cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10840577
title: Data for "Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition"

description: Data for "Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition".

neutron_data.zip --> neutron data in .nxspe form. S(Q,E) calculated using the DAVE software. Includes logbook spreadsheet. 

Training_Data.xyz --> xyz file containing training data used to generate Allegro machine learning forcefield in the paper

nh3_pimd.deploy --> Trained Allegro model to that can be used in LAMMPS and RXMD software a ML forcefield 

POSCAR_UNIT_CELL_AMMONIA --> NH3 unit cell in solid phase in POSCAR format that can be read by the VASP software used to perform the DFT simmulations.
DOI: 10.3886/e186841
title: A retrospective 10 year survival analysis of 1340 Her-2 low positive breast cancer patients

description: A retrospective 10 year survival analysis of 1340 Her-2 low positive breast cancer patients
DOI: 10.3886/e186841v1-147206
title: A retrospective 10 year survival analysis of 1340 Her-2 low positive breast cancer patients

description: A retrospective 10 year survival analysis of 1340 Her-2 low positive breast cancer patients
DOI: 10.6084/m9.figshare.25466356
title: CHM for anxiety disorders - dataset

description: This is the dataset of the article "Chinese Herbal Medicine for Anxiety Disorders and Obsessive-Compulsive Disorder: A Systematic Review with Meta-Analysis"
DOI: 10.6084/m9.figshare.25466308
title: 2024, UVA EV Workshop, EV Flow Cytometry

description: This workshop’s protocols were developed based on the published protocols in: Cook S, Tang VA, Lannigan J, Jones JC, Welsh JA. <b><i>Quantitative flow cytometry enables end-to-end optimization of cross-platform extracellular vesicle studies.</i></b> Cell Rep Methods. 2023 Dec 18;3(12):100664. doi: 10.1016/j.crmeth.2023.100664.
DOI: 10.25345/c5125qm7j
title: MassIVE MSV000094390 - Activity-dependent synthesis of Emerin gates neuronal plasticity via proteostasis regulatio
title: Neurons dynamically regulate their proteome in response to sensory input, a key process underlying experience-dependent structural and functional plasticity. Here, we characterized the visual experience-dependent nascent proteome within a brief, defined time window using an optimized metabolic labeling approach. Visual experience induces cell type-specific and age-dependent alterations in the nascent proteome and recruits proteostasis-related processes. We identified Emerin as the top activity-induced candidate plasticity protein and demonstrated that its activity-induced synthesis is transcription-independent. In contrast to its well-studied nuclear localization and function in myocytes, activity-induced neuronal Emerin is abundant in the ER and broadly inhibits protein synthesis, including synaptic proteins. Downregulating Emerin increases synaptic density, however, it shifts dendritic spines from predominantly mushroom morphology to filopodia, leading to decreased network connectivity, visual responses and visual information processing. Our findings support a visual experience-dependent feed-forward role for Emerin in gating neuronal plasticity through negative regulation of translation.
DOI: 10.6084/m9.figshare.25466362
title: Data From: Light and Dark Fur Cats - Total Body Scores

description: Limited data exists within the forensic veterinary medicine discipline about the differences between the decomposition of animals with fur. Due to the sheer number of animals used as animal models and the number of animals that exist, determining the stages of decomposition that is applicable for all species is difficult. Typically, assessing what stage of decomposition a decedent is in is subjective due to the visual assessment of decompositional changes. A method developed to rectify this issue was the total body score (TBS) method, which assigns a numerical value based of the degree of decomposition to the head, torso, and limbs. The purpose of this study was to examine the decomposition of cats, identify any unique decomposition characteristics, and determine the rate of decomposition using total body score and accumulated degree days (ADD). Twelve domestic short haired cats were placed in a grassy field in West Lafayette, IN. An assessment of TBS was documented for each cat and each experimental group. An exponential relationship between TBS and ADD was documented. Overall, there was not a significant difference in the rate of decomposition or total body scores between the groups (Z = -91.00, p = 0.0672).
DOI: 10.5517/ccdc.csd.cc2fx8wj
title: CSD 2261508: Experimental Crystal Structure Determination

description: Related Article: Juhe Liu, Yuwei Chen, Mengran Sun, Wenhao Liu, Xianghe Meng, Jiyong Yao|2024|Cryst.Growth Des.|24|2343|doi:10.1021/acs.cgd.3c01122
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.18112/openneuro.ds004995.v1.0.1
title: The Time-Course of Food Representation in the Human Brain
DOI: 10.5281/zenodo.10864674
title: lippia_alba_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.10864675
title: lippia_alba_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.10864680
title: zingiber_zerumbet_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.10864681
title: zingiber_zerumbet_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.10530385
title: Training and test data for antibody humanness evaluation

description: ### Training and test data for humanness evaluation

This data was collected in conjunction with and used fortraining and testing for Parkinson / Wang et al 2024. Thedata is organized as follows:

- Heavy chain training and multispecies test data (under the heavy chain folder)    - The conslidated cAb rep file contains training human sequences    - The test sample sequences folder contains fasta files with test sequences for each species- Light chain training and multispecies test data (under the light chain folder)    - The conslidated cAb rep file contains training human sequences    - The test sample sequences folder contains fasta files with test sequences for each species- Abybank data (under the abybank compiled data folder)    - This folder contains separate folders for heavy and light chain    - Each subfolder contains test data for a more diverse species set under fasta files for each species- Humanization test data (under the humanization test data folder)    - The sequences in the parental.fa file were originally humanized as part of drug discovery programs    - The experimental.fa file contains the humanization results- IMGT and ADA data (under the imgt test data folder)    - The imgt mab db fa and tsv files contain sequences and species assignments for IMGT mAb DB    - The thera ada fa file contains sequences evaluated in the clinic    - The Therapeutic ADA txt file contains anti drug antibody results for those antibodies

The data was retrieved from the following sources.

1. All heavy and light chain training data is from the cAb-Rep database from [Guo et al.](https://pubmed.ncbi.nlm.nih.gov/31649674/)2. All testing data is from the Observed Antibody Space [(OAS) database](https://opig.stats.ox.ac.uk/webapps/oas/)

The training and test data show is after filtering for quality. The testing data was additionally randomly sampled to yield a set of 50,000 sequences for each species, then filtered to remove duplicates. The human test data was checked to ensure no overlap with the human training set.

The IMGT, ADA and humanization test data was retrieved from Prihoda et al. andthe associated [Github repo](https://github.com/Merck/BioPhi-2021-publication).

See Parkinson et al. 2024 and the associated github repos for more details on how models other thanSAM / AntPack were evaluated on this data.
DOI: 10.5281/zenodo.10819061
title: Training and test data for antibody humanness evaluation

description: ### Training and test data for humanness evaluation

This data was collected in conjunction with and used fortraining and testing for Parkinson / Wang et al 2024. Thedata is organized as follows:

- Heavy chain training and multispecies test data (under the heavy chain folder)    - The conslidated cAb rep file contains training human sequences    - The test sample sequences folder contains fasta files with test sequences for each species- Light chain training and multispecies test data (under the light chain folder)    - The conslidated cAb rep file contains training human sequences    - The test sample sequences folder contains fasta files with test sequences for each species- Abybank data (under the abybank compiled data folder)    - This folder contains separate folders for heavy and light chain    - Each subfolder contains test data for a more diverse species set under fasta files for each species- Humanization test data (under the humanization test data folder)    - The sequences in the parental.fa file were originally humanized as part of drug discovery programs    - The experimental.fa file contains the humanization results- IMGT and ADA data (under the imgt test data folder)    - The imgt mab db fa and tsv files contain sequences and species assignments for IMGT mAb DB    - The thera ada fa file contains sequences evaluated in the clinic    - The Therapeutic ADA txt file contains anti drug antibody results for those antibodies- VDJ statistics (under the vdj_statistics_eval folder)

The data was retrieved from the following sources.

1. All heavy and light chain training data is from the cAb-Rep database from [Guo et al.](https://pubmed.ncbi.nlm.nih.gov/31649674/)2. All testing data is from the Observed Antibody Space [(OAS) database](https://opig.stats.ox.ac.uk/webapps/oas/)

The training and test data show is after filtering for quality. The testing data was additionally randomly sampled to yield a set of 50,000 sequences for each species, then filtered to remove duplicates. The human test data was checked to ensure no overlap with the human training set.

The IMGT, ADA and humanization test data was retrieved from Prihoda et al. andthe associated [Github repo](https://github.com/Merck/BioPhi-2021-publication).

See Parkinson et al. 2024 and the associated github repos for more details on how models other thanSAM / AntPack were evaluated on this data.
DOI: 10.5281/zenodo.10864595
title: Training and test data for antibody humanness evaluation

description: ### Training and test data for humanness evaluation

This data was collected in conjunction with and used fortraining and testing for Parkinson / Wang et al 2024. Thedata is organized as follows:

- Heavy chain training and multispecies test data (under the heavy chain folder)    - The conslidated cAb rep file contains training human sequences    - The test sample sequences folder contains fasta files with test sequences for each species- Light chain training and multispecies test data (under the light chain folder)    - The conslidated cAb rep file contains training human sequences    - The test sample sequences folder contains fasta files with test sequences for each species- Abybank data (under the abybank compiled data folder)    - This folder contains separate folders for heavy and light chain    - Each subfolder contains test data for a more diverse species set under fasta files for each species- Humanization test data (under the humanization test data folder)    - The sequences in the parental.fa file were originally humanized as part of drug discovery programs    - The experimental.fa file contains the humanization results- IMGT and ADA data (under the imgt test data folder)    - The imgt mab db fa and tsv files contain sequences and species assignments for IMGT mAb DB    - The thera ada fa file contains sequences evaluated in the clinic    - The Therapeutic ADA txt file contains anti drug antibody results for those antibodies- VDJ statistics (under the vdj_statistics_eval folder)

The data was retrieved from the following sources.

1. All heavy and light chain training data is from the cAb-Rep database from [Guo et al.](https://pubmed.ncbi.nlm.nih.gov/31649674/)2. All testing data is from the Observed Antibody Space [(OAS) database](https://opig.stats.ox.ac.uk/webapps/oas/)

The training and test data show is after filtering for quality. The testing data was additionally randomly sampled to yield a set of 50,000 sequences for each species, then filtered to remove duplicates. The human test data was checked to ensure no overlap with the human training set.

The IMGT, ADA and humanization test data was retrieved from Prihoda et al. andthe associated [Github repo](https://github.com/Merck/BioPhi-2021-publication).

See Parkinson et al. 2024 and the associated github repos for more details on how models other thanSAM / AntPack were evaluated on this data.
DOI: 10.5281/zenodo.10530384
title: Training and test data for antibody humanness evaluation

description: ### Training and test data for humanness evaluation

This data was collected in conjunction with and used fortraining and testing for Parkinson / Wang et al 2024. Thedata is organized as follows:

- Heavy chain training and multispecies test data (under the heavy chain folder)    - The conslidated cAb rep file contains training human sequences    - The test sample sequences folder contains fasta files with test sequences for each species- Light chain training and multispecies test data (under the light chain folder)    - The conslidated cAb rep file contains training human sequences    - The test sample sequences folder contains fasta files with test sequences for each species- Abybank data (under the abybank compiled data folder)    - This folder contains separate folders for heavy and light chain    - Each subfolder contains test data for a more diverse species set under fasta files for each species- Humanization test data (under the humanization test data folder)    - The sequences in the parental.fa file were originally humanized as part of drug discovery programs    - The experimental.fa file contains the humanization results- IMGT and ADA data (under the imgt test data folder)    - The imgt mab db fa and tsv files contain sequences and species assignments for IMGT mAb DB    - The thera ada fa file contains sequences evaluated in the clinic    - The Therapeutic ADA txt file contains anti drug antibody results for those antibodies- VDJ statistics (under the vdj_statistics_eval folder)

The data was retrieved from the following sources.

1. All heavy and light chain training data is from the cAb-Rep database from [Guo et al.](https://pubmed.ncbi.nlm.nih.gov/31649674/)2. All testing data is from the Observed Antibody Space [(OAS) database](https://opig.stats.ox.ac.uk/webapps/oas/)

The training and test data show is after filtering for quality. The testing data was additionally randomly sampled to yield a set of 50,000 sequences for each species, then filtered to remove duplicates. The human test data was checked to ensure no overlap with the human training set.

The IMGT, ADA and humanization test data was retrieved from Prihoda et al. andthe associated [Github repo](https://github.com/Merck/BioPhi-2021-publication).

See Parkinson et al. 2024 and the associated github repos for more details on how models other thanSAM / AntPack were evaluated on this data.
DOI: 10.5281/zenodo.10562968
title: Training and test data for antibody humanness evaluation

description: ### Training and test data for humanness evaluation

This data was collected in conjunction with and used fortraining and testing for Parkinson / Wang et al 2024. Thedata is organized as follows:

- Heavy chain training and multispecies test data (under the heavy chain folder)    - The conslidated cAb rep file contains training human sequences    - The test sample sequences folder contains fasta files with test sequences for each species- Light chain training and multispecies test data (under the light chain folder)    - The conslidated cAb rep file contains training human sequences    - The test sample sequences folder contains fasta files with test sequences for each species- Abybank data (under the abybank compiled data folder)    - This folder contains separate folders for heavy and light chain    - Each subfolder contains test data for a more diverse species set under fasta files for each species- Humanization test data (under the humanization test data folder)    - The sequences in the parental.fa file were originally humanized as part of drug discovery programs    - The experimental.fa file contains the humanization results- IMGT and ADA data (under the imgt test data folder)    - The imgt mab db fa and tsv files contain sequences and species assignments for IMGT mAb DB    - The thera ada fa file contains sequences evaluated in the clinic    - The Therapeutic ADA txt file contains anti drug antibody results for those antibodies

The data was retrieved from the following sources.

1. All heavy and light chain training data is from the cAb-Rep database from [Guo et al.](https://pubmed.ncbi.nlm.nih.gov/31649674/)2. All testing data is from the Observed Antibody Space [(OAS) database](https://opig.stats.ox.ac.uk/webapps/oas/)

The training and test data show is after filtering for quality. The testing data was additionally randomly sampled to yield a set of 50,000 sequences for each species, then filtered to remove duplicates. The human test data was checked to ensure no overlap with the human training set.

The IMGT, ADA and humanization test data was retrieved from Prihoda et al. andthe associated [Github repo](https://github.com/Merck/BioPhi-2021-publication).

See Parkinson et al. 2024 and the associated github repos for more details on how models other thanSAM / AntPack were evaluated on this data.
DOI: 10.5281/zenodo.10864692
title: teaching portfolio

description: This file contains coding data from the study titled "Using a teaching portfolio as a professional development tool for Turkish early childhood teachers "
DOI: 10.5281/zenodo.10864693
title: teaching portfolio

description: This file contains coding data from the study titled "Using a teaching portfolio as a professional development tool for Turkish early childhood teachers "
DOI: 10.5517/ccdc.csd.cc2h2k8f
title: CCDC 2296364: Experimental Crystal Structure Determination

description: Related Article: Han-Qing Li, Jia-Yin Xu, Shan-Shan Wu, Liang Jin|2024|ACS Omega|9|11925|doi:10.1021/acsomega.3c09696
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: 10.5517/ccdc.csd.cc2h2n08
title: CCDC 2296449: Experimental Crystal Structure Determination

description: Related Article: Han-Qing Li, Jia-Yin Xu, Shan-Shan Wu, Liang Jin|2024|ACS Omega|9|11925|doi:10.1021/acsomega.3c09696
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: 10.5517/ccdc.csd.cc2h2n19
title: CCDC 2296450: Experimental Crystal Structure Determination

description: Related Article: Han-Qing Li, Jia-Yin Xu, Shan-Shan Wu, Liang Jin|2024|ACS Omega|9|11925|doi:10.1021/acsomega.3c09696
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: 10.5517/ccdc.csd.cc2h8rbw
title: CCDC 2302318: Experimental Crystal Structure Determination

description: Related Article: Mahendra Godi, Hyukmin Kwon, Sangwook Park, Sunwoo Park, Hayoon Lee, Kiho Lee, Jongwook Park|2024|RSC Advances|14|8135|doi:10.1039/D3RA07937F
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: 10.5517/ccdc.csd.cc2hk1ch
title: CCDC 2310286: Experimental Crystal Structure Determination

description: Related Article: Bo Yang, Suqiong Yan, Yuan Zhang, Shirong Ban, Hui Ma, Fanda Feng, Wei Huang|2024|J.Am.Chem.Soc.|146|7668|doi:10.1021/jacs.3c14262
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: 10.5517/ccdc.csd.cc2hk1dj
title: CCDC 2310287: Experimental Crystal Structure Determination

description: Related Article: Bo Yang, Suqiong Yan, Yuan Zhang, Shirong Ban, Hui Ma, Fanda Feng, Wei Huang|2024|J.Am.Chem.Soc.|146|7668|doi:10.1021/jacs.3c14262
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: 10.5517/ccdc.csd.cc2hk1fk
title: CCDC 2310288: Experimental Crystal Structure Determination

description: Related Article: Bo Yang, Suqiong Yan, Yuan Zhang, Shirong Ban, Hui Ma, Fanda Feng, Wei Huang|2024|J.Am.Chem.Soc.|146|7668|doi:10.1021/jacs.3c14262
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: 10.5517/ccdc.csd.cc2hk1gl
title: CCDC 2310289: Experimental Crystal Structure Determination

description: Related Article: Bo Yang, Suqiong Yan, Yuan Zhang, Shirong Ban, Hui Ma, Fanda Feng, Wei Huang|2024|J.Am.Chem.Soc.|146|7668|doi:10.1021/jacs.3c14262
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.