cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5sq8qn1m
title: MassIVE MSV000089473 - A data-independent acquisition-based urinary extracellular vesicle phosphoproteomics system enables renal cell carcinoma grade differentiation
title: Early diagnosing and monitoring cancer through blood or urine tests have been a decades-long aim of medical diagnostics. However, translating our research capability and knowledge in cancer signaling into clinical settings has been slow and ineffective. Recently, extracellular Vesicles (EVs) have emerged as promising sources for developing disease phosphoprotein markers based on the knowledge that phosphorylation events are directly responsible for many signaling pathways at the cellular level. This study focused on optimizing and applying robust data-independent acquisition using mass spectrometry for urinary phosphoproteomic EVs profiling for renal cell cancer (RCC) grades differentiation. We compared several methods for DIA quantification, such as using the gas-phase fractionated (GPF) library, direct DIA, forbidden zones, and several different windowing schemes. After finding the optimized DIA mass spectrometry method, we applied the strategy to identify and quantify urinary EV phosphoproteome from 57 individuals representing four different urine samples from low-grade clear cell RCC, high-grade clear cell RCC, chronic kidney disease (CKD), and healthy control (HC) individuals. For these samples, we utilized the EVtrap capture method for EV enrichment and PolyMAC for phosphopeptides enrichment. After careful data analyses, we quantified 4,057 unique phosphosites. Several RNA-related pathways, such as RNA splicing, mRNA processing, and mRNA metabolic process, were significantly upregulated in CKD. Meanwhile, several prominent cancer-related pathways, such as ErbB signaling, renal cell carcinoma, and regulation of actin cytoskeleton, were only upregulated in high-grade clear cell RCC but not in CKD and low-grade clear cell RCC. These results show that EV phosphoproteome quantification utilizing our optimized EV isolation, phosphopeptides enrichment, and DIA method could be further developed for RCC grade differentiation to benefit many newly diagnosed RCC patients.
DOI: 10.6084/m9.figshare.19767289
title: Relación entre estrategias interpersonales y emociones

description: Se presenta la relación encontrada entre las emociones de alegría, ira,miedo y tristeza y las estrategias empleadas por los niños cuando experimentan estas emociones.
DOI: 10.6084/m9.figshare.19767289.v1
title: Relación entre estrategias interpersonales y emociones

description: Se presenta la relación encontrada entre las emociones de alegría, ira,miedo y tristeza y las estrategias empleadas por los niños cuando experimentan estas emociones.
DOI: 10.6084/m9.figshare.19767301
title: Estrategias interpersonales en niños y niñas

description: La tabla presenta la categorización realizada con las estrategias que los niños y niñas de 5 y 6 años verbalizan para la gestión de alegría, ira, miedo y tristeza
DOI: 10.6084/m9.figshare.19767301.v1
title: Estrategias interpersonales en niños y niñas

description: La tabla presenta la categorización realizada con las estrategias que los niños y niñas de 5 y 6 años verbalizan para la gestión de alegría, ira, miedo y tristeza
DOI: 10.6084/m9.figshare.19767307
title: Relaciones estrategias parentales, intrapersonales e interpersonales

description: La tabla muestra la relación existente entre las estrategias que emplean los padres para ayudar a sus hijos, las estrategias que emplean los niños por si mismos y las que usan para ayudar a otros.
DOI: 10.6084/m9.figshare.19767307.v1
title: Relaciones estrategias parentales, intrapersonales e interpersonales

description: La tabla muestra la relación existente entre las estrategias que emplean los padres para ayudar a sus hijos, las estrategias que emplean los niños por si mismos y las que usan para ayudar a otros.
DOI: 10.5281/zenodo.6532013
title: Code and data sets for "MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates"

description: Code used to prepare data sets, train and evaluate new MS²PIP models, evaluate MS²Rescore for immunopeptidomics, and generate figures. See README.md for more information on how to use these files and reproduce the results reported in the manuscript titled "MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates".
DOI: 10.5281/zenodo.5615049
title: Code and data sets for "MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates"

description: Code used to prepare data sets, train and evaluate new MS²PIP models, evaluate MS²Rescore for immunopeptidomics, and generate figures. See README.md for more information on how to use these files and reproduce the results reported in the manuscript titled "MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates".
DOI: 10.25838/d5p-32
title: Uncoupling of voltage- and ligand-induced activation in HCN2 channels by glycine inserts v2

description: Hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels are tetramers that generate electrical rhythmicity in special brain neurons and cardiomyocytes. The channels are activated by membrane hyperpolarization. The binding of cAMP to the four available cyclic nucleotide-binding domains (CNBD) enhances channel activation. We analyzed in the present study the mechanism of how the effect of cAMP binding is transmitted to the pore domain (PD). Our strategy was to uncouple the C-linker (CL) from the channel core by inserting one to five glycine residues between the S6 gate and the A’-helix (constructs 1G to 5G). We quantified in full-length HCN2 channels the resulting functional effects of the inserted glycines by current activation as well as the structural dynamics and statics using molecular dynamics simulations and Constraint Network Analysis (CNA). We show functionally that already in 1G the cAMP effect on activation is lost and that with the exception of 3G and 5G the concentration-activation relationships are shifted to depolarized voltages with respect to HCN2. The strongest effect was found for 4G. Accordingly, the activation kinetics were accelerated by all constructs, again with the strongest effect in 4G. The simulations reveal that the average residue mobility of the CL and CNBD domains is increased in all constructs and that the junction between the S6 and A’-helix is turned into a flexible hinge, resulting in a destabilized gate in all constructs. Moreover, for 3G and 4G, there is a stronger downward displacement of the CL-CNBD than in HCN2 and the other constructs, resulting in an increased kink angle between S6 and A’-helix, which in turn loosens contacts between the S4-helix and the CL. This is suggested to promote a downward movement of the S4-helix, similar to the effect of hyperpolarization. In addition, exclusively in 4G, the selectivity filter in the upper pore region and parts of the S4-helix are destabilized. The results provide new insights into the intricate activation of HCN2 channels.
DOI: 10.6084/m9.figshare.14301257.v3
title: Data of: Cellulose in secondary xylem of Cactaceae: chemical composition and anatomical distribution

description: Raw data from the infrared spectra of twenty-five species of Cactaceae with which the cristallinity indexes were obtained.
DOI: 10.5281/zenodo.6547650
title: Genome Annotation Workshop 2022 - Test data

description: Test datasets for the Genome Annotation Workshop 2022
DOI: 10.5281/zenodo.4638951
title: Genome Annotation Workshop 2022 - Test data

description: Test datasets for the Genome Annotation Workshop 2022
DOI: 10.5517/ccdc.csd.cc282bg5
title: CCDC 2087616: Experimental Crystal Structure Determination

description: Related Article: Gokanapalli Anusha, Meeniga Indira, Irla Siva Kumar, Loka Subramanyam Sarma, Kakarla Raghava Reddy, Peddiahgari Vasu Govardhana Reddy, Tejraj M. Aminabhavi|2022|Chemosphere|301|134751|doi:10.1016/j.chemosphere.2022.134751
DOI: 10.5517/ccdc.csd.cc28c4ld
title: CCDC 2096083: Experimental Crystal Structure Determination

description: Related Article: Hyo Moon Cho, Eun Jin Park, Yeon Joo Park, Jorge Ponce-Zea, Van Hieu Mai, Thi Phuong Doan, Byeol Ryu, Young Won Chin, Won Keun Oh|2022|Phytochemistry|200|113211|doi:10.1016/j.phytochem.2022.113211
DOI: 10.5517/ccdc.csd.cc28wx14
title: CCDC 2112186: Experimental Crystal Structure Determination

description: Related Article: Hye Jin Shin, Yoon Jung Jang, Hikaru Zenno, Shinya Hayami, Kil Sik Min|2022|J.Ind.Eng.Chem.(Seoul, Repub.Korea)|110|345|doi:10.1016/j.jiec.2022.03.007
DOI: 10.5517/ccdc.csd.cc28wx58
title: CCDC 2112190: Experimental Crystal Structure Determination

description: Related Article: Hye Jin Shin, Yoon Jung Jang, Hikaru Zenno, Shinya Hayami, Kil Sik Min|2022|J.Ind.Eng.Chem.(Seoul, Repub.Korea)|110|345|doi:10.1016/j.jiec.2022.03.007
DOI: 10.5517/ccdc.csd.cc28wx25
title: CCDC 2112187: Experimental Crystal Structure Determination

description: Related Article: Hye Jin Shin, Yoon Jung Jang, Hikaru Zenno, Shinya Hayami, Kil Sik Min|2022|J.Ind.Eng.Chem.(Seoul, Repub.Korea)|110|345|doi:10.1016/j.jiec.2022.03.007
DOI: 10.5517/ccdc.csd.cc28wx47
title: CCDC 2112189: Experimental Crystal Structure Determination

description: Related Article: Hye Jin Shin, Yoon Jung Jang, Hikaru Zenno, Shinya Hayami, Kil Sik Min|2022|J.Ind.Eng.Chem.(Seoul, Repub.Korea)|110|345|doi:10.1016/j.jiec.2022.03.007
DOI: 10.5517/ccdc.csd.cc28wx36
title: CCDC 2112188: Experimental Crystal Structure Determination

description: Related Article: Hye Jin Shin, Yoon Jung Jang, Hikaru Zenno, Shinya Hayami, Kil Sik Min|2022|J.Ind.Eng.Chem.(Seoul, Repub.Korea)|110|345|doi:10.1016/j.jiec.2022.03.007
DOI: 10.5517/ccdc.csd.cc29zpqq
title: CCDC 2144664: Experimental Crystal Structure Determination

description: Related Article: Jinxu Qi, Yunyun Zheng, Bin Li, Lai Wei, Jiuling Li, Xiangxiang Xu, Shiru Zhao, Xinhua Zheng, Yihong Wang|2022|Eur.J.Med.Chem.|237|114415|doi:10.1016/j.ejmech.2022.114415
DOI: 10.5517/ccdc.csd.cc29zprr
title: CCDC 2144665: Experimental Crystal Structure Determination

description: Related Article: Jinxu Qi, Yunyun Zheng, Bin Li, Lai Wei, Jiuling Li, Xiangxiang Xu, Shiru Zhao, Xinhua Zheng, Yihong Wang|2022|Eur.J.Med.Chem.|237|114415|doi:10.1016/j.ejmech.2022.114415
DOI: 10.5517/ccdc.csd.cc2b7n3c
title: CCDC 2152302: Experimental Crystal Structure Determination

description: Related Article: Argyro Chatziadi, Eliska Skorepova, Jan Jirat, Jan Rohlíček, Miroslav Šoóš|2022|Cryst.Growth Des.|22|3395|doi:10.1021/acs.cgd.2c00207
DOI: 10.5517/ccdc.csd.cc2b7n8j
title: CCDC 2152307: Experimental Crystal Structure Determination

description: Related Article: Argyro Chatziadi, Eliska Skorepova, Jan Jirat, Jan Rohlíček, Miroslav Šoóš|2022|Cryst.Growth Des.|22|3395|doi:10.1021/acs.cgd.2c00207
DOI: 10.5517/ccdc.csd.cc2b7v2j
title: CCDC 2152487: Experimental Crystal Structure Determination

description: Related Article: Argyro Chatziadi, Eliska Skorepova, Jan Jirat, Jan Rohlíček, Miroslav Šoóš|2022|Cryst.Growth Des.|22|3395|doi:10.1021/acs.cgd.2c00207
DOI: 10.5519/qd.16rl287r
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (13544 records)
DOI: 10.5281/zenodo.5018340
title: Experiments of Multiple Decision Making in CDCL SAT Solvers

description: With these experiments (submission), we show that Multiple Decision Making (MDM) has a positive impact on CDCL, for many different SAT application problems when alternating between different decision queues and frequently running the WalkSAT strategy. Overall, MDM allowed the CDCL search to solve extra 10 formulas in the SAT competition 2020 benchmark set, and achieves a minimum PAR-2 score of 3,473 compared to the state of the art solver Kissat.
DOI: 10.5281/zenodo.5018339
title: Experiments of Multiple Decision Making in CDCL SAT Solvers

description: With these experiments (submission), we show that Multiple Decision Making (MDM) has a positive impact on CDCL, for many different SAT application problems when alternating between different decision queues and frequently running the WalkSAT strategy. Overall, MDM allowed the CDCL search to solve extra 10 formulas in the SAT competition 2020 benchmark set, and achieves a minimum PAR-2 score of 3,473 compared to the state of the art solver Kissat.
DOI: 10.17632/6pwd2s9rff.1
title: The liver x receptor is selectively modulated by different ligands to differentially alter breast cancer metastasis-associated myeloid immune cells - Supplemental Data

description: This is supplemental data corresponding to the manuscript titled The liver x receptor is selectively modulated by different ligands to differentially alter breast cancer metastasis-associated myeloid immune cells.

Authors: 
Liqian Ma1, Hashni Epa Vidana Gamage1, Srishti Tiwari1, Chaeyeon Han1, Madeline A Henn1, Natalia Krawczynska1, Payam Dibaeinia2, Graeme J. Koelwyn3,†, Anasuya Das Gupta1, Rafael Ovidio Bautista Rivas1,  Chris L. Wright4, Fangxiu Xu4, Kathryn J. Moore3,5, Saurabh Sinha2,6,7 and Erik R. Nelson1,6-10,*

Affiliations:
1 Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL
2 Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL
3 NYU Cardiovascular Research Center, Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY
4 Roy J. Carver Biotechnology Center DNA Services, University of Illinois Urbana-Champaign, Urbana, IL
5 Department of Cell Biology, New York University School of Medicine, New York, NY
6 Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL
7 Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL
8 Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL
9 University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL
10 Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL



*To whom correspondence and reprint requests should be addressed: Erik R. Nelson. University of Illinois at Urbana-Champaign. 407 S Goodwin Ave (MC-114), Urbana, IL, 61801. Phone: 217-244-5477. Fax: 217-333-1133. ORCiD: 0000-0002-8887-1905. E-mail: enels@illinois.edu
DOI: 10.6084/m9.figshare.19767481
title: Mtr_GFF.tar.gz

description: The Gene and TE annotation of the genome of <em>Musa troglodytarum</em> L.
DOI: 10.6084/m9.figshare.19767481.v1
title: Mtr_GFF.tar.gz

description: The Gene and TE annotation of the genome of <em>Musa troglodytarum</em> L.
DOI: 10.6084/m9.figshare.19767559
title: Mtr_supplementary_seqs.fasta

description: The cDNA sequences of <em>MtrSSUIIs and MtrGALK. </em>The promoter sequences of <em>MtrACO1</em> and <em>MtrACS1</em>.
DOI: 10.6084/m9.figshare.19767553.v2
title: Parameters of tested system

description: Parameters of tested system
DOI: 10.6084/m9.figshare.19767553.v1
title: Parameters of tested system

description: Parameters of tested system
DOI: 10.6084/m9.figshare.18737369.v1
title: Analysis code and data

description: Data for "Differences in social network structure and implications for reproductive isolation in a pair of stickleback ecotypes"
DOI: 10.6084/m9.figshare.16786558
title: R Code for analysis - The effect of resource availability on interspecific competition between a native and an invasive ant

description: R Code for "The effect of resource availability on interspecific<br>competition between a native and an invasive ant"
DOI: 10.6084/m9.figshare.16786558.v2
title: R Code for analysis - "The effect of resource availability on interspecific competition between a native and an invasive ant"

description: R Code for "The effect of resource availability on interspecific<br>competition between a native and an invasive ant"
DOI: 10.6084/m9.figshare.19767652.v1
title: Arctic Ocean Amplification in a warming climate in CMIP6 models

description: The codes used in the main data processing and visualization in paper entitled "Arctic Ocean Amplification in a warming climate in CMIP6 models" by Shu et al. (2022)
DOI: 10.34740/kaggle/dsv/3637657
title: BBC News
DOI: 10.34740/kaggle/dsv/3637741
title: Michelin Guide Restaurants 2021
DOI: 10.34848/czcki6/xcigc7
title: Respuesta al derecho de petición 202172011138561.pdf

description: :unav
DOI: 10.34848/czcki6/2hiykn
title: Base de datos procesamiento derecho de petición UARIV.tab

description: :unav
DOI: 10.6084/m9.figshare.19747204
title: Rdata_files

description: Rdata files releted to the single cell RNA-seq of human erythroid cells.
DOI: 10.5281/zenodo.6549690
title: GPT-J Code Clone Detection

description: This is the dataset of GPT-J code clone detection. 'data/' folder contains the data to replicate our study. 'code/' folder contains the code to replicate our study. `rebuttal/` folder contains the results of the rebuttal. Each folder has its own README, please check the details there.
DOI: 10.5281/zenodo.6366686
title: GPT-J Code Clone Detection

description: This is the dataset of GPT-J code clone detection. 'data/' folder contains the data to replicate our study. 'code/' folder contains the code to replicate our study. `rebuttal/` folder contains the results of the rebuttal. Each folder has its own README, please check the details there.
DOI: 10.6084/m9.figshare.19767724.v1
title: Additional file 3 of Transcriptome profiling and proteomic validation reveals targets of the androgen receptor signaling in the BT-474 breast cancer cell line

description: Additional file 3. Additional Tables S1-S6.
DOI: 10.6084/m9.figshare.19767724
title: Additional file 3 of Transcriptome profiling and proteomic validation reveals targets of the androgen receptor signaling in the BT-474 breast cancer cell line

description: Additional file 3. Additional Tables S1-S6.
DOI: 10.6084/m9.figshare.19767770
title: Additional file 1 of ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

description: Additional file 1. Appendix 1: A complete list of names and URIs s of all included EC forms from MDM Portal.
DOI: 10.6084/m9.figshare.19767770.v1
title: Additional file 1 of ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

description: Additional file 1. Appendix 1: A complete list of names and URIs s of all included EC forms from MDM Portal.
DOI: 10.6084/m9.figshare.19767773
title: Additional file 2 of ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

description: Additional file 2. Appendix 2A. A list of unique UMLS concepts of group A sorted by absolute frequency. B: A list of unique UMLS concepts of group B sorted by absolute frequency.
DOI: 10.6084/m9.figshare.19767773.v1
title: Additional file 2 of ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

description: Additional file 2. Appendix 2A. A list of unique UMLS concepts of group A sorted by absolute frequency. B: A list of unique UMLS concepts of group B sorted by absolute frequency.
DOI: 10.6084/m9.figshare.19767776
title: Additional file 3 of ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

description: Additional file 3. Appendix 3: A complete detailed list of all occurrences of all UMLS concepts identified within EC forms. This database includes details like the question text, names and IDs of all item groups and items as well as UMLS preferred definition of every single UMLS concept occurrence identified within EC forms.
DOI: 10.6084/m9.figshare.19767776.v1
title: Additional file 3 of ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

description: Additional file 3. Appendix 3: A complete detailed list of all occurrences of all UMLS concepts identified within EC forms. This database includes details like the question text, names and IDs of all item groups and items as well as UMLS preferred definition of every single UMLS concept occurrence identified within EC forms.
DOI: 10.6084/m9.figshare.19767800
title: Additional file 7 of ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

description: Additional file 7. Appendix 7: A complete list of all UMLS primary and secondary laboratory concepts used in the manual analysis to produce the dataset of top 55 most common Laboratory Procedures. This includes 703 unique UMLS concepts, among which 311 concepts belong to Group A (Concepts of laboratory semantic types). Concepts are sorted in 55 Ranks according to the nTotal of primary and secondary concepts of each Laboratory Procedure.
DOI: 10.6084/m9.figshare.19767800.v1
title: Additional file 7 of ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

description: Additional file 7. Appendix 7: A complete list of all UMLS primary and secondary laboratory concepts used in the manual analysis to produce the dataset of top 55 most common Laboratory Procedures. This includes 703 unique UMLS concepts, among which 311 concepts belong to Group A (Concepts of laboratory semantic types). Concepts are sorted in 55 Ranks according to the nTotal of primary and secondary concepts of each Laboratory Procedure.
DOI: 10.6084/m9.figshare.19767803
title: Additional file 8 of ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

description: Additional file 8. Appendix 8A: The final dataset, ELaPro, in CSV format after complete mapping to LOINC. B: The final dataset, ELaPro, reported as ODM file (CDASH standard). 8C. The final dataset, ELaPro, in in FHIR format (HL7 standard).
DOI: 10.6084/m9.figshare.19767803.v1
title: Additional file 8 of ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

description: Additional file 8. Appendix 8A: The final dataset, ELaPro, in CSV format after complete mapping to LOINC. B: The final dataset, ELaPro, reported as ODM file (CDASH standard). 8C. The final dataset, ELaPro, in in FHIR format (HL7 standard).
DOI: 10.6084/m9.figshare.19767892.v1
title: Additional file 10 of Mouse Chd4-NURD is required for neonatal spermatogonia survival and normal gonad development

description: Additional file 10: Table S3. List of annotated Chd4-bounded genes possibly implicated in stem cell survival and/differentiation.
DOI: 10.6084/m9.figshare.19767892
title: Additional file 10 of Mouse Chd4-NURD is required for neonatal spermatogonia survival and normal gonad development

description: Additional file 10: Table S3. List of annotated Chd4-bounded genes possibly implicated in stem cell survival and/differentiation.
DOI: 10.6084/m9.figshare.19767898
title: Additional file 12 of Mouse Chd4-NURD is required for neonatal spermatogonia survival and normal gonad development

description: Additional file 12: Table S5. Mapping statistics corresponding to Chd4 ChIP-seq.
DOI: 10.6084/m9.figshare.19767898.v1
title: Additional file 12 of Mouse Chd4-NURD is required for neonatal spermatogonia survival and normal gonad development

description: Additional file 12: Table S5. Mapping statistics corresponding to Chd4 ChIP-seq.
DOI: 10.6084/m9.figshare.19767922
title: Additional file 8 of Mouse Chd4-NURD is required for neonatal spermatogonia survival and normal gonad development

description: Additional file 8: Table S1. List of Chd4 ChIP-seq signal.
DOI: 10.6084/m9.figshare.19767922.v1
title: Additional file 8 of Mouse Chd4-NURD is required for neonatal spermatogonia survival and normal gonad development

description: Additional file 8: Table S1. List of Chd4 ChIP-seq signal.
DOI: 10.6084/m9.figshare.19767925
title: Additional file 9 of Mouse Chd4-NURD is required for neonatal spermatogonia survival and normal gonad development

description: Additional file 9: Table S2. Gene ontology analysis.