cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24248734.v1
title: Supplementary Material for: Pregnancy outcomes in females with eosinophilic esophagitis – a nationwide population-based study

description: Background and Aims: Eosinophilic esophagitis (EoE) is a chronic, allergic inflammatory disease of the esophagus. It has a peak incidence in the 2nd and 3rd decades of life. Despite this, little is known about pregnancy outcomes in patients with EoE. Methods: Using a validated histopathologic and nationwide population-based cohort for the diagnosis of EoE, we examined maternal and fetal outcomes, with preterm birth as the primary outcome, in females with EoE compared to matched controls. Odds ratios (OR) were calculated using logistic regression. Results: Between 1992 and 2016 we identified 19 females with EoE who gave birth to 23 children (reference births: n=115). There was 1 (4.3%) preterm birth in the EoE cohort vs. 8 (7.0%) in the reference cohort (OR = 0.60; 95%CI = 0.07-5.14). Secondary fetal outcomes included stillbirth, neonatal death, small for gestational age, low birth weight (LBW) and low Apgar score. Of these, LBW (&lt;2500g) in patients with EoE compared to controls correlated to an OR of 12.42 (95%CI = 1.26-122.42), however this finding was based on very low numbers. The remaining fetal outcomes were not significantly different between females with EoE and controls. Secondary pregnancy and maternal outcomes including induction of labor, instrumental delivery, gestational diabetes, or pre-eclampsia were not significantly different between patients with EoE and controls. Conclusion: Overall in this nationwide cohort study, we did not find increased association of preterm birth in patients with EoE.
DOI: 10.6084/m9.figshare.24241693
title: Automatic Identification of Illegal Construction and Demolition Waste Landfills: A Computer Vision Approach

description: This link contains the raw data, which includes 35 environmental reports for construction and demolition waste landfills, data information for 231 landfills, and 360 raw images of construction and demolition waste landfills used for the experiments and the corresponding labels.
DOI: 10.6084/m9.figshare.24241693.v1
title: Automatic Identification of Illegal Construction and Demolition Waste Landfills: A Computer Vision Approach

description: This link contains the raw data, which includes 35 environmental reports for construction and demolition waste landfills, data information for 231 landfills, and 360 raw images of construction and demolition waste landfills used for the experiments and the corresponding labels.
DOI: 10.34820/fk2/ghjyx9/bn08ds
title: 25.finishing.jpg

description: sabut kelapa cup finishing
DOI: 10.34820/fk2/ghjyx9/dorx9m
title: 22.HasilAkhirPengamplasan.jpg

description: sabut kelapa cup dempul
DOI: 10.34820/fk2/ghjyx9
title: Sabut kelapa

description: File sabut kelapa
DOI: 10.5519/qd.svi4cd76
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (873 records)
DOI: 10.6084/m9.figshare.24248758
title: Supplementary Material for: Overexpression of VSNL1 enhances cell proliferation in colorectal carcinogenesis

description: Introduction: We have previously reported that overexpression of VSNL1 (Visinin-like protein 1) is frequently observed in advanced colorectal adenocarcinomas and correlates with poorer prognosis. In this study, we determined the levels of VSNL1 expression in the earlier stages of colorectal tumors including adenomas and adenocarcinomas, and attempted to clarify the functional significance of VSNL1 overexpression in colorectal carcinogenesis. Methods: Levels of VSNL expression in colorectal tumor tissues were analyzed using immunohistochemistry. The effects of VSNL1 downregulation and overexpression on cell proliferation, resistance to apoptosis and invasiveness were determined using two VSNL1-overexpressing colorectal cancer cell lines, CW-2 and HCT116 and VSNL1 inducibly expressing SNU-C5, respectively. Gene expression signatures in VSNL1-downregulated CW-2 and HCT116 were identified using transcriptome and gene set enrichment analyses. Results: VSNL1 expression was restricted to only a few crypt cells in the non-tumorous epithelium, whereas it became enhanced in adenomas and adenocarcinomas with the progression of tumorigenesis. Downregulation of VSNL1 in CW-2 and HCT116 cells suppressed their proliferation through induction of apoptosis. Conversely, overexpression of VSNL1 in SNU-C5 cells enhanced resistance to anoikis. Transcriptome and gene set enrichment analyses revealed that downregulation of VSNL1 altered the expression level of the apoptosis-related gene set in CW-2 and HCT116 cells. Conclusion: VSNL1 plays a role in both the development and progression of colorectal tumors by enhancing cell viability.
DOI: 10.6084/m9.figshare.24248758.v1
title: Supplementary Material for: Overexpression of VSNL1 enhances cell proliferation in colorectal carcinogenesis

description: Introduction: We have previously reported that overexpression of VSNL1 (Visinin-like protein 1) is frequently observed in advanced colorectal adenocarcinomas and correlates with poorer prognosis. In this study, we determined the levels of VSNL1 expression in the earlier stages of colorectal tumors including adenomas and adenocarcinomas, and attempted to clarify the functional significance of VSNL1 overexpression in colorectal carcinogenesis. Methods: Levels of VSNL expression in colorectal tumor tissues were analyzed using immunohistochemistry. The effects of VSNL1 downregulation and overexpression on cell proliferation, resistance to apoptosis and invasiveness were determined using two VSNL1-overexpressing colorectal cancer cell lines, CW-2 and HCT116 and VSNL1 inducibly expressing SNU-C5, respectively. Gene expression signatures in VSNL1-downregulated CW-2 and HCT116 were identified using transcriptome and gene set enrichment analyses. Results: VSNL1 expression was restricted to only a few crypt cells in the non-tumorous epithelium, whereas it became enhanced in adenomas and adenocarcinomas with the progression of tumorigenesis. Downregulation of VSNL1 in CW-2 and HCT116 cells suppressed their proliferation through induction of apoptosis. Conversely, overexpression of VSNL1 in SNU-C5 cells enhanced resistance to anoikis. Transcriptome and gene set enrichment analyses revealed that downregulation of VSNL1 altered the expression level of the apoptosis-related gene set in CW-2 and HCT116 cells. Conclusion: VSNL1 plays a role in both the development and progression of colorectal tumors by enhancing cell viability.
DOI: 10.25919/cqnt-x005
title: Parkes observations for project P1176 semester 2023APRS_09

description: Pulsars and their winds are among nature's most powerful particle accelerators, producing particles with energies up to a few PeVatrons. In addition to high-energy radiation from the magnetosphere, the rotational energy of a neutron star is carried away in the form of magnetized ultra-relativistic pulsar winds. Investigation of pulsar wind nebula (PWN) offers an excellent chance to determine the interaction details of relativistic flows with their surroundings that may never be possible in other classes of source. Our recent analyses of ASKAP observations of Galactic Plane uncovered previously known X-ray PWN CXOU J163802.6-471358 (nicknamed as Potoroo). Recently, we have successfully detected a pulsar candidate associated with Potoroo with Parkes telescope. It is detected at 3 GHz with a dispersion measure of DM = 1553 pc cm-3 and a rotation period of 65.74 ms. Here we propose timing observations for this pulsar with the Parkes Ultra-Wideband Low (UWL) receiver. Through pulsar timing, we will be able to obtain precise measurements of the pulsar position and proper motions, and the spin-down of the pulsar which enables us to independently estimate the age of the system. Long-term timing will also enable us to measure the parallax of the system and search for pulsation at high energies (i.e. X-ray and gamma-ray)
DOI: 10.5281/zenodo.7909638
title: rCRUX Generated MiFish Universal 12S Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: MiFish Universal<br> Gene: 12S<br> Length of Target: 163–185<br> get_seeds_local() minimum length: 170<br> get_seeds_local() maximum length: 250<br> blast_seeds() minimum length: 140<br> blast_seeds() maximum length: 250<br> max_to_blast: 1000<br> Forward Sequence (5'-3'): GTGTCGGTAAAACTCGTGCCAGC<br> Reverse Sequence (5'-3'): CATAGTGGGGTATCTAATCCCAGTTTG<br> Reference: Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., ... & Kondoh, M. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society open science, 2(7), 150088. https://doi.org/10.1098/rsos.150088 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7915855
title: rCRUX Generated 18s SSU3/SSU4 Metazoan Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: 18s SSU3/SSU4 Metazoan<br> Gene: 18S v7<br> Length of Target: 170<br> get_seeds_local() minimum length: 120<br> get_seeds_local() maximum length: 220<br> blast_seeds() minimum length: 98<br> blast_seeds() maximum length: 200<br> max_to_blast: 100<br> Forward Sequence (5'-3'): GGTCTGTGATGCCCTTAGATG<br> Reverse Sequence (5'-3'): GGTGTGTACAAAGGGCAGGG<br> Reference: McInnes, J. C., Alderman, R., Deagle, B. E., Lea, M. A., Raymond, B., & Jarman, S. N. (2017). Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates. Methods in Ecology and Evolution, 8(2), 192-202. http://dx.doi.org/10.1111/2041-210X.12677 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8322517
title: PetHIS

description: The data originates from the Laboratory of Veterinary Medicine of the State University of Maranhão as part of a research project conducted at a Federal Institute of Maranhão. The histopathological image database was created to train CNN models for pet cancer classification. The image database was created from 82 original images that were enlarged using data augmentation such as vertical flip, horizontal flip, and random crop(px(0.50)), totaling 592 histopathological images divided into benign and malignant.
description: Research project funded by Fundação de Amparo à Pesquisa e ao Desenvolvimento Científico e Tecnológico do Maranhão - FAPEMA.
DOI: 10.5281/zenodo.8322516
title: PetHIS

description: The data originates from the Laboratory of Veterinary Medicine of the State University of Maranhão as part of a research project conducted at a Federal Institute of Maranhão. The histopathological image database was created to train CNN models for pet cancer classification. The image database was created from 82 original images that were enlarged using data augmentation such as vertical flip, horizontal flip, and random crop(px(0.50)), totaling 592 histopathological images divided into benign and malignant.
description: Research project funded by Fundação de Amparo à Pesquisa e ao Desenvolvimento Científico e Tecnológico do Maranhão - FAPEMA.
DOI: 10.5281/zenodo.7909701
title: rCRUX Generated trnl plants Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: trnl plants<br> Gene: trnl<br> Length of Target: ~85<br> get_seeds_local() minimum length: 60<br> get_seeds_local() maximum length: 110<br> blast_seeds() minimum length: 23<br> blast_seeds() maximum length: 73<br> max_to_blast: 250<br> Forward Sequence (5'-3'): GGGCAATCCTGAGCCAA<br> Reverse Sequence (5'-3'): TTTGAGTCTCTGCACCTATC<br> Reference: Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., ... & Willerslev, E. (2007). Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research 3 (35),.(2007). https://doi.org/10.1093%2Fnar%2Fgkl938 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909698
title: rCRUX Generated Teleo Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: teleo L1848/H1913<br> Gene: 12S<br> Length of Target: 100<br> get_seeds_local() minimum length: 70<br> get_seeds_local() maximum length: 130<br> blast_seeds() minimum length: 40<br> blast_seeds() maximum length: 100<br> max_to_blast: 100<br> Forward Sequence (5'-3'): ACACCGCCCGTCACTCT<br> Reverse Sequence (5'-3'): CTTCCGGTACACTTACCATG<br> Reference: Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., ... & Gaboriaud, C. (2016). Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929-942. https://doi.org/10.1111/mec.13428 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909696
title: rCRUX Generated Taberlet c/h trnl Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Taberlet c/h trnl<br> Gene: trnl<br> Length of Target: 150<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 150<br> blast_seeds() minimum length: 85<br> blast_seeds() maximum length: 128<br> max_to_blast: 100<br> Forward Sequence (5'-3'): CGAAATCGGTAGACGCTACG<br> Reverse Sequence (5'-3'): CCATTGAGTCTCTGCACCTATC<br> Reference: Taberlet, P., Gielly, L., Pautou, G., & Bouvet, J. (1991). Universal primers for amplification of three non-coding regions of. Plant molecular biology, 17, 1105-1109. & Taberlet, Pierre, Eric Coissac, François Pompanon, Ludovic Gielly, Christian Miquel, Alice Valentini, Thierry Vermat, Gerard Corthier, Christian Brochmann, and Eske Willerslev. "Power and limitations of the chloroplast trn L (UAA) intron for plant DNA barcoding." Nucleic acids research 35, no. 3 (2007): e14-e14. We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909692
title: rCRUX Generated Baker Dlp1.5-H/Oordlp4 Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Scott Baker Dlp1.5-H/Oordlp4<br> Gene: D loop<br> Length of Target: 350-390<br> get_seeds_local() minimum length: 245<br> get_seeds_local() maximum length: 495<br> blast_seeds() minimum length: 205<br> blast_seeds() maximum length: 455<br> max_to_blast: 100<br> Forward Sequence (5'-3'): TCACCCAAAGCTGRARTTCTA<br> Reverse Sequence (5'-3'): GCGGGTTGCTGGTTTCACG<br> Reference: Baker, C. S., Steel, D., Nieukirk, S., & Klinck, H. (2018). Environmental DNA (eDNA) from the wake of the whales: Droplet digital PCR for detection and species identification. Frontiers in Marine Science, 5, 133. https://doi.org/10.3389/fmars.2018.00133 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8401469
title: UniFMIR: Pre-training a Foundation Model for Universal Fluorescence Microscopy Image Restoration

description: This repository contains the preprocessed dataset for [UniFMIR](https://github.com/cxm12/UNiFMIR/). All training and test data involved in the experiments are publicly available datasets. Licenses of the original dataset are applied. You can refer to the Github repository for details. * The 3D denoising/isotropic reconstruction/projection datasets can be downloaded from [Content Aware Image Restoration dataset](https://publications.mpi-cbg.de/publications-sites/7207/). `Projection_Flywing/train_data/my_training_data.npz` are generated according to the [CSBDeep](http://csbdeep.bioimagecomputing.com/doc/). * The SR dataset can be downloaded from [BioSR dataset](https://doi.org/10.6084/m9.figshare.13264793). The dataset is augmented according to the instructions in [DFCAN](https://github.com/qc17-THU/DL-SR/tree/main#train-a-new-model) and `my_training_data.npz` files are generated following [CSBDeep](http://csbdeep.bioimagecomputing.com/doc/datagen.html). * The Volumetric reconstruction dataset are from [VCD-LFM dataset](https://doi.org/10.5281/zenodo.4390067). The dataset is prepared according to the instructions in [VCD-Net](https://github.com/feilab-hust/VCD-Net). * DeepBacs dataset can be downloaded from [DeepBacs dataset](https://zenodo.org/record/6460867). We split the dataset into 5 folds for cross-validation. Shareloc dataset can be downloaded from [Shareloc dataset](https://zenodo.org/record/7234161). The data paths should be as follows: ``` VCD/vcdnet/ CSB/DataSet/ Denoising_Planaria/ Denoising_Tribolium/ Isotropic/Isotropic_Liver/ Projection_Flywing/ BioSR_WF_to_SIM/DL-SR-main/dataset/ Synthetic_tubulin_gfp/ Synthetic_tubulin_granules/ DeepBacs/ Shareloc/ ```
DOI: 10.5281/zenodo.8408449
title: Dataset for Peptide binder design with inverse folding and protein structure prediction

description: Dataset for a paper on peptide design <br> mutated_peptides - results for randomly intriduced mutations in protein-peptide complexes that can be predicted at 2 Å (Figure 1)<br> pdb_peptide - variation in the number of recycles (1-10) for 96 peptides (Figure 1)<br> minibinder - results for the minibinder set (Figure 2)<br> Pfam - results for the Pfam set (Figures 4+5)<br> protein_mpnn - results on protein_mpnn test set (Figure 6)
DOI: 10.5281/zenodo.8408448
title: Dataset for Peptide binder design with inverse folding and protein structure prediction

description: Dataset for a paper on peptide design <br> mutated_peptides - results for randomly intriduced mutations in protein-peptide complexes that can be predicted at 2 Å (Figure 1)<br> pdb_peptide - variation in the number of recycles (1-10) for 96 peptides (Figure 1)<br> minibinder - results for the minibinder set (Figure 2)<br> Pfam - results for the Pfam set (Figures 4+5)<br> protein_mpnn - results on protein_mpnn test set (Figure 6)
DOI: 10.5281/zenodo.7909664
title: rCRUX Generated MarVer3 Marine Mammal Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: MarVer3 Marine Mammal<br> Gene: 16S<br> Length of Target: 232-274<br> get_seeds_local() minimum length: 160<br> get_seeds_local() maximum length: 345<br> blast_seeds() minimum length: 124<br> blast_seeds() maximum length: 309<br> max_to_blast: 100<br> Forward Sequence (5'-3'): AGACGAGAAGACCCTRTG<br> Reverse Sequence (5'-3'): GGATTGCGCTGTTATCCC<br> Reference: Valsecchi, E., Bylemans, J., Goodman, S. J., Lombardi, R., Carr, I., Castellano, L., ... & Galli, P. (2020). Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates. Environmental DNA, 2(4), 460-476. https://doi.org/10.1002/edn3.72 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.6673185
title: Collider Datasets for Simplified Dark Matter models

description: This is a set of datasets containing MonoJet and DiJet interpolation grids. When using the simplified dark matter models in gambit, the backend "DMsimp_data" must be made first, which will download these datasets to the correct folder.
DOI: 10.5281/zenodo.6999436
title: Collider Datasets for Simplified Dark Matter models

description: This is a set of datasets containing MonoJet and DiJet interpolation grids. When using the simplified dark matter models in gambit, the backend "DMsimp_data" must be made first, which will download these datasets to the correct folder.
DOI: 10.5281/zenodo.6673184
title: Collider Datasets for Simplified Dark Matter models

description: This is a set of datasets containing MonoJet and DiJet interpolation grids. When using the simplified dark matter models in gambit, the backend "DMsimp_data" must be made first, which will download these datasets to the correct folder. If using monojet data outside of GAMBIT, please use the files in the DMsimp_monojet_data folder, which have been formatted with appropriate headings. Vector DM data is not included in this additional folder due to additional unitarity considerations required to use the data. If using this data, please cite this zenodo record, along with the gambit simplified model study (https://arxiv.org/abs/2209.13266).
DOI: 10.5281/zenodo.7614468
title: Collider Datasets for Simplified Dark Matter models

description: This is a set of datasets containing MonoJet and DiJet interpolation grids. When using the simplified dark matter models in gambit, the backend "DMsimp_data" must be made first, which will download these datasets to the correct folder.
DOI: 10.5281/zenodo.7619478
title: Collider Datasets for Simplified Dark Matter models

description: This is a set of datasets containing MonoJet and DiJet interpolation grids. When using the simplified dark matter models in gambit, the backend "DMsimp_data" must be made first, which will download these datasets to the correct folder.
DOI: 10.5281/zenodo.8409171
title: Collider Datasets for Simplified Dark Matter models

description: This is a set of datasets containing MonoJet and DiJet interpolation grids. When using the simplified dark matter models in gambit, the backend "DMsimp_data" must be made first, which will download these datasets to the correct folder. If using monojet data outside of GAMBIT, please use the files in the DMsimp_monojet_data folder, which have been formatted with appropriate headings. Vector DM data is not included in this additional folder due to additional unitarity considerations required to use the data. If using this data, please cite this zenodo record, along with the gambit simplified model study (https://arxiv.org/abs/2209.13266).