cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19113054.v1
title: Additional file 1 of Cyclic multiplex fluorescent immunohistochemistry and machine learning reveal distinct states of astrocytes and microglia in normal aging and Alzheimer’s disease

description: Additional File 1: Table S1. Demographic and neuropathological characteristics of study subjects. Description: Abbreviations: ADNC = AD neuropathological changes; APOE = Apolipoprotein E genotype; CAA = cerebral amyloid angiopathy; CVD = cerebrovascular disease; F = female; LBD = Lewy body disease; M = male; NA = Not available/applicable; NOS = not otherwise specified; NP Dx = neuropathological diagnosis. Table S2. Primary and secondary antibodies used in this study and sequence of immunohistochemistry cycles. Description: Note: GFAP and DAPI detection are needed in all the cycles to guarantee an adequate alignment of the images. Abbreviations: AF488 = AlexaFluor 488; Cy = cyanine; Dk = donkey; Gt = goat; Ms = mouse; Rb = rabbit. All secondary antibodies were purchased from Jackson ImmunoResearch Labs, West Grove, PA. Table S3. Results of mixed effects regression models. Description: Results of mixed effects regression models with diagnosis (CTRL vs. AD) or state (homeostatic vs. intermediate vs. reactive) as a fixed effect, respectively, and subject ID as random effect in both cases, are reported. Table S4. Model performance statistics for CTRL vs. AD binary classifiers. Description: Model performance statistics for the binary classification task of CTRL vs. AD for both the gradient boosting machine (GBM) and the convolutional neural network (CNN) machine learning models are reported. For all heuristics except for AUC and AUCPR (which are not threshold-dependent), the threshold was chosen by maximizing the accuracy. 95% confidence intervals were estimated by bootstrapping the hold-out test set across 500 iterations. Table S5. Results of Bayesian hyperparameter optimization. Description: The final hyperparameters determined by the Optuna hyperparameter tuning framework are reported. The Optuna optimizer maximized the out-of-sample area under the receiver operating characteristic (ROC) curve (AUC), which in turn was determined by 3-fold cross-validation for each trial.
DOI: 10.6084/m9.figshare.6530114
title: Additional file 6: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S5. Differentially expressed genes involved in protein kinases and transcription factors. (XLSX 225 kb)
DOI: 10.6084/m9.figshare.19113034
title: Additional file 3 of Identification and validation of serum autoantibodies in children with B-cell acute lymphoblastic leukemia by serological proteome analysis

description: Additional file 3. Raw data of mass spectrometry.
DOI: 10.6084/m9.figshare.6530267
title: Additional file 6: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: g:Pprofiler enrichment for the FTD IIHs. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.6530267.v1
title: Additional file 6: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: g:Pprofiler enrichment for the FTD IIHs. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.6530126
title: Additional file 13: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: List of PD network proteins responsible for the enrichment of the terms in Supplementary FileÂ 6. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.6530126.v1
title: Additional file 13: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: List of PD network proteins responsible for the enrichment of the terms in Supplementary FileÂ 6. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.6530135.v1
title: Additional file 7: of Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana

description: Table S6. Expression information of DEGs in Figs.Â 5 and 6. (XLSX 123 kb)
DOI: 10.6084/m9.figshare.6530177
title: Additional file 16: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: Functions of newly prioritized candidate genes. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6530177.v1
title: Additional file 16: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: Functions of newly prioritized candidate genes. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6530351.v1
title: Additional file 5: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table. Always-neighboring gene pairs with intrachromosomal colocalization. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6530333.v1
title: Additional file 15: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S9. Contians 268 serine and phosphatases enriched common genes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6530333
title: Additional file 15: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S9. Contians 268 serine and phosphatases enriched common genes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6530336
title: Additional file 1: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S1. Intrachromosomal colocalized gene pairs which were not linear neighbors. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.6530342.v1
title: Additional file 3: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S3. Evolutionary neighboring gene pairs without intrachromosomal colocalization. (XLSX 131 kb)
DOI: 10.6084/m9.figshare.6530336.v1
title: Additional file 1: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S1. Intrachromosomal colocalized gene pairs which were not linear neighbors. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.6530351
title: Additional file 5: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table. Always-neighboring gene pairs with intrachromosomal colocalization. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6530363
title: Additional file 7: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S6. Gene pairs with both always-neighboring and evolutionary neighboring colocalizations. (XLSX 118 kb)
DOI: 10.5517/ccp9xlg
title: CCDC 635146: Experimental Crystal Structure Determination

description: Related Article: Bo Liu, Xiu-Mei Li, Yun-Cheng Cui, Ming Feng|2007|Jiegou Huaxue|26|184|
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.cc2d7y9x
title: CCDC 2212169: Experimental Crystal Structure Determination

description: Related Article: Ya-Nan Dong, Zhi-Kun Liu, Jin-Peng Xue, Yun Li, Ke Sun, Zi-Shuo Yao, Jun Tao|2022|Inorg.Chem.|61|20232|doi:10.1021/acs.inorgchem.2c03626
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.cc2f2dtr
title: CCDC 2236644: Experimental Crystal Structure Determination

description: Related Article: Li Tang, Yuting Luo, Xiaoshuang Ma, Bin Wang, Mei Ding, Ru Wang, Pu Wang, Yong Pei, Shuxin Wang|2023|Angew.Chem.,Int.Ed.|62|e202300553|doi:10.1002/anie.202300553
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.6530342
title: Additional file 3: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S3. Evolutionary neighboring gene pairs without intrachromosomal colocalization. (XLSX 131 kb)
DOI: 10.6084/m9.figshare.6530369
title: Additional file 8: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S7. Gene pairs with all three kinds of colocalization. (XLSX 15 kb)
DOI: 10.5517/ccdc.csd.cc2f7hls
title: CCDC 2241535: Experimental Crystal Structure Determination

description: Related Article: Yan Li, Fei Gao, Juanjuan Xue, Guo-Ping Yang, Yao-Yu Wang|2023|Cryst.Growth Des.|23|3702|doi:10.1021/acs.cgd.3c00120
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.6530369.v1
title: Additional file 8: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S7. Gene pairs with all three kinds of colocalization. (XLSX 15 kb)
DOI: 10.5517/ccdc.csd.cc2fj1st
title: CCDC 2249756: Experimental Crystal Structure Determination

description: Related Article: W. Clegg, R.W. Harrington|2023|CSD Communication|||
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.cc2fj1vw
title: CCDC 2249758: Experimental Crystal Structure Determination

description: Related Article: W. Clegg|2023|CSD Communication|||
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.cc2g05rf
title: CCDC 2264294: Experimental Crystal Structure Determination

description: Related Article: Avazbek B. Ibragimov, Jamshid M. Ashurov, Bakhtiyar T. Ibragimov, Alisher G. Eshimbetov, Shaxnoz S. Аzimova, Zavkibek G. Tilyakov, Aziz F. Dusmatov|2023|J.Mol.Struct.|1292|136105|doi:10.1016/j.molstruc.2023.136105
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.cc2g752z
title: CCDC 2271000: Experimental Crystal Structure Determination

description: Related Article: Jing Du, Shi-Yi Zhao, Zhi-Chao Hu, Zhi-Bing Dong|2023|Asian J.Org.Chem|12|e202300499|doi:10.1002/ajoc.202300499
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.cc2g7bwy
title: CCDC 2271180: Experimental Crystal Structure Determination

description: Related Article: Vinod G. Landge, Ankita Mishra, Waruna Thotamune, Audrey L. Bonds, Indunil Alahakoon, Ajith Karunarathne, Michael C. Young|2023|Chem Cat.|3|100809|doi:10.1016/j.checat.2023.100809
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.6530357
title: Additional file 6: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S5. Evolutionary neighboring gene pairs with intrachromosomal colocalization. (XLSX 15 kb)
DOI: 10.5517/ccdc.csd.cc2fyx5h
title: CCDC 2263067: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.cc2h7xh5
title: CCDC 2301517: Experimental Crystal Structure Determination

description: Related Article: Abdur Rahim, Shuming Zhan, Biqiong Hong, Longhui Duan, Zhenhua Gu|2024|Org.Chem.Front.|11|1225|doi:10.1039/D3QO01846F
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.6530357.v1
title: Additional file 6: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S5. Evolutionary neighboring gene pairs with intrachromosomal colocalization. (XLSX 15 kb)
DOI: 10.5517/ccdc.csd.cc2fyx9m
title: CCDC 2263071: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.6530363.v1
title: Additional file 7: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S6. Gene pairs with both always-neighboring and evolutionary neighboring colocalizations. (XLSX 118 kb)
DOI: 10.5517/ccdc.csd.cc2fywy7
title: CCDC 2263060: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.cc2fyxcp
title: CCDC 2263073: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.cc2fywx6
title: CCDC 2263059: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.cc2fyx4g
title: CCDC 2263066: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.cc2fztfp
title: CCDC 2263943: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.cc2fztgq
title: CCDC 2263944: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.cc2fyx2d
title: CCDC 2263064: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.cc2fyx6j
title: CCDC 2263068: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.cc2fyxfr
title: CCDC 2263075: Experimental Crystal Structure Determination

description: Related Article: M. Woińska, A.A. Hoser, M.L. Chodkiewicz, K. Woźniak|2023|IUCrJ|11|45|doi:10.1107/S205225252300951X
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.cc2hg7y5
title: CCDC 2307607: Experimental Crystal Structure Determination

description: Related Article: Constantin G. Daniliuc, Patrick Liptau, Roland Fröhlich, Gerhard Erker|2023|CSD Communication|||
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.6530285.v1
title: Additional file 8: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: g:Pprofiler enrichment for the PD IIHs. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.6530258.v1
title: Additional file 5: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: g:Pprofiler enrichment for the entire network. (XLSX 172 kb)
DOI: 10.6084/m9.figshare.6530279.v1
title: Additional file 7: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: g:Pprofiler enrichment for the PS IIHs. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.6530285
title: Additional file 8: of Stratification of candidate genes for Parkinsonâ s disease using weighted protein-protein interaction network analysis

description: g:Pprofiler enrichment for the PD IIHs. (XLSX 25 kb)