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I am a computer science researcher with a master's in Biomedical Engineering from the University of Porto and a PhD in Computer Science from the University of Aveiro. Currently, I am working as a Researcher on the GDI - Genomic Data Infrastructure project. My main research focuses on the development and application of machine learning and information theory concepts in bioinformatics. I have published numerous papers in quality venues and participated in significant European projects besides GDI, such as EHDEN, SCREEN-DR, MMIR, and EMIF. I actively collaborate with many international and national institutions and researchers and am a reviewer for esteemed scientific journals. I have received an IEEE Best Paper award for my research and have won 2 BioASQ challenges.
Identification

Personal identification

Full name
JORGE MIGUEL FERREIRA DA SILVA

Citation names

  • Jorge Miguel Silva

Author identifiers

Ciência ID
7319-3EDC-9A88
ORCID iD
0000-0002-6331-6091
Google Scholar ID
N6ZzRPEAAAAJ&hl
Scopus Author Id
57194129937

Telephones

Fax
  • (+351) 234378157 (Professional)
Telephone
  • (+351) 234 370 50 (Professional)

Addresses

  • Campus Universitário de Santiago, 3810-193, Aveiro, Aveiro, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Italian Upper intermediate (B2) Elementary (A2) Beginner (A1) Intermediate (B1) Beginner (A1)
Education
Degree Classification
2023/04/18
Concluded
Doctorate in Computer Engineering (Doutoramento)
Major in Complexidade de Kolmogorov
Universidade de Aveiro, Portugal
"Algorithmic information approximations in data analysis" (THESIS/DISSERTATION)
Aprovado
2016
Concluded
Integrated Master in Bioengineering (Mestrado)
Major in Área de especialização: Engenharia Biomédica
Universidade do Porto Faculdade de Engenharia, Portugal

Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
"Automatic Analysis of Glial Cells and Photoreception in Drosophila Melanogaster" (THESIS/DISSERTATION)
15
2014 - 2014
Concluded
Evaluation of brain cell biomarkers using mRNA gene expression human brain atlas (Outros)
Major in Bioinformatica
Università degli Studi di Padova Dipartimento di Ingegneria Dell'Informazione, Italy
Affiliation

Science

Category
Host institution
Employer
2023/07/15 - Current Researcher (Research) Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal
Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal

Others

Category
Host institution
Employer
2023/03/01 - 2023/07/15 Research Fellow Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal
Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal
2018/12/01 - 2023/01/31 PhD Scholarship Holder Fundação para a Ciência e a Tecnologia, Portugal
Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal
2016/06/01 - 2018/11/30 Research Fellow Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal
Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal
Projects

Grant

Designation Funders
2023/03/01 - Current GDI - Genomic Data Infrastructure
Researcher
Universidade de Aveiro, Portugal
European Commission
Ongoing
2018/12/01 - 2023/01/31 Patient Diagnosis Prediction in Multimodal Medical Information
SFRH/BD/141851/2018
Universidade de Aveiro, Portugal
Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2023/10 - Current Mapping the Knowledge Landscape of Language Models
FCT.CPCA.2022.01
Co-Principal Investigator (Co-PI)
Fundacao de Computacao Cientifica Nacional, Portugal

Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal

Fundação para a Ciência e a Tecnologia, Portugal
Fundação para a Ciência e a Tecnologia

Fundacao de Computacao Cientifica Nacional

Rede Nacional de Computação Avançada
Ongoing
2023 - 2023 TMFinder
2022.27068.CPCA.A0
Co-Principal Investigator (Co-PI)
Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal

Rede Nacional de Computação Avançada, Portugal

Fundacao de Computacao Cientifica Nacional, Portugal
Fundação para a Ciência e a Tecnologia

Fundacao de Computacao Cientifica Nacional

Rede Nacional de Computação Avançada
Ongoing
2018/12/01 - 2022/11/30 Patient Diagnosis Prediction in Multimodal Medical Information
SFRH/BD/141851/2018
Universidade de Aveiro, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016/04/01 - 2020/12/01 Plataforma de Análise de Imagem e de Aprendizagem Computacional para a Inovação no Rastreio da Retinopatia Diabética
CMUP-ERI/TIC/0028/2014
Instituto de Engenharia de Sistemas e Computadores, Portugal

Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência, Portugal

Administração Regional de Saúde do Norte IP, Portugal

Universidade de Aveiro, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016/07/01 - 2019/12/31 Recuperação de Informação Multimodal em Repositórios de Imagem Médica
PTDC/EEI-ESS/6815/2014
Universidade de Aveiro, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2018 - 2018 EMIF (European Medical Information Framework)
Research Fellow
Universidade de Aveiro, Portugal
European Commission
Concluded

Other

Designation Funders
2018 - Current EHDEN European Health Data & Evidence Network
Research Fellow
Ongoing
Outputs

Publications

Book chapter
  1. Silva, Jorge Miguel; Pratas, Diogo; Caetano, Tânia; Matos, Sérgio. "Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods". In Pattern Recognition and Image Analysis, 309-320. Aveiro, Portugal: Springer International Publishing, 2022.
    Published • 10.1007/978-3-031-04881-4_25
Conference paper
  1. Silva, J.M.; Almeida, J.R.; Oliveira, J.L.. "Classifying and discovering genomic sequences in metagenomic repositories". 2023.
    10.1016/j.procs.2023.01.441
  2. Pinheiro, M.; Silva, J.M.; Oliveira, J.L.. "Optimizing Variant Calling for Human Genome Analysis: A Comprehensive Pipeline Approach". 2023.
    10.1007/978-3-031-34960-7_6
  3. Silva, J.M.; Pratas, D.; Matos, S.. "Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications". 2023.
    10.1007/978-3-031-36007-7_12
  4. Almeida, J.R.; Silva, J.M.; Oliveira, J.L.. "A FAIR Approach to Real-World Health Data Management and Analysis". 2023.
    10.1109/CBMS58004.2023.00338
  5. Almeida, T.; Jonker, R.A.A.; Poudel, R.; Silva, J.M.; Matos, S.. "BIT.UA at MedProcNer: Discovering Medical Procedures in Spanish Using Transformer Models with MCRF and Augmentation". 2023.
  6. Almeida, T.; Jonker, R.A.A.; Poudel, R.; Silva, J.M.; Matos, S.. "BIT.UA at BioASQ 11B: Two-Stage IR with Synthetic Training and Zero-Shot Answer Generation". 2023.
  7. Jorge Miguel Silva; Almeida, João Rafael. Corresponding author: Jorge Miguel Silva. "Characterizing Genomics Repositories Using Feature-Based Classification". 2022.
    10.3233/shti220932
  8. Silva, Jorge Miguel; Almeida, Joao Rafael. "The value of compression for taxonomic identification". Paper presented in IEEE 35th International Symposium on Computer-Based Medical Systems (CBMS), 2022.
    Published • 10.1109/cbms55023.2022.00055
  9. Lebre, Rui; Pinho, Eduardo; Jorge Miguel Silva; Costa, Carlos. "Dicoogle Framework for Medical Imaging Teaching and Research". 2020.
    Published • 10.1109/iscc50000.2020.9219545
  10. Silva, Joao Figueira; Jorge Miguel Silva; Guerra, Antonio; Matos, Sergio; Costa, Carlos. "Ejection Fraction Classification in Transthoracic Echocardiography Using a Deep Learning Approach". Paper presented in IEEE 31th International Symposium on Computer-Based Medical Systems (CBMS), 2018.
    Published • 10.1109/cbms.2018.00029
  11. Jorge Miguel Silva; Guerra, Antonio; Silva, Joao Figueira; Pinho, Eduardo; Costa, Carlos. "Face De-Identification Service for Neuroimaging Volumes". 2018.
    Published • 10.1109/cbms.2018.00032
  12. Jorge Miguel Silva; Joao F. Silva; Carlos Costa; Michael Pedrosa. "A novel 3D-CNN approach for ejection fraction classification in transthoracic echocardiography". Paper presented in CARS 2018—Computer Assisted Radiology and Surgery Proceedings of the 32nd International Congress and Exhibition Berlin, Germany, June 20–23, 2018, Berlin, 2018.
    Published • 10.1007/s11548-018-1766-x
  13. Pedrosa, Micael; Jorge Miguel Silva; Costa, Carlos. "Reactive Through Services - Opinionated Framework for Developing Reactive Services". 2018.
    10.5220/0006661403300337
  14. Pedrosa M; Jorge Miguel Silva; Matos S; Costa C. Corresponding author: Jorge Miguel Silva. "SCREEN-DR - Software Architecture for the Diabetic Retinopathy Screening.". 2018.
    10.3233/978-1-61499-852-5-396
  15. Jorge Miguel Silva. Corresponding author: Jorge Miguel Silva. "Research PACS for diabetic retinopathy screening". Paper presented in CARS2018 - Computer Assisted Radiology and Surgery Proceedings of the 32nd International Congress and Exhibition, Berlim, 2018.
    Published • 10.1007/s11548-018-1766-y
  16. Pinho, E.; Silva, J.F.; Jorge Miguel Silva; Costa, C.. "Towards representation learning for biomedical concept detection in medical images: UA.PT bioinformatics in ImageCLEF 2017". Paper presented in Conference and Labs of the Evaluation Forum, Dublin, 2017.
    Published
  17. Silva, J.F.; Jorge Miguel Silva; Pinho, E.; Costa, C.. "3D-CNN in drug resistance detection and tuberculosis classification". Paper presented in Conference and Labs of the Evaluation Forum, Dublin, 2017.
    Published
  18. Jorge Miguel Silva; Tiago, Marques Godinho; David, Silva; Carlos, Costa; Silva, J.M.; Marques Godinho, T.; Silva, D.; Costa, C.. Corresponding author: Jorge Miguel Silva. "Web Validation Service for Ensuring Adherence to the DICOM Standard.". Paper presented in Studies in health technology and informatics, 2017.
    Published • 10.3233/978-1-61499-753-5-38
Conference poster
  1. Jorge Miguel Silva. "Exploring Kolmogorov Complexity Approximations for Data Analysis". Paper presented in Encontro Ciência 2023, 2023.
Journal article
  1. Jorge M, Silva; Weihong, Qi; Armando J, Pinho; Diogo, Pratas. "AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.". GigaScience 12 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85159449092&partnerID=MN8TOARS.
    Open access • Accepted
  2. Cruz DB; Almeida JR; Silva JM; Oliveira JL. "A Reliable and Secure Method for Sharing Genomic Data.". Studies in health technology and informatics (2023): http://europepmc.org/abstract/med/37203584.
    10.3233/shti230350
  3. Silva JM; Pratas D; Caetano T; Matos S; Jorge Miguel Silva. "The complexity landscape of viral genomes.". GigaScience (2022): http://europepmc.org/abstract/med/35950839.
    10.1093/gigascience/giac079
  4. Pratas, Diogo; Jorge Miguel Silva. "Persistent minimal sequences of SARS-CoV-2". Bioinformatics 36 21 (2020): 5129-5132. http://dx.doi.org/10.1093/bioinformatics/btaa686.
    Open access • Published • 10.1093/bioinformatics/btaa686
  5. Jorge Miguel Silva; Eduardo Pinho; Sérgio Matos; D. Pratas. "Statistical Complexity Analysis of Turing Machine tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model". Entropy (2020): https://www.mdpi.com/1099-4300/22/1/105.
    10.3390/e22010105
  6. D. Pratas; Morteza Hosseini; Jorge Miguel Silva; Armando J Pinho. "A Reference-Free Lossless Compression Algorithm for DNA Sequences Using a Competitive Prediction of Two Classes of Weighted Models". Entropy (2019): https://www.mdpi.com/1099-4300/21/11/1074.
    10.3390/e21111074
  7. Jorge Miguel Silva; Godinho, Tiago Marques; Silva, David; Costa, Carlos. "A community-driven validation service for standard medical imaging objects". Computer Standards & Interfaces 61 (2019): 121-128. http://dx.doi.org/10.1016/j.csi.2018.06.003.
    10.1016/j.csi.2018.06.003
  8. Pedrosa, Micael; Jorge Miguel Silva; Silva, João Figueira; Matos, Sérgio; Costa, Carlos. "SCREEN-DR: Collaborative platform for diabetic retinopathy". International Journal of Medical Informatics 120 (2018): 137-146. http://dx.doi.org/10.1016/j.ijmedinf.2018.10.005.
    10.1016/j.ijmedinf.2018.10.005
  9. Jorge Miguel Silva; Pinho, Eduardo; Monteiro, Eriksson; Silva, João Figueira; Costa, Carlos. Corresponding author: Jorge Miguel Silva. "Controlled searching in reversibly de-identified medical imaging archives". Journal of Biomedical Informatics 77 (2018): 81-90. http://dx.doi.org/10.1016/j.jbi.2017.12.002.
    10.1016/j.jbi.2017.12.002
Newsletter article
  1. Jorge Miguel Silva; Diogo Pratas; Tania Caetano; Sérgio Matos. "Archaea Taxonomic Classification.", 27th Portuguese Conference on Pattern Recognition, 2021
  2. Jorge Miguel Silva; Diogo Pratas; Sérgio Matos. "Comparison and Evaluation of Information-based Measures in Images.", 26th Portuguese Conference on Pattern Recognition, 2020
  3. Jorge Miguel Silva; Diogo Pratas; Sérgio Matos. "Evaluation of Statistical Complexity in Viral Genome Sequences", 25th Portuguese Conference on Pattern Recognition, 2019
  4. Jorge Miguel Silva; Augusto Silva; Pedro Vilela. "Enhanced Cerebral Vascular Segmentation with Harmonic Constraints.", The 23rd Portuguese Conference on Pattern Recognition, 2017
Thesis / Dissertation
  1. "Algorithmic information approximations in data analysis". PhD, Universidade de Aveiro, 2023.
  2. "Automatic Analysis of Glial Cells and Photoreception in Drosophila Melanogaster". Master, Universidade do Porto Faculdade de Engenharia, 2016. https://hdl.handle.net/10216/83253.
Website
  1. Jorge Miguel Silva; Pratas, Diogo; Rui Antunes; Matos, Sérgio; Armando J Pinho. Automatic analysis of artistic paintings using information-based measures. 2021. http://panther.web.ua.pt.
    10.1016/j.patcog.2021.107864

Other

Software
  1. Jorge Miguel Silva; Diogo Pratas. "AltaiR: a C toolkit for alignment-free and spatial-temporal analysis of multi-FASTA data". 1.0.1. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/cobilab/altair. 2023.
  2. Luis Bastiao; Eduardo Pinho; Godinho, Tiago Marques; Jorge Miguel Silva; Rui Lebre; Rui Jesus; Tibério Baptista; et al. "dicoogle: An extensible, platform-independent, open-source PACS archive.". 3.2.2. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/bioinformatics-ua/dicoogle.git. 2023.
  3. Jorge Miguel Silva; Lourenço, Alexandre; Joao Almeida; Diogo Pratas. "RFSC: Reference-Free Sequence Classification". Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/cobilab/RFSC.git. 2022.
  4. Jorge Miguel Silva; Diogo Pratas. "AlcoR: Alignment-free simulation, mapping, and visualization of low-complexity regions in FASTA data.". 1.9. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/cobilab/alcor. 2022.
  5. Jorge Miguel Silva. "xgtaxonomy: Cross-reference of Genomic Taxonomy". 1.0. Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro. https://github.com/ieeta-pt/xgTaxonomy.git. 2022.
  6. Jorge Miguel Silva; Joao Almeida. "SecureFASTA". 1.0. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/bioinformatics-ua/SecureFASTA. 2022.
  7. Jorge Miguel Silva; Joao Almeida. "COMPACT: COMPressor tAxonomic ClassificaTion". 1.0. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/bioinformatics-ua/COMPACT. 2022.
  8. Jorge Miguel Silva; Pratas, Diogo. "canvas: Complexity Analysis Viral Sequences". 1.0. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/jorgeMFS/canvas. 2022.
  9. Jorge Miguel Silva; Tiago Almeida. "tm-neural-finder". 0.1. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/bioinformatics-ua/TM-Neural-Finder. 2022.
  10. Jorge Miguel Silva; Tiago Almeida. "SPTTM". 1.0. Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro. https://github.com/jorgeMFS/spttm. 2022.
  11. Jorge Miguel Silva. "Archaea2". 2.0. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/jorgeMFS/Archaea2. 2021.
  12. Jorge Miguel Silva; Diogo Pratas; Sérgio Matos. "PANThER". 1.0. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/asilab/panther. 2021.
  13. Jorge Miguel Silva. "TMRecreator". 1.0. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/jorgeMFS/TMRecreator. 2019.
  14. Jorge Miguel Silva. "TMCompress". 1.0. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/asilab/TMCompression. 2018.
  15. David Silva; Jorge Miguel Silva; Godinho, Tiago Marques. "Dicom Validator". 1.0. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://bioinformatics.ua.pt/dicomvalidator/#/. 2018.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2020/07/24 Patient Diagnosis Prediction in Multimodal Medical Information Research Summit 2020
Universidade de Aveiro (Aveiro, Portugal)
2019/10/19 Algorithmic-Statistical Learning DSPT Day 2019
DSPT Day (Porto, Portugal)
2019/10 Evaluation of Statistical Complexity in Viral Genome Sequences RECPAD 2019
Faculty of Sciences of the University of Porto (Porto, Portugal)
2019/07/03 Patient Diagnosis Prediction Using Multimodal Medical Information Research Summit 2019
Universidade de Aveiro (Aveiro, Portugal)

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2024/02/20 - Current Enhancing Genomic Discovery through Taxonomic Identification Tools
Co-supervisor
Mestrado em Engenharia Biomédica (Master)
Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal

Event organisation

Event name
Type of event (Role)
Institution / Organization
2023/09/13 - 2023/11/15 ELIXIR Portugal All Hands 3rd Edition (2023/11/13 - 2023/11/17)
Workshop (Co-organisor)
BioData.pt, Portugal

Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro, Portugal
2014 - 2014 Symposium on Bioengineering (2014 - 2016)
Symposium (Member of the Organising Committee)
Universidade do Porto Faculdade de Engenharia, Portugal

Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal

Event participation

Activity description
Type of event
Event name
Institution / Organization
2024/07/03 - Current Presentation of the work: "Unlocking Genomic Data with Genomic Data Infrastructure project"
Exhibition
Encontro Ciência 2024
Fundação para a Ciência e a Tecnologia, Portugal
2024/01/22 - 2024/01/24 Pillar II and III joint Workshop
Workshop
Pillar II and III joint workshop
ELIXIR, United Kingdom
2023/11/07 - 2023/11/10 Pillar II 2nd GDI Workshop
Workshop
Pillar II 2nd GDI Workshop
BioData.pt, Portugal

ELIXIR, United Kingdom
2023/07/05 - 2023/07/07 Encontro Ciência 2023
Congress
Encontro Ciência 2023
Universidade de Aveiro, Portugal
2023/03/08 - 2023/03/10 Pillar II 1st GDI Workshop
Workshop
Pillar II 1st GDI Workshop
National Bioinformatics Infrastructure Sweden, Sweden

ELIXIR, United Kingdom

Association member

Society Organization name Role
2021 - Current Portuguese Association for Pattern Recognition (APRP) member
2013 - 2015 Núcleo de Estudantes de Bioengenharia - FEUP/ICBAS Co-Founder and President of the Supervisory board

Committee member

Activity description
Role
Institution / Organization
2023 - 2023 Federated European Genome-phenome Archive (FEGA) Operations Committee
Coordinator
ELIXIR, United Kingdom

Conference scientific committee

Conference name Conference host
2021 - 2023 Computer-Based Medical Systems (IEEE CBMS)

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2023/02/01 BioASK Winners Diario de Aveiro
2022/07/31 Software da UA identifica autores de pinturas e classifica correntes artísticas AveiroMag
2022/07/29 Criado em Aveiro programa para identificar pintores, correntes, e falsificações observador

Journal scientific committee

Journal title (ISSN) Publisher
2018 - Current Journal of Digital Imaging (8971889) Springer
2018 - Current Journal of Biomedical Imaging (1532-0480) Elsevier
2019 - 2023 Artificial Intelligence in Medicine (0933-3657) Elsevier

Mentoring / Tutoring

Topic Student name
2021 - 2021 Reference-Free Sequence Classification Tool Alexandre Emanuel Monteiro Lourenço
2017 - 2018 Dicom Validator David Silva
Distinctions

Award

2023 Winner of the BIOASQ Challenge 2023 Task 11B
Ethniko Kentro Ereunas Physikon Epistemon Demokritos, Greece

Google Inc, United States

Éditions Scientifiques Elsevier, France

Centro Nacional de Supercomputación, Spain
2023 Winner of the BIOASQ Challenge 2023 Task MedProcNER
Ethniko Kentro Ereunas Physikon Epistemon Demokritos, Greece

Google Inc, United States

Éditions Scientifiques Elsevier, France

Centro Nacional de Supercomputación, Spain
2018 TCCLS Best Student Paper Award
IEEE, United States