cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.23719/1529362
title: Evaluating structure-based activity in a high-throughput assay for steroid biosynthesis

description: Dataset from Foster, M.J., et al., Evaluating structure-based activity in a high-throughput assay for steroid biosynthesis, Computational Toxicology, Vol 24, No. 100245, Nov 2022, DOI https://doi.org/10.1016/j.comtox.2022.100245

The work described herein was conducted in R software (version 4.0.2) and is available at GitHub (https://github.com/USEPA/CompTox-HTH295R-SAR) and the US EPA Clowder repository as well as in Supplemental File 1 as an html file including code and resultant output.
DOI: 10.5066/p92izpid
title: Whole Rock Geochemistry and Uranium Lead Isotopic Data from the Dinwiddie Terrane, Virginia, USA

description: This data release includes whole rock geochemical data, and uranium-lead isotopic data collected by both Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) and Sensitive High Resolution Ion Microprobe-Reverse Geometry (SHRIMP-RG) methods. Whole rock geochemistry was collected by Activation Laboratories in Ancaster, Ontario. LA-ICP-MS data was collected at the PLASMA at the USGS in Denver, Colorado. SHRIMP-RG data was collected at the USGS-Stanford SHRIMP-RG in Palo Alto, California. Rock samples for all methods were collected by Mark Carter of the USGS. The whole rock geochemistry and uranium lead isotopic data constrain the age and origin of rocks in the newly defined Dinwiddie Terrane of eastern Virginia.
DOI: 10.5066/p9g4a2e3
title: Hawai&amp;amp;lsquo;i Island ??pe?ape?a (Hawaiian hoary bat; Lasiurus semotus) mist netting effort, capture, and tag retention, 2018&amp;amp;ndash;2021

description: ‘?pe‘ape‘a (Hawaiian hoary bats; Lasiurus semotus) were surveyed at 23 sites on Hawai?i Island from 33 to 2,341 m elevation from May 2018 to August 2021. Of the 23 sites, 8 were established as fixed survey sites for sampling at repeated intervals from January 2019 through January 2021. We surveyed each fixed site at least once per four-month period (January–April, May–August, September–December), with a survey comprising one to three netting events. Additional opportunistic surveys were conducted at alternate sites or on alternate dates. We captured 138 unique bats (37 female, 101 male) and recaptured 10 bats over 224 mist-netting events. Of the total 148 captured bats we affixed 131 with radio transmitters and attempted to relocate 127 (38 female; 89 male; 120 adult; 7 juvenile) bats in trees or forest stands used for day roosts on subsequent days of tracking. Of 91 bats (32 female; 59 male) relocated, males retained transmitters longer than females with a mean low estimate of 9 ± 6 days for males and 6 ± 4 days for females (time from capture to the last day a signal was confirmed). This data release consists of three tabular datasets: (1) Hawai?i Island ??pe?ape?a mist netting effort, 2018–2021, (2) Hawai‘i Island ??pe?ape?a captures, 2018–2021, and (3) Hawai?i Island ??pe?ape?a transmitter retention, 2018-2021.
DOI: 10.6084/m9.figshare.24078474
title: EMNPD Download Data

description: Data is also available at https://bddg.hznu.edu.cn/emnpd/download/
DOI: 10.6084/m9.figshare.24078474.v1
title: EMNPD Download Data

description: Data is also available at https://bddg.hznu.edu.cn/emnpd/download/
DOI: 10.5281/zenodo.8227862
title: multi-table-corpus

description: table pretraining corpus
DOI: 10.5281/zenodo.8227861
title: multi-table-corpus

description: table pretraining corpus
DOI: 10.21227/qt26-yp32
title: Pokemon-Zero-Neg

description: To thoroughly investigate the non-overlapping registration problem, we created our own datasets: Pokemon-Zero for zero overlap and Pokemon-Neg for negative overlap. In this section, we describe the process of dataset creation. First, we obtained five Pokemon models: “Charizard”, “Bulbasaur”, “Mew”, “Nidoking”, and “Pikachu”. Using FPS (Farthest Point Sampling) , we sampled each model to obtain 4096 points. Next, we randomly split each downsampled model into two non-overlapping parts and sampled 1024 points from each part to construct sparse point clouds, increasing the difficulty of registration. Finally, we randomly rotated and translated one of the parts to create the source point cloud and ground truth transformation matrix. Since both the second and third steps involve randomness, theoretically, our training set is infinitely large. To remove randomness during testing, we randomly generated 450 pairs of point clouds using this method and stored them as the test set.
DOI: 10.15151/esrf-es-1300235907
title: Structural Biology in Marseille

description: The BAG groups 11 teams from 6 Marseille laboratories. It has lately been reorganized, with 2 PIs changing affiliation, and 2 laboratories revisiting internal organisation, but mutual understanding amongst all PIs provides a solid base for efficient organization of the BAG. Research revolves around infection, health and biotechnology. For the next beam time allocation period we could make efficient use of 10 MX and 2 SAXS shifts. This amount of beam time reflects what we had asked for in previous rounds. 3 teams combine structural biology with medicinal chemistry and beam time at MASSIF for large ligand-screening campaigns will mostly suit their purpose. Access to beamlines with tuneable energy will be instrumental for projects requiring experimental phasing. One team uses exclusively Bio-SAXS and allocation of one shift/session would be welcomed. Remote access for MX sessions has become very popular whereas scientists prefer to be on-site for Bio-SAXS experiments.
DOI: 10.6084/m9.figshare.24077859
title: Chukar variants

description: This vcf file contains the SNP and Indel information of six chukar subspecies (pubescens, potanini, pallida, falki, pallescens, and domestic) .
DOI: 10.6084/m9.figshare.24077859.v1
title: Chukar variants

description: This vcf file contains the SNP and Indel information of six chukar subspecies (pubescens, potanini, pallida, falki, pallescens, and domestic) .
DOI: 10.6084/m9.figshare.24078519.v1
title: Graph of exposure light and concentration of Centella asiatica extract.xlsx

description: <b>Abstract</b><i>Background:</i> Insomnia is difficulty initiating or maintaining sleep for at least three nights a week or more and lasting for at least 3 months. One of the molecules that play a role in the circadian rhythm of arousal system is <i>hypocretin/orexin</i>. Orexin activates the p38-MAPK signaling pathway and increases phosphorylated ERK1/2 levels. <i>Centella asiatica</i> (CA) has a role in the signal work of the MAPK/ERK, Akt, and p38 path in many various diseases.<i>Methods:</i> The research method used is true laboratory experimental. The research approach used was randomized control group post-test only. Zebrafish embryos aged 0-7 dpf were used in this study. The treatment group consisted of 5 groups: normal, insomnia, insomnia + 2.5 μg/mL CA, insomnia + 5 μg/mL CA, and insomnia + 10 μg/mL CA. The locomotor motion of zebrafish larvae was observed using Basler cameras on days five-, six- and seven-day post fertilization (dpf), then analyzed by using Western Blot method.<i>Results:</i> The results proved that exposure to CA extract was able to reduce the expression of orexin (91963 ± 9129) and p38 (117425 ± 6398) as an arousal trigger in the sleep-wake cycle, with the most optimal concentration of CA 5 μg/mL. Exposure to CA extract was also able to reduce the expression of ERK (94795 ± 30830) and Akt (60113.5 ± 27833.5) with an optimum concentration of CA 2.5 μg/mL.<i>Conclusion:</i> Exposure to CA extract was able to improve the sleep activity of zebrafish larvae insomnia model by extending the total inactivity time (<i>cumulative duration</i>) and shortening the duration of first sleep (<i>latency to first</i>) in light and dark phases through inhibition of orexin, ERK, p38, and Akt.
DOI: 10.5281/zenodo.8312565
title: data (simulation)

description: The supporting information files are named "resultanddata(2).xlsx" and "fundamentionresult.xlsx". The file "resultanddata(2)" contains both experimental and simulation results. On the other hand, the file "fundamentionresult" comprises simulation results related to fundamental diagrams on stairs in the section titled "Findings from the comparison with study [35]".
DOI: 10.5281/zenodo.8312564
title: data (simulation)

description: The supporting information files are named "resultanddata(2).xlsx" and "fundamentionresult.xlsx". The file "resultanddata(2)" contains both experimental and simulation results. On the other hand, the file "fundamentionresult" comprises simulation results related to fundamental diagrams on stairs in the section titled "Findings from the comparison with study [35]".
DOI: 10.5517/ccdc.csd.cc2bb5jd
title: CCDC 2154733: Experimental Crystal Structure Determination

description: Related Article: Weerapat Foytong, Supak Pattaweepaiboon, Narongpol Kaewchangwat, Khomson Suttisintong, Weekit Sirisaksoontorn|2023|Supramol.Chem.|34|46|doi:10.1080/10610278.2023.2221365
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.24078519
title: data supporting research results Effect of <i>Centella asiatica</i> ethanol extract on zebrafish larvae (<i>Danio rerio</i>) insomnia model through inhibition of Orexin, ERK, Akt and p38

description: <b>Abstract</b><i>Background:</i> Insomnia is difficulty initiating or maintaining sleep for at least three nights a week or more and lasting for at least 3 months. One of the molecules that play a role in the circadian rhythm of arousal system is <i>hypocretin/orexin</i>. Orexin activates the p38-MAPK signaling pathway and increases phosphorylated ERK1/2 levels. <i>Centella asiatica</i> (CA) has a role in the signal work of the MAPK/ERK, Akt, and p38 path in many various diseases.<i>Methods:</i> The research method used is true laboratory experimental. The research approach used was randomized control group post-test only. Zebrafish embryos aged 0-7 dpf were used in this study. The treatment group consisted of 5 groups: normal, insomnia, insomnia + 2.5 μg/mL CA, insomnia + 5 μg/mL CA, and insomnia + 10 μg/mL CA. The locomotor motion of zebrafish larvae was observed using Basler cameras on days five-, six- and seven-day post fertilization (dpf), then analyzed by using Western Blot method.<i>Results:</i> The results proved that exposure to CA extract was able to reduce the expression of orexin (91963 ± 9129) and p38 (117425 ± 6398) as an arousal trigger in the sleep-wake cycle, with the most optimal concentration of CA 5 μg/mL. Exposure to CA extract was also able to reduce the expression of ERK (94795 ± 30830) and Akt (60113.5 ± 27833.5) with an optimum concentration of CA 2.5 μg/mL.<i>Conclusion:</i> Exposure to CA extract was able to improve the sleep activity of zebrafish larvae insomnia model by extending the total inactivity time (<i>cumulative duration</i>) and shortening the duration of first sleep (<i>latency to first</i>) in light and dark phases through inhibition of orexin, ERK, p38, and Akt.
DOI: 10.6084/m9.figshare.24078519.v2
title: Graph of exposure light and concentration of Centella asiatica extract.xlsx

description: <b>Abstract</b><i>Background:</i> Insomnia is difficulty initiating or maintaining sleep for at least three nights a week or more and lasting for at least 3 months. One of the molecules that play a role in the circadian rhythm of arousal system is <i>hypocretin/orexin</i>. Orexin activates the p38-MAPK signaling pathway and increases phosphorylated ERK1/2 levels. <i>Centella asiatica</i> (CA) has a role in the signal work of the MAPK/ERK, Akt, and p38 path in many various diseases.<i>Methods:</i> The research method used is true laboratory experimental. The research approach used was randomized control group post-test only. Zebrafish embryos aged 0-7 dpf were used in this study. The treatment group consisted of 5 groups: normal, insomnia, insomnia + 2.5 μg/mL CA, insomnia + 5 μg/mL CA, and insomnia + 10 μg/mL CA. The locomotor motion of zebrafish larvae was observed using Basler cameras on days five-, six- and seven-day post fertilization (dpf), then analyzed by using Western Blot method.<i>Results:</i> The results proved that exposure to CA extract was able to reduce the expression of orexin (91963 ± 9129) and p38 (117425 ± 6398) as an arousal trigger in the sleep-wake cycle, with the most optimal concentration of CA 5 μg/mL. Exposure to CA extract was also able to reduce the expression of ERK (94795 ± 30830) and Akt (60113.5 ± 27833.5) with an optimum concentration of CA 2.5 μg/mL.<i>Conclusion:</i> Exposure to CA extract was able to improve the sleep activity of zebrafish larvae insomnia model by extending the total inactivity time (<i>cumulative duration</i>) and shortening the duration of first sleep (<i>latency to first</i>) in light and dark phases through inhibition of orexin, ERK, p38, and Akt.
DOI: 10.6084/m9.figshare.24078519.v3
title: data supporting research results Effect of <i>Centella asiatica</i> ethanol extract on zebrafish larvae (<i>Danio rerio</i>) insomnia model through inhibition of Orexin, ERK, Akt and p38

description: <b>Abstract</b><i>Background:</i> Insomnia is difficulty initiating or maintaining sleep for at least three nights a week or more and lasting for at least 3 months. One of the molecules that play a role in the circadian rhythm of arousal system is <i>hypocretin/orexin</i>. Orexin activates the p38-MAPK signaling pathway and increases phosphorylated ERK1/2 levels. <i>Centella asiatica</i> (CA) has a role in the signal work of the MAPK/ERK, Akt, and p38 path in many various diseases.<i>Methods:</i> The research method used is true laboratory experimental. The research approach used was randomized control group post-test only. Zebrafish embryos aged 0-7 dpf were used in this study. The treatment group consisted of 5 groups: normal, insomnia, insomnia + 2.5 μg/mL CA, insomnia + 5 μg/mL CA, and insomnia + 10 μg/mL CA. The locomotor motion of zebrafish larvae was observed using Basler cameras on days five-, six- and seven-day post fertilization (dpf), then analyzed by using Western Blot method.<i>Results:</i> The results proved that exposure to CA extract was able to reduce the expression of orexin (91963 ± 9129) and p38 (117425 ± 6398) as an arousal trigger in the sleep-wake cycle, with the most optimal concentration of CA 5 μg/mL. Exposure to CA extract was also able to reduce the expression of ERK (94795 ± 30830) and Akt (60113.5 ± 27833.5) with an optimum concentration of CA 2.5 μg/mL.<i>Conclusion:</i> Exposure to CA extract was able to improve the sleep activity of zebrafish larvae insomnia model by extending the total inactivity time (<i>cumulative duration</i>) and shortening the duration of first sleep (<i>latency to first</i>) in light and dark phases through inhibition of orexin, ERK, p38, and Akt.
DOI: 10.25345/c5nv99n0p
title: MassIVE MSV000092811 - Site-specific glycoproteomic modifications are associated with cognitive decline in older adults with type 2 diabetes
title: Type 2 diabetes (T2D) is a metabolic disorder associated with cognitive decline and an increased risk of dementia. The molecular mechanisms linking T2D to cognitive decline remain unclear. Here, we investigated site-specific glycoproteomic modifications as potential contributors to cognitive decline in older adults with T2D. We analyzed protein glycosylation and glycation using mass spectrometry-based glycoproteomics in serum samples from initially cognitively normal T2D patients, eight of whom declined cognitively over a period of 36 months and 15 of whom maintained normal cognition over time. Our results reveal quantitative changes in glycopeptiforms--i.e. specific glycan compositions on amino acid sites of proteins--associated with cognitive decline in T2D. These findings suggest that aberrant protein glycosylation may play a role in the development of cognitive impairment in T2D. Our study provides valuable insights into the molecular mechanisms underlying cognitive decline in T2D and highlights the potential of glycoproteomic modifications as biomarkers for early identification of cognitive decline in T2D patients. Further research is warranted to elucidate the functional implications of these glycoproteomic changes and their role in T2D-related cognitive decline.
DOI: 10.6084/m9.figshare.13726375
title: Benchmark datasets

description: 20 benchmark datasets for DeepEukFinder. The name of each file"a_b_c_d_e_test.fasta"a: number of prokaryotesb: number of prokaryotic-virusesc: number of plasmidsd: number of eukaryotese: number of eukaryotic-viruses
DOI: 10.6084/m9.figshare.13726375.v2
title: Benchmark datasets

description: 20 benchmark datasets for DeepEukFinder. The name of each file"a_b_c_d_e_test.fasta"a: number of prokaryotesb: number of prokaryotic-virusesc: number of plasmidsd: number of eukaryotese: number of eukaryotic-viruses
DOI: 10.6084/m9.figshare.13726375.v1
title: test-data.zip

description: 20 test datasets for DeepEukFinder. The name of each file"a_b_c_d_e_test.fasta"<br>a: number of prokaryotes b: number of prokaryotic-virusesc: number of plasmids d: number of eukaryotese: number of eukaryotic-viruses
DOI: 10.6084/m9.figshare.14576193.v1
title: Test Data and Script for DeepEukFinder

description: batch_predict_def.sh: script to get results from the test files, usage: (after environment is set to have DeepEukFinder in PATH) bash batch_predict_def.sh. <br>test-data.zip: 20 test datasets for DeepEukFinder. The name of each file"a_b_c_d_e_test.fasta"<br>a: number of prokaryotesb: number of prokaryotic-virusesc: number of plasmidsd: number of eukaryotese: number of eukaryotic-viruses<br>
DOI: 10.6084/m9.figshare.14576193.v2
title: Benchmark datasets and Script for DeepEukFinder

description: batch_predict_def.sh: script to get results from the test files, usage: (after environment is set to have DeepEukFinder in PATH) bash batch_predict_def.sh.test-data.zip: 20 benchmark datasets for DeepEukFinder. The name of each file"a_b_c_d_e_test.fasta"a: number of prokaryotesb: number of prokaryotic-virusesc: number of plasmidsd: number of eukaryotese: number of eukaryotic-viruses<br><br>
DOI: 10.6084/m9.figshare.14576193
title: Benchmark datasets for DeepMicroClass

description: Usage: DeepMicroClass predict [-h] --input INPUT --output_dir OUTPUT_DIR [--model MODEL] [--encoding {onehot,embedding}] [--mode {hybrid,single}] [--single-len SINGLE_LEN] [--device {cpu,cuda}]Benchmark_datasets.zip: 20 benchmark datasets for DeepMicroClass. Prokaryote:PROK ProkaryoteVirus: PROKVIR Plasmid: PLSMD Eukaryote:EUK EukaryoteVirus: EUKVIREach row of the output prediction file contains the scores from the neural network for class label assignment. The higher the score, the more likely the class label for a given sequence.<br>
DOI: 10.6084/m9.figshare.14576193.v3
title: Benchmark datasets and Script for DeepMicroClass

description: batch_predict_def.sh: script to get results from the test files, usage: (after environment is set to have DeepEukFinder in PATH) bash batch_predict_def.sh.test-data.zip: 20 benchmark datasets for DeepEukFinder. The name of each file"a_b_c_d_e_test.fasta"a: number of prokaryotesb: number of prokaryotic-virusesc: number of plasmidsd: number of eukaryotese: number of eukaryotic-viruses<br><br>
DOI: 10.18434/mds2-2387
title: Suspect List of Possible Per- and Polyfluoroalkyl Substances (PFAS)
DOI: 10.6073/pasta/3760eec82562e0a8b7cd493c0a3e3ef4
title: Settlement Trees, Northern Michigan Level 0

description: We provide a Level 0 record of trees from 43 counties Michigan's Upper Peninsual and the northern one-third of Michigan's Lower Peninsula from Public Land Surveys conducted by surveyors from the General Land Office of the United States in the 1800s. Posts were set every half mile in townships that were typically 6 miles by 6 miles square. Surveyors recorded details about the one to four trees closest (but typically recorded information for the two closest trees) to the posts and included information about the tree name (taxonomic specificity ranged by surveyor), tree diameter (inches), and distance and bearing from the post. Our records include the tree information and the location of the posts from which the tree information came from. These Level 0 tree data were aggregated to the 8km grid resolution Level 1 product (see msb-paleon.26 package). That product was then statistically smoothed using a statistical model that accounts for zero-inflated continuous data with smoothing based on generalized additive modeling techniques and approximate Bayesian uncertainty estimates for the Level 2 products estimating aboveground biomass (msb-paleon.23), density (msb-paleon.24), and basal area (msb-paleon.25). The data processing steps and associated code are available in the GitHub repository: https://github.com/PalEON-Project/PLS_products. These products are used in the manucript, Paciorek et al., 2020, Statistically-estimated tree biomass, stem, and basal area for the upper Midwestern United States at the time of Euro-American settlement (https://www.biorxiv.org/content/10.1101/856526v1). This material is based upon work supported by the National Science Foundation under grants #DEB-1241874, 1241868, 1241870, 1241851, 1241891, 1241846, 1241856, 1241930.
DOI: 10.6073/pasta/409ec6dfb218b6a3e98022916d2b4438
title: Settlement Trees, Southeastern Michigan Level 0

description: We provide a Level 0 record of trees for 27 townships in the southeastern area of Michigan's Lower Peninsula, south of the Detroit River transcribed from Public Land Surveys conducted by surveyors from the General Land Office of the United States in the 1800s. Posts were set every half mile in townships that were typically 6 miles by 6 miles square. Surveyors recorded details about the two closest trees to the posts and included information about the tree name (taxonomic specificity ranged by surveyor), tree diameter (inches), and distance and bearing from the post. Our records include the tree information and the location of the posts from which the tree information came from. These Level 0 tree data were aggregated to the 8km grid resolution Level 1 product (see msb-paleon.26 package). That product was then statistically smoothed using a statistical model that accounts for zero-inflated continuous data with smoothing based on generalized additive modeling techniques and approximate Bayesian uncertainty estimates for the Level 2 products estimating aboveground biomass (msb-paleon.23), density (msb-paleon.24), and basal area (msb-paleon.25). The data processing steps and associated code are available in the GitHub repository: https://github.com/PalEON-Project/PLS_products. These products are used in the manucript, Paciorek et al., 2020, Statistically-estimated tree biomass, stem, and basal area for the upper Midwestern United States at the time of Euro-American settlement (https://www.biorxiv.org/content/10.1101/856526v1). This material is based upon work supported by the National Science Foundation under grants #DEB-1241874, 1241868, 1241870, 1241851, 1241891, 1241846, 1241856, 1241930.