cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10551522
title: Hybrid pKa Dataset for Acid Molecules

description: This hybrid dataset is composed of a collection of 13460 acid molecules with their corresponding dissociation constant (\(\rm{p}\it{K}_\rm{a}\)) and the temperature in which the dissociation constant was measured.

This dataset was created in two different steps. The first step came from two different sources, one from literature digitization [1], and the second source was a chemical intelligence support software that predicts the \(\rm{p}\it{K}_\rm{a}\) [2].

Among other variables in this first step, both datasets contained information regarding the SMILES representation of the molecules, \(\rm{p}\it{K}_\rm{a}\), and temperature, see the table below. A preprocessing was done to remove duplicated compounds, but only when the temperatures were the same, otherwise, repeated molecules were kept. Finally, the resulting dataset from this first step ended with 6030 entries.

The second step was an extension of the dataset, done in two ways. The first way was using the dataset from [3], and the second way was by the use of the results coming from simulations that we did using a conditional variational autoencoder (CVAE). The CVAE was trained with the dataset from step 1. The final hybrid dataset possesses  13460 molecules.

 




Parameter
Description


SMILES
String molecular representation of molecules.


\(\rm{p}\it{K}_\rm{a}\)
The negative base-10 logarithm of the acid dissociation constant \(\it{K}_\rm{a}\) of a solution.


Temperature (°C)
The temperature at which \(\rm{p}\it{K}_\rm{a}\) was measured in degrees Celsius.




 

This hybrid dataset was created to be used within the framework of the MOZART project with Grant Agreement 101058450, website: Mozart-Project.

 

[1] Jonathan Zheng. (2022). IUPAC/Dissociation-Constants: v1.0 (v1-0_initial-release) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7236453

[2] DataWarrior: An Open-Source Program For Chemistry Aware Data Visualization And Analysis. Thomas Sander, Joel Freyss, Modest von Korff, and Christian Rufener. Journal of Chemical Information and Modeling 2015 55 (2), 460-473. DOI: 10.1021/ci500588j. Website: www.openmolecules.org.

[3] Python script to lookup pKa values. Repository: GitHub - khoivan88/pka_lookup: Python script to lookup pKa values
DOI: 10.5281/zenodo.8374046
title: NutriGreen Image Dataset: A Collection of Annotated Nutrition, Organic, and Vegan Food Products

description: The generated dataset is an annotated collection, with each image carrying labels (NutriScore, V-label and Bio). The presence of annotated data is essential for developing a supervised machine-learning model capable of automatically identifying labels in new images. In our case, we utilize this data to train a model that can autonomously recognize labels on new images not present in the dataset, achieving a model accuracy of 94%. In the future, you have the option to train a new model using the dataset to achieve higher accuracy or employ the existing model to automatically identify bio and nutri labels in newly collected images, eliminating the need for manual review. We should emphasize that these resources should be utilized by a data science team. There is an opportunity for this model to be integrated with a mobile app, but this is a direction for future work, we included in the revised version.

In this research, we introduce the NutriGreen dataset, which is a collection of images representing packaged food products. Each image in the dataset comes with three distinct labels: one indicating its nutritional value using the Nutri-Score, another denoting whether it's vegan or vegetarian with the V-label, and a third displaying the EU organic certification (BIO) logo. The dataset comprises a total of 10,472 images. Among these, the Nutri-Score label is distributed across five sub-labels: A with 1,250 images, B with 1,107 images, C with 867 images, D with 1,001 images, and E with 967 images. Additionally, there are 870 images featuring the V-Label, 2,328 images showcasing the BIO label, and 3201 images with no labels. Furthermore, we have fine-tuned the YOLOv5 model to demonstrate the practicality of using these annotated datasets, achieving an impressive accuracy of 94.0%. These promising results indicate that this dataset has significant potential for training innovative systems capable of detecting food labels. Moreover, it can serve as a valuable benchmark dataset for emerging computer vision systems.
DOI: 10.5281/zenodo.8374047
title: NutriGreen Image Dataset: A Collection of Annotated Nutrition, Organic, and Vegan Food Products

description: In this research, we introduce the NutriGreen dataset, which is a collection of images representing packaged food products. Each image in the dataset comes with three distinct labels: one indicating its nutritional value using the Nutri-Score, another denoting whether it's vegan or vegetarian with the V-label, and a third displaying the EU organic certification (BIO) logo. The dataset comprises a total of 10,472 images. Among these, the Nutri-Score label is distributed across five sub-labels: A with 1,250 images, B with 1,107 images, C with 867 images, D with 1,001 images, and E with 967 images. Additionally, there are 870 images featuring the V-Label, 2,328 images showcasing the BIO label, and 3201 images with no labels. Furthermore, we have fine-tuned the YOLOv5 model to demonstrate the practicality of using these annotated datasets, achieving an impressive accuracy of 94.0%. These promising results indicate that this dataset has significant potential for training innovative systems capable of detecting food labels. Moreover, it can serve as a valuable benchmark dataset for emerging computer vision systems.
DOI: 10.5281/zenodo.10617846
title: Oculated Idols DATASET

description: Images of oculated Idols in JPG format
DOI: 10.5281/zenodo.10617845
title: Oculated Idols DATASET

description: Images of oculated Idols in JPG format
DOI: 10.24403/jp.1321689
title: Wer war Dr. phil. Carl Leonhardt, der Verfasser der „Flora von Jena“ aus dem Jahre 1900? / Wolfgang Heinrich
DOI: 10.5281/zenodo.10617827
title: Cyclone labels, associated cluster, and location at classification time

description: This dataset is related to the following article:

Givon, Y., Hess, O., Flaounas, E., Catto, J. L., Sprenger, M., and Raveh-Rubin, S.: Process-based classification of Mediterranean cyclones using potential vorticity, Weather Clim. Dynam., 5, 133–162, https://doi.org/10.5194/wcd-5-133-2024, 2024.

Each row corresponds to a certain Mediterranean cyclone track labeled consistently as is Flaounas et al., 2023 dataset at confidence level 5 (left column).

The attributed PV cluster to each cyclone track is provided in the second column, followed by the location of the cyclone center at classification time (longitude, latitude).
DOI: 10.5281/zenodo.10617828
title: Cyclone labels, associated cluster, and location at classification time

description: This dataset is related to the following article:

Givon, Y., Hess, O., Flaounas, E., Catto, J. L., Sprenger, M., and Raveh-Rubin, S.: Process-based classification of Mediterranean cyclones using potential vorticity, Weather Clim. Dynam., 5, 133–162, https://doi.org/10.5194/wcd-5-133-2024, 2024.

Each row corresponds to a certain Mediterranean cyclone track labeled consistently as is Flaounas et al., 2023 dataset at confidence level 5 (left column).

The attributed PV cluster to each cyclone track is provided in the second column, followed by the location of the cyclone center at classification time (longitude, latitude).
DOI: 10.6084/m9.figshare.12586400
title: Additional file 8 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 8: Table S5. Targeting relationships between miRNAs and lncRNAs/mRNAs
DOI: 10.6084/m9.figshare.12586400.v1
title: Additional file 8 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 8: Table S5. Targeting relationships between miRNAs and lncRNAs/mRNAs
DOI: 10.6084/m9.figshare.12586403
title: Additional file 9 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 9: Table S6. Parental expression level dominance lncRNAs and its target mRNAs in three progenies
DOI: 10.6084/m9.figshare.12586403.v1
title: Additional file 9 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 9: Table S6. Parental expression level dominance lncRNAs and its target mRNAs in three progenies
DOI: 10.5522/04/25102538
title: Synchrotron Micro-Tomography of NMC811 Particles

description: 3D tiff stacks of tomographic data used within "Non-Linear Damage Response to Voltage Revealed by Operando X-ray Tomography in Polycrystalline NMC811". Within this dataset is a series of 3D tiff stacks that contain tomograms from I13-2 at Diamond Light Source, with a spatial resolution of 325 nm using a pco.edge.5.5 CMOS full field X-ray detector. The NMC811 particles are taken at multiple states-of-charge during the first charge cycle, and using a particle grey level analysis algorithm we have looked to understand the cracking behaviour on a particle-by-particle basis.
DOI: 10.5522/04/25102538.v1
title: Synchrotron Micro-Tomography of NMC811 Particles

description: 3D tiff stacks of tomographic data used within "Non-Linear Damage Response to Voltage Revealed by Operando X-ray Tomography in Polycrystalline NMC811". Within this dataset is a series of 3D tiff stacks that contain tomograms from I13-2 at Diamond Light Source, with a spatial resolution of 325 nm using a pco.edge.5.5 CMOS full field X-ray detector. The NMC811 particles are taken at multiple states-of-charge during the first charge cycle, and using a particle grey level analysis algorithm we have looked to understand the cracking behaviour on a particle-by-particle basis.
DOI: 10.6084/m9.figshare.12586420
title: Additional file 2 of Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

description: Additional file 2: Table S1. Locations of C2 domains and transmembrane regions in GhMCTP proteins.
DOI: 10.6084/m9.figshare.12586420.v1
title: Additional file 2 of Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

description: Additional file 2: Table S1. Locations of C2 domains and transmembrane regions in GhMCTP proteins.
DOI: 10.6084/m9.figshare.12586429
title: Additional file 5 of Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

description: Additional file 5: Table S2. Coding sequence divergence between syntenic MCTPs in G. barbadense, G. raimondii and G. arboreum.
DOI: 10.6084/m9.figshare.12586429.v1
title: Additional file 5 of Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

description: Additional file 5: Table S2. Coding sequence divergence between syntenic MCTPs in G. barbadense, G. raimondii and G. arboreum.
DOI: 10.6084/m9.figshare.12586432
title: Additional file 6 of Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

description: Additional file 6: Table S3. Physicochemical properties of the N-terminus and C-terminus of GhMCTP proteins.
DOI: 10.6084/m9.figshare.12586432.v1
title: Additional file 6 of Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

description: Additional file 6: Table S3. Physicochemical properties of the N-terminus and C-terminus of GhMCTP proteins.
DOI: 10.6084/m9.figshare.12586438
title: Additional file 8 of Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

description: Additional file 8: Table S4. Information about 27 plant species used in identifying MCTPs.
DOI: 10.6084/m9.figshare.12586438.v1
title: Additional file 8 of Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

description: Additional file 8: Table S4. Information about 27 plant species used in identifying MCTPs.
DOI: 10.6084/m9.figshare.12586441
title: Additional file 9 of Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

description: Additional file 9: Table S5. Primer pairs used for gene clone in yeast two-hybrid assay.
DOI: 10.6084/m9.figshare.12586441.v1
title: Additional file 9 of Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

description: Additional file 9: Table S5. Primer pairs used for gene clone in yeast two-hybrid assay.
DOI: 10.6084/m9.figshare.7867859
title: A novel in-frame mutation in <i>CLN3</i> leads to Juvenile neuronal ceroid lipofuscinosis in a large Pakistani family

description: <b>Aim:</b> Neuronal ceroid lipofuscinosis (NCLs) are the most common neurodegenerative disorders, with global incidence of 1 in 100,000 live births. NCLs affect central nervous system, primarily cerebellar and cerebral cortices. Juvenile neuronal ceroid lipofuscinosis (JNCL), also known as Batten disease, is the most common form of NCLs. JNCL is primarily caused by pathogenic mutations in <i>CLN3</i> gene, which encodes a transporter transmembrane protein of uncertain function. The 1.02 kb deletion is the most common mutation in <i>CLN3</i> that results in frame shift and a premature termination leading to nonfunctional protein. Here, we invetigated a large consanguineous family consisting of four affected individuals with clincal symptoms suggestive of Juvenile neuronal ceroid lipofuscinosis. <b>Materials and methods:</b> We conducted clinial and radilogical investigation of the family and performed NGS based Gene Panel sequencing comprising of five hundred and forty five candidate genes to characterize it at genetic level. <b>Results:</b> We identified a novel homozygous c.181_183delGAC mutation in the <i>CLN3</i> gene seggregating witht the disorder in the family. The mutation induces in-frame deletion, deleting one amino acid (p.Asp61del) in CLN3 protein. The deleted amino acid aspartic acid plays an important role as general acid in enzymes active centers as well as in maintaining the ionic character of proteins. <b>Conclusion:</b> Our finding adds to genetic variability of Juvenile neuronal ceroid lipofuscinosis associated with <i>CLN3</i> gene and a predicted CLN3 protein interacting domain site.
DOI: 10.6084/m9.figshare.7867859.v1
title: A novel in-frame mutation in <i>CLN3</i> leads to Juvenile neuronal ceroid lipofuscinosis in a large Pakistani family

description: <b>Aim:</b> Neuronal ceroid lipofuscinosis (NCLs) are the most common neurodegenerative disorders, with global incidence of 1 in 100,000 live births. NCLs affect central nervous system, primarily cerebellar and cerebral cortices. Juvenile neuronal ceroid lipofuscinosis (JNCL), also known as Batten disease, is the most common form of NCLs. JNCL is primarily caused by pathogenic mutations in <i>CLN3</i> gene, which encodes a transporter transmembrane protein of uncertain function. The 1.02 kb deletion is the most common mutation in <i>CLN3</i> that results in frame shift and a premature termination leading to nonfunctional protein. Here, we invetigated a large consanguineous family consisting of four affected individuals with clincal symptoms suggestive of Juvenile neuronal ceroid lipofuscinosis. <b>Materials and methods:</b> We conducted clinial and radilogical investigation of the family and performed NGS based Gene Panel sequencing comprising of five hundred and forty five candidate genes to characterize it at genetic level. <b>Results:</b> We identified a novel homozygous c.181_183delGAC mutation in the <i>CLN3</i> gene seggregating witht the disorder in the family. The mutation induces in-frame deletion, deleting one amino acid (p.Asp61del) in CLN3 protein. The deleted amino acid aspartic acid plays an important role as general acid in enzymes active centers as well as in maintaining the ionic character of proteins. <b>Conclusion:</b> Our finding adds to genetic variability of Juvenile neuronal ceroid lipofuscinosis associated with <i>CLN3</i> gene and a predicted CLN3 protein interacting domain site.
DOI: 10.6084/m9.figshare.12586447
title: Additional file 1 of Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome

description: Additional file 1: Table S1. Clinical parameters of the 58 subjects. N = uninfected group, P = infected group, PE = pre-eradicated group, E = eradicated group.
DOI: 10.6084/m9.figshare.12586447.v1
title: Additional file 1 of Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome

description: Additional file 1: Table S1. Clinical parameters of the 58 subjects. N = uninfected group, P = infected group, PE = pre-eradicated group, E = eradicated group.
DOI: 10.6084/m9.figshare.12586450
title: Additional file 2 of Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome

description: Additional file 2: Table S2. Barcodes of all samples subjected to multiplex sequencing. N = uninfected group, P = infected group, E = eradicated group.
DOI: 10.6084/m9.figshare.12586450.v1
title: Additional file 2 of Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome

description: Additional file 2: Table S2. Barcodes of all samples subjected to multiplex sequencing. N = uninfected group, P = infected group, E = eradicated group.
DOI: 10.6084/m9.figshare.12586453
title: Additional file 3 of Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome

description: Additional file 3: Table S3. Sequences and modified OTUs of all saliva samples from sequencing at 97% identity. N = uninfected group, P = infected group, E = eradicated group.
DOI: 10.6084/m9.figshare.12586453.v1
title: Additional file 3 of Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome

description: Additional file 3: Table S3. Sequences and modified OTUs of all saliva samples from sequencing at 97% identity. N = uninfected group, P = infected group, E = eradicated group.
DOI: 10.6084/m9.figshare.6294998
title: Optimal Designs for Multi-Response Nonlinear Regression Models With Several Factors via Semidefinite Programming

description: We use semidefinite programming (SDP) to find a variety of optimal designs for multi-response linear models with multiple factors, and for the first time, extend the methodology to find optimal designs for multi-response nonlinear models and generalized linear models with multiple factors. We construct transformations that (i) facilitate improved formulation of the optimal design problems into SDP problems, (ii) enable us to extend SDP methodology to find optimal designs from linear models to nonlinear multi-response models with multiple factors and (iii) correct erroneously reported optimal designs in the literature caused by formulation issues. We also derive invariance properties of optimal designs and their dependence on the covariance matrix of the correlated errors, which are helpful for reducing the computation time for finding optimal designs. Our applications include finding A-, A<sub><i>s</i></sub>-, c-, and D-optimal designs for multi-response multi-factor polynomial models, locally c- and D-optimal designs for a bivariate Emax response model and for a bivariate Probit model useful in the biosciences.
DOI: 10.6084/m9.figshare.12586459
title: Additional file 5 of Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome

description: Additional file 5: Table S4. Modified OTU table at 97% identity. N = uninfected group, P = infected group, E = eradicated group.
DOI: 10.6084/m9.figshare.12586459.v1
title: Additional file 5 of Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome

description: Additional file 5: Table S4. Modified OTU table at 97% identity. N = uninfected group, P = infected group, E = eradicated group.
DOI: 10.6084/m9.figshare.7867916
title: Overexpression of lncRNA GAS5 suppresses prostatic epithelial cell proliferation by regulating COX-2 in chronic non-bacterial prostatitis

description: Chronic non-bacterial prostatitis (CNP) is a common urologic disease that is linked to the development of prostate cancer. Long non-coding RNA (lncRNA) GAS5 has been identified to mediate cell proliferation in prostate cancer, although its role in CNP is still unclear. Human prostate epithelial cell line RWPE-1 was induced by lipopolysaccharide (LPS) to mimic CNP model <i>in vitro</i>. Real-time PCR was performed to determine the expression of GAS5 and COX-2, while western blotting was used to evaluate the protein expression of COX-2. The interaction between GAS5 and COX-2 was determined using RNA pull-down and RNA immunoprecipitation (RIP). Cell proliferation was determined using MTT assay. The expression of GAS5 was decreased, while COX-2 was increased in prostatitis tissues and in LPS-induced RWPE-1 cells. The overexpression of GAS5 suppressed the protein level of COX-2, and inhibited cell proliferation of LPS-induced RWPE-1 cells and HPECs, which was rescued by the co-transfection with pcDNA-GAS5 and pcDNA-COX-2. GAS5 was confirmed to promote the ubiquitination of COX-2, and the <i>in vivo</i> GAS5-overexpressed CNP rat model decreased the motor scores, the volume of prostate tissues, the average number of inflammatory cells, prostatic proliferation, and COX-2 expression. Our findings revealed that overexpression of GAS5 inhibited cell proliferation via negatively regulating the expression of COX-2, thus alleviating the progression of CNP.
DOI: 10.6084/m9.figshare.7867916.v2
title: Overexpression of lncRNA GAS5 suppresses prostatic epithelial cell proliferation by regulating COX-2 in chronic non-bacterial prostatitis

description: Chronic non-bacterial prostatitis (CNP) is a common urologic disease that is linked to the development of prostate cancer. Long non-coding RNA (lncRNA) GAS5 has been identified to mediate cell proliferation in prostate cancer, although its role in CNP is still unclear. Human prostate epithelial cell line RWPE-1 was induced by lipopolysaccharide (LPS) to mimic CNP model <i>in vitro</i>. Real-time PCR was performed to determine the expression of GAS5 and COX-2, while western blotting was used to evaluate the protein expression of COX-2. The interaction between GAS5 and COX-2 was determined using RNA pull-down and RNA immunoprecipitation (RIP). Cell proliferation was determined using MTT assay. The expression of GAS5 was decreased, while COX-2 was increased in prostatitis tissues and in LPS-induced RWPE-1 cells. The overexpression of GAS5 suppressed the protein level of COX-2, and inhibited cell proliferation of LPS-induced RWPE-1 cells and HPECs, which was rescued by the co-transfection with pcDNA-GAS5 and pcDNA-COX-2. GAS5 was confirmed to promote the ubiquitination of COX-2, and the <i>in vivo</i> GAS5-overexpressed CNP rat model decreased the motor scores, the volume of prostate tissues, the average number of inflammatory cells, prostatic proliferation, and COX-2 expression. Our findings revealed that overexpression of GAS5 inhibited cell proliferation via negatively regulating the expression of COX-2, thus alleviating the progression of CNP.