cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12062040
title: Additional file 6 of Dafachronic acid and temperature regulate canonical dauer pathways during Nippostrongylus brasiliensis infectious larvae activation

description: Additional file 6: Data S6.Nippostrongylus brasiliensis StringTie-predicted EdgeR-normalized transcript counts.
DOI: 10.6084/m9.figshare.21499233
title: Enrichment of GO and KEGG of gene faimlies with expansion of Megalurothrips usitatus

description:  <em>Megalurothrips usitatus</em>, with small size, high concealment, and strong fertility, is a staple pest of cowpea, causing dramatic economic losses. Despite its huge damage, genetic studies of this species remain limited. To better understand genetics evolution and the eventual development of novel management options, an availability of genome will help to illustrate and achieve. Here, we generated a chromosome-level genome of the thrips using a combination strategy of PacBio and Hi-C technologies.
DOI: 10.6084/m9.figshare.12062040.v1
title: Additional file 6 of Dafachronic acid and temperature regulate canonical dauer pathways during Nippostrongylus brasiliensis infectious larvae activation

description: Additional file 6: Data S6.Nippostrongylus brasiliensis StringTie-predicted EdgeR-normalized transcript counts.
DOI: 10.6084/m9.figshare.12062043
title: Additional file 7 of Dafachronic acid and temperature regulate canonical dauer pathways during Nippostrongylus brasiliensis infectious larvae activation

description: Additional file 7: Data S7.Nippostrongylus brasiliensis EdgeR differentially expressed transcripts.
DOI: 10.6084/m9.figshare.12062043.v1
title: Additional file 7 of Dafachronic acid and temperature regulate canonical dauer pathways during Nippostrongylus brasiliensis infectious larvae activation

description: Additional file 7: Data S7.Nippostrongylus brasiliensis EdgeR differentially expressed transcripts.
DOI: 10.6084/m9.figshare.21499248
title: Enrichment of GO and KEGG of gene family with contraction of Megalurothrips usitatus

description:  <em>Megalurothrips usitatus</em>, with small size, high concealment, and strong fertility, is a staple pest of cowpea, causing dramatic economic losses. Despite its huge damage, genetic studies of this species remain limited. To better understand genetics evolution and the eventual development of novel management options, an availability of genome will help to illustrate and achieve. Here, we generated a chromosome-level genome of the thrips using a combination strategy of PacBio and Hi-C technologies. The genome assembled 238.14 Mb with scaffold N50 of 13.85 Mb, and the final genome was anchored into 16 pseudo-chromosomes.
DOI: 10.6084/m9.figshare.12586370
title: Additional file 10 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 10: Table S7. The primers used for quantitative real-time PCR
DOI: 10.6084/m9.figshare.12586370.v1
title: Additional file 10 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 10: Table S7. The primers used for quantitative real-time PCR
DOI: 10.6084/m9.figshare.23596426
title: Spatio-Temporal Analysis and Prediction of Mass Telecommunication Base Station Failure Events

description: Large-scale telecommunication systems are lifeline infrastructure in modern society. A telecommunication system typically consists of a huge number of base stations with diverse geographical locations across a country, which highly complicates maintenance operations. To allocate maintenance resource properly, it is important to have a good understanding on the failure pattern of these base stations. Statistical inference of recurrent failures of these base stations is challenging because of the large number of base stations and the spatial correlation of their failure processes. Based on eight-month failure data of telecommunication base stations in Harbin, China, we propose a customized nonhomogeneous Poisson process (NHPP) model for recurrent failure data from telecommunication systems. The model consists of two layers, where the temporal layer applies an NHPP with station-specific frailty for failures of each base station, and the spatial layer uses a multivariate lognormal distribution to characterize the correlation among the frailties. The Monte Carlo EM (MCEM) algorithm is applied to estimate parameters included in the proposed model. We demonstrate the proposed model using the Harbin telecommunication system example with 7725 base stations and 4615 failure records.
DOI: 10.6084/m9.figshare.23596426.v1
title: Spatio-Temporal Analysis and Prediction of Mass Telecommunication Base Station Failure Events

description: Large-scale telecommunication systems are lifeline infrastructure in modern society. A telecommunication system typically consists of a huge number of base stations with diverse geographical locations across a country, which highly complicates maintenance operations. To allocate maintenance resource properly, it is important to have a good understanding on the failure pattern of these base stations. Statistical inference of recurrent failures of these base stations is challenging because of the large number of base stations and the spatial correlation of their failure processes. Based on eight-month failure data of telecommunication base stations in Harbin, China, we propose a customized nonhomogeneous Poisson process (NHPP) model for recurrent failure data from telecommunication systems. The model consists of two layers, where the temporal layer applies an NHPP with station-specific frailty for failures of each base station, and the spatial layer uses a multivariate lognormal distribution to characterize the correlation among the frailties. The Monte Carlo EM (MCEM) algorithm is applied to estimate parameters included in the proposed model. We demonstrate the proposed model using the Harbin telecommunication system example with 7725 base stations and 4615 failure records.
DOI: 10.6084/m9.figshare.12586382
title: Additional file 4 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 4: Table S1. Summary of sequencing reads in fifteen libraries
DOI: 10.6084/m9.figshare.12586382.v1
title: Additional file 4 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 4: Table S1. Summary of sequencing reads in fifteen libraries
DOI: 10.6084/m9.figshare.12586388
title: Additional file 5 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 5: Table S2. The statistical analysis of assembled 16,038 novel transcripts
DOI: 10.6084/m9.figshare.12586388.v1
title: Additional file 5 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 5: Table S2. The statistical analysis of assembled 16,038 novel transcripts
DOI: 10.6084/m9.figshare.12586391
title: Additional file 6 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 6: Table S3. The normalized FPKM values for all lncRNAs and mRNAs in all samples
DOI: 10.6084/m9.figshare.12586391.v1
title: Additional file 6 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 6: Table S3. The normalized FPKM values for all lncRNAs and mRNAs in all samples
DOI: 10.6084/m9.figshare.19926429
title: Carboplatin-loaded surface modified-PLGA nanoparticles confer sustained inhibitory effect against retinoblastoma cell in vitro

description: ABSTRACT Purpose: To investigate the antiproliferative effect of carboplatin-loaded surface-modified poly(lactide-co-glycolide) on retinoblastoma cells. Methods: Carboplatin-loaded poly(lactide-co-glycolide) with or without sodium alginate surface modification was prepared using sodium alginate-poly(lactide-co-glycolide) and poly(lactide-co-glycolide). The zeta potential and carboplatin release behavior were investigated. The cellular uptake of the released drug was observed in the retinoblastoma cell line Y79. The inhibitory effect of carboplatin-loaded nanoparticles against the Y79 cell line was evaluated using methyl thiazolyl tetrazolium assay and western blot. Native carboplatin and void nanoparticles without carboplatin loading were used as controls. Results: The zeta potential was -(26.1 ± 3.1) mV for carboplatin-loaded poly(lactide-co-glycolide) and-(43.1 ± 8.1) mV for carboplatin-loaded sodium alginate-poly(lactide-co-glycolide). The burst release percentages of carboplatin-loaded poly(lactide-co-glycolide) and sodium alginate-poly(lactide-co-glycolide) were (40.0% ± 8.2%) and (18.9% ± 4.3%) at 24 hours, respectively. A significant difference was identified regarding drug release between carboplatin-loaded sodium alginate-poly(lactide-co-glycolide) and carboplatin-loaded poly(lactide-co-glycolide). Fluorescence detection revealed that intense uptake of carboplatin into the cytoplasm of the Y79 cell line that was exposed to carboplatin-loaded sodium alginate-poly(lactide-co-glycolide). Carboplatin-loaded poly(lactide-co-glycolide) or sodium alginate-poly(lactide-co-glycolide) exposure inhibited proliferating cell nuclear antigen expression in Y79 cells on day 3. Extension of exposure to day 5 revealed that the sodium alginate-poly(lactide-co-glycolide) surface modification was superior to that of poly(lactide-co-glycolide) in terms of proliferating cell nuclear antigen inhibition. The cell viability test using methyl thiazolyl tetrazolium revealed a similar inhibitory effect. Furthermore, the carboplatin-loaded nanoparticles of lower concentration inhibited cell viability more strongly than native carboplatin of higher concentration in methyl thiazolyl tetrazolium assay. Conclusions: Carboplatin-loaded sodium alginate-poly(lactide-co-glycolide) inhibited retinoblastoma cell proliferation with superior effect as compared with poly(lactide-co-glycolide) and native carboplatin. Sodium alginate surface modification offers a potential strategy for the sustained carboplatin release system.
DOI: 10.6084/m9.figshare.19926429.v1
title: Carboplatin-loaded surface modified-PLGA nanoparticles confer sustained inhibitory effect against retinoblastoma cell in vitro

description: ABSTRACT Purpose: To investigate the antiproliferative effect of carboplatin-loaded surface-modified poly(lactide-co-glycolide) on retinoblastoma cells. Methods: Carboplatin-loaded poly(lactide-co-glycolide) with or without sodium alginate surface modification was prepared using sodium alginate-poly(lactide-co-glycolide) and poly(lactide-co-glycolide). The zeta potential and carboplatin release behavior were investigated. The cellular uptake of the released drug was observed in the retinoblastoma cell line Y79. The inhibitory effect of carboplatin-loaded nanoparticles against the Y79 cell line was evaluated using methyl thiazolyl tetrazolium assay and western blot. Native carboplatin and void nanoparticles without carboplatin loading were used as controls. Results: The zeta potential was -(26.1 ± 3.1) mV for carboplatin-loaded poly(lactide-co-glycolide) and-(43.1 ± 8.1) mV for carboplatin-loaded sodium alginate-poly(lactide-co-glycolide). The burst release percentages of carboplatin-loaded poly(lactide-co-glycolide) and sodium alginate-poly(lactide-co-glycolide) were (40.0% ± 8.2%) and (18.9% ± 4.3%) at 24 hours, respectively. A significant difference was identified regarding drug release between carboplatin-loaded sodium alginate-poly(lactide-co-glycolide) and carboplatin-loaded poly(lactide-co-glycolide). Fluorescence detection revealed that intense uptake of carboplatin into the cytoplasm of the Y79 cell line that was exposed to carboplatin-loaded sodium alginate-poly(lactide-co-glycolide). Carboplatin-loaded poly(lactide-co-glycolide) or sodium alginate-poly(lactide-co-glycolide) exposure inhibited proliferating cell nuclear antigen expression in Y79 cells on day 3. Extension of exposure to day 5 revealed that the sodium alginate-poly(lactide-co-glycolide) surface modification was superior to that of poly(lactide-co-glycolide) in terms of proliferating cell nuclear antigen inhibition. The cell viability test using methyl thiazolyl tetrazolium revealed a similar inhibitory effect. Furthermore, the carboplatin-loaded nanoparticles of lower concentration inhibited cell viability more strongly than native carboplatin of higher concentration in methyl thiazolyl tetrazolium assay. Conclusions: Carboplatin-loaded sodium alginate-poly(lactide-co-glycolide) inhibited retinoblastoma cell proliferation with superior effect as compared with poly(lactide-co-glycolide) and native carboplatin. Sodium alginate surface modification offers a potential strategy for the sustained carboplatin release system.
DOI: 10.6084/m9.figshare.12586397
title: Additional file 7 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 7: Table S4. The regulatory relationship types of lncRNA-mRNA pairs
DOI: 10.6084/m9.figshare.12586397.v1
title: Additional file 7 of Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

description: Additional files 7: Table S4. The regulatory relationship types of lncRNA-mRNA pairs
DOI: 10.25625/v7htb8
title: Generalisation Tagger CV Models

description: These models were downloaded from https://gitlab.gwdg.de/tillmann.doenicke/thesis/-/tree/v1.0/deep_learning/models/cv. Version 1.0 contains the multi-class and the binary model. Version 2.0 contains only the multi-class model (that should be used for binary tagging as well).
DOI: 10.6084/m9.figshare.12062097
title: Additional file 5 of Detrimental effects of excessive fatty acid secretion on female sperm storage in chickens

description: Additional file 5: Table S3. Metabolome profile of the UVJ tissue.
DOI: 10.6084/m9.figshare.12062106
title: Additional file 6 of Detrimental effects of excessive fatty acid secretion on female sperm storage in chickens

description: Additional file 6: Table S4. Pathway analysis of differentially expressed metabolites.
DOI: 10.6084/m9.figshare.12062082.v1
title: Additional file 2 of Detrimental effects of excessive fatty acid secretion on female sperm storage in chickens

description: Additional file 2: Table S1. Descriptive statistics of duration of fertility and hatching egg production (HEP) in the two test periods.
DOI: 10.6084/m9.figshare.12062082
title: Additional file 2 of Detrimental effects of excessive fatty acid secretion on female sperm storage in chickens

description: Additional file 2: Table S1. Descriptive statistics of duration of fertility and hatching egg production (HEP) in the two test periods.
DOI: 10.6084/m9.figshare.12062097.v1
title: Additional file 5 of Detrimental effects of excessive fatty acid secretion on female sperm storage in chickens

description: Additional file 5: Table S3. Metabolome profile of the UVJ tissue.
DOI: 10.6084/m9.figshare.12062091
title: Additional file 4 of Detrimental effects of excessive fatty acid secretion on female sperm storage in chickens

description: Additional file 4: Table S2. Physiological parameters and duration of fertility of hens that used for metabolomics study.
DOI: 10.6084/m9.figshare.12062106.v1
title: Additional file 6 of Detrimental effects of excessive fatty acid secretion on female sperm storage in chickens

description: Additional file 6: Table S4. Pathway analysis of differentially expressed metabolites.
DOI: 10.6084/m9.figshare.12062091.v1
title: Additional file 4 of Detrimental effects of excessive fatty acid secretion on female sperm storage in chickens

description: Additional file 4: Table S2. Physiological parameters and duration of fertility of hens that used for metabolomics study.
DOI: 10.5281/zenodo.10617801
title: Dynamics of Antibiotic resistance genes in Plasmids and Bacteriophages

description: Supplementary data for review article 'Dynamics of Antibiotic Resistance Genes in Plasmids and Bacteriophages'
DOI: 10.5281/zenodo.10617802
title: Dynamics of Antibiotic resistance genes in Plasmids and Bacteriophages

description: Supplementary data for review article 'Dynamics of Antibiotic Resistance Genes in Plasmids and Bacteriophages'
DOI: 10.5281/zenodo.10572179
title: Data used in manuscript CO2 uptake of urban vegetation in a warming Nordic city

description: Model runs used in manuscript "CO2 uptake of urban vegetation in a warming Nordic city". This data set includes spatial model runs for the Surface Urban Energy and Water balance Scheme (SUEWS) for two scenarios in Helsinki, Finland.



For 2014-2019 using MEPS:



Input_met includes the input files needed to run SUEWS for 6 years, with 2014 used as a spinup period.



For the 2050s with the RCP8.5 scenario:



Input_rcp includes the input files needed to run SUEWS for 1 year, with initial conditions the same as for Input_met year 2015.




The additional data files are:

SourceCode Fortran source code version used in the manuscript.

Runcontrol.nmlSUEWS_V2020b
DOI: 10.5281/zenodo.10572180
title: Data used in manuscript CO2 uptake of urban vegetation in a warming Nordic city

description: Model runs used in manuscript "CO2 uptake of urban vegetation in a warming Nordic city". This data set includes spatial model runs for the Surface Urban Energy and Water balance Scheme (SUEWS) for two scenarios in Helsinki, Finland.



For 2014-2019 using MEPS:



Input_met includes the input files needed to run SUEWS for 6 years, with 2014 used as a spinup period.



For the 2050s with the RCP8.5 scenario:



Input_rcp includes the input files needed to run SUEWS for 1 year, with initial conditions the same as for Input_met year 2015.




The additional data files are:

SourceCode Fortran source code version used in the manuscript.

Runcontrol.nmlSUEWS_V2020b
DOI: 10.5281/zenodo.10020545
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.10551521
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