailed data contact the authors

Acknowledgments This research was funded by Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria with the project RTA2011-00062 and GRU 15112 and AGROS financed by Gobierno de Extremadura. These projects were co-funded by the Fondo Europeo de Desarrollo Regional (FEDER, EU).

  


Valcárcel, M., Lahoz, I., Campillo, C., Martí, R., Leiva-Brondo, M., Rosello, S. and Cebolla-Cornejo, J., 2020. Controlled deficit irrigation as a water-saving strategy for processing tomato. Scientia Horticulturae, 261, p.108972.


Link to publication:
https://www.sciencedirect.com/science/article/pii/S0304423819308581


Link to repository:
https://riunet.upv.es/handle/10251/171697
DOI: 10.5281/zenodo.10633841
title: Controlled deficit irrigation as a water-saving strategy for processing tomato

description: In a complex scenario characterized by climate change and increasing population demand, it is necessary to adopt production strategies involving a lower use of water. For this purpose, controlled deficit irrigation, CDI, strategies with an initial full irrigation covering 100% crop evapotranspiration (ETc) followed by mild (50%ETc) and moderate (75%ETc) irrigation restrictions after the fruit set stage were evaluated. The study was performed during two years in two growing areas of processing tomato in Spain, using conventional and high-lycopene cultivars. With moderate levels of CDI an average saving of water of 26.1% was achieved, but productivity was reduced on average by 10.7%. It should be considered though, that the effect was dependent on the environment and genotype, and high-yield cultivars seemed to be more sensitive to the negative effects of moderate CDI on productivity. In contrast, mild CDI levels did not affect productivity and still entailed a water saving of 13%. Moderate CDI levels increased soluble solids content, but this increase was not due to a higher accumulation of taste-related compounds, such as sugars and acids. Indeed, irrigation dose had no significant effect on the levels of fructose, glucose, citric and glutamic acid nor on derived variables related to tomato acceptability and CDI decreased the levels of malic acid. Considering previous results, mild CDI strategies would be preferred to continuous deficit irrigation strategies as the former contribute to reduce the use of water, an increasingly scarce resource, avoiding negative impacts on productivity, a key parameter to promote farmer adoption of CDI strategies. 

For more detailed data contact the authors

Acknowledgments This research was funded by Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria with the project RTA2011-00062 and GRU 15112 and AGROS financed by Gobierno de Extremadura. These projects were co-funded by the Fondo Europeo de Desarrollo Regional (FEDER, EU).

  


Valcárcel, M., Lahoz, I., Campillo, C., Martí, R., Leiva-Brondo, M., Rosello, S. and Cebolla-Cornejo, J., 2020. Controlled deficit irrigation as a water-saving strategy for processing tomato. Scientia Horticulturae, 261, p.108972.


Link to publication:
https://www.sciencedirect.com/science/article/pii/S0304423819308581


Link to repository:
https://riunet.upv.es/handle/10251/171697
DOI: 10.6084/m9.figshare.10566959
title: MOESM1 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 1. Throughput and quality of RNA-Seq data in apricot fruit.