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1. NAB2::STAT6 fusions and genome-wide DNA methylation profiling: Predictors of patient outcomes in meningeal solitary fibrous tumors.

Author

Eschbacher, Kathryn, Tran, Quynh, Moskalev, Evgeny, Jenkins, Sarah, Fritchie, Karen, Stoehr, Robert, Caron, Alissa, Link, Michael, Brown, Paul, Guajardo, Andrew, Brat, Daniel, Wu, Ashley, Santagata, Sandro, Louis, David, Brastianos, Priscilla, Kaplan, Alexander, Alexander, Brian, Rossi, Sabrina, Ferrarese, Fabio, Raleigh, David, Nguyen, Minh, Gross, John, Velazquez Vega, Jose, Rodriguez, Fausto, Perry, Arie, Martinez-Lage, Maria, Orr, Brent, Haller, Florian, and Giannini, Caterina

Subjects
CNS WHO grade, NAB2::STAT6, TERT, meningeal solitary fibrous tumor, solitary fibrous tumor, Humans, Female, Male, Middle Aged, Solitary Fibrous Tumors, DNA Methylation, STAT6 Transcription Factor, Adult, Repressor Proteins, Aged, Meningeal Neoplasms, Young Adult, Adolescent, Aged, 80 and over, Child, Prognosis, Telomerase
Abstract

Meningeal solitary fibrous tumors (SFT) are rare and have a high frequency of local recurrence and distant metastasis. In a cohort of 126 patients (57 female, 69 male; mean age at surgery 53.0 years) with pathologically confirmed meningeal SFTs with extended clinical follow-up (median 9.9 years; range 15 days-43 years), we performed extensive molecular characterization including genome-wide DNA methylation profiling (n = 80) and targeted TERT promoter mutation testing (n = 98). Associations were examined with NAB2::STAT6 fusion status (n = 101 cases; 51 = ex5-7::ex16-17, 26 = ex4::ex2-3; 12 = ex2-3::exANY/other and 12 = no fusion) and placed in the context of 2021 Central Nervous System (CNS) WHO grade. NAB2::STAT6 fusion breakpoints (fusion type) were significantly associated with metastasis-free survival (MFS) (p = 0.03) and, on multivariate analysis, disease-specific survival (DSS) when adjusting for CNS WHO grade (p = 0.03). DNA methylation profiling revealed three distinct clusters: Cluster 1 (n = 38), Cluster 2 (n = 22), and Cluster 3 (n = 20). Methylation clusters were significantly associated with fusion type (p

Published
2024

3. Sigma basis sets: a new family of GTO basis sets for molecular calculations

Author

Ema, Ignacio, Ramírez, Guillermo, López, Rafael, and de la Vega, José Manuel García

Subjects
Physics - Computational Physics
Abstract

A new family of Gaussian-type basis sets named sigma basis sets is presented and preliminarily tested. Sigma basis sets for H, C, N, O and P are reported and their performance is tested in some atomic and molecular calculations., Comment: 6 pages, 5 tables, no figures

Published
2022

16. Diabetic ketoacidosis drives COVID-19 related hospitalizations in children with type 1 diabetes.

Author

Alonso, Guy Todd, Ebekozien, Osagie, Gallagher, Mary Pat, Rompicherla, Saketh, Lyons, Sarah K, Choudhary, Abha, Majidi, Shideh, Pinnaro, Catherina T, Balachandar, Sadana, Gangat, Mariam, Curda Roberts, Alissa Jeanne, Marks, Brynn E, Creo, Ana, Sanchez, Janine, Seeherunvong, Tossaporn, Jimenez-Vega, Jose, Patel, Neha S, Wood, Jamie R, Gabriel, Liana, Sumpter, Kathryn M, Wilkes, Meredith, Rapaport, Robert, Cymbaluk, Anna, Wong, Jenise C, Sanda, Srinath, and Albanese-O'neill, Anastasia

Subjects
Humans, Diabetic Ketoacidosis, Diabetes Mellitus, Type 1, Disease Progression, Hospitalization, Registries, Risk Assessment, Risk Factors, Cross-Sectional Studies, Age Factors, Up-Regulation, Adolescent, Child, Child, Preschool, Infant, Infant, Newborn, United States, Female, Male, Biomarkers, COVID-19, Glycated Hemoglobin, 1型糖尿病, DKA, pediatric, type 1 diabetes, 儿科, 新型冠状病毒肺炎, Diabetes, Pediatric, Prevention, Metabolic and endocrine, Clinical Sciences, Public Health and Health Services
Abstract

BackgroundDiabetes is a risk factor for poor COVID-19 outcomes, but pediatric patients with type 1 diabetes are poorly represented in current studies.MethodsT1D Exchange coordinated a US type 1 diabetes COVID-19 registry. Forty-six diabetes centers submitted pediatric cases for patients with laboratory confirmed COVID-19. Associations between clinical factors and hospitalization were tested with Fisher's Exact Test. Logistic regression was used to calculate odds ratios for hospitalization.ResultsData from 266 patients with previously established type 1 diabetes aged

Published
2021

19. Methodological Approach to the Evaluation of Scientific Journals

Author

Montoya-Roncancio, Valeria, Merlo-Vega, José Antonio, Huang, Ronghuai, Series Editor, Kinshuk, Series Editor, Jemni, Mohamed, Series Editor, Chen, Nian-Shing, Series Editor, Spector, J. Michael, Series Editor, García-Peñalvo, Francisco José, editor, and García-Holgado, Alicia, editor

Published
2023
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20. Prototyping with Blockchain: A Case Study for Teaching Blockchain Application Development at University

Author

Froehlich, Michael, Vega, Jose, Pahl, Amelie, Lotz, Sergej, Alt, Florian, Schmidt, Albrecht, Welpe, Isabell, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Auer, Michael E., editor, Pachatz, Wolfgang, editor, and Rüütmann, Tiia, editor

Published
2023
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22. Real-world apremilast use in biologic-naïve psoriatic arthritis patients. Data from Spanish clinical practice

Author

Gratacós-Masmitja, Jordi, Beltrán Catalán, Emma, Álvarez Vega, José Luis, Urruticoechea-Arana, Ana, Fito, Concepción, Maceiras, Francisco, Belzunegui Otano, Joaquín María, Fernández Melón, Julia, Chamizo Carmona, Eugenio, Abad Hernández, Miguel Ángel, Ros Vilamajó, Inmaculada, Castro Oreiro, Sonia, Pascual Alfonso, Eva, and Torre Alonso, Juan Carlos

Published
2024
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23. Inequities in Health Outcomes in Children and Adults With Type 1 Diabetes: Data From the T1D Exchange Quality Improvement Collaborative.

Author

Majidi, Shideh, Ebekozien, Osagie, Noor, Nudrat, Lyons, Sarah, McDonough, Ryan, Gandhi, Kajal, Izquierdo, Roberto, Demeterco-Berggren, Carla, Polsky, Sarit, Basina, Marina, Desimone, Marisa, Thomas, Inas, Rioles, Nicole, Jimenez-Vega, Jose, Malik, Faisal, Miyazaki, Brian, Albanese-ONeill, Anastasia, and Jones, Nana-Hawa

Abstract

Health care inequities among racial and ethnic groups remain prevalent. For people with type 1 diabetes who require increased medical access and care, disparities are seen in access to care and health outcomes. This article reports on a study by the T1D Exchange Quality Improvement Collaborative evaluating differences in A1C, diabetic ketoacidosis (DKA), severe hypoglycemia, and technology use among racial and ethnic groups. In a diverse cohort of nearly 20,000 children and adults with type 1 diabetes, A1C was found to differ significantly among racial and ethnic groups. Non-Hispanic Blacks had higher rates of DKA and severe hypoglycemia and the lowest rate of technology use. These results underscore the crucial need to study and overcome the barriers that lead to inequities in the care and outcomes of people with type 1 diabetes.

Published
2021

30. Somatosensation

Author

Martín-Alguacil, Nieves, de Gaspar, Ignacio, Schober, Justine M., Pfaff, Donald W., Vega, José A., Pfaff, Donald W., editor, Volkow, Nora D., editor, and Rubenstein, John L., editor

Published
2022
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31. The Almina of Ceuta. Graphic Analysis of Its Historical Cartography

Author

de la Vega, José Fco. Montes, Cano, María Teresa Pérez, Quijada, Ramón Queiro, Tosi, Francesca, Editor-in-Chief, Germak, Claudio, Series Editor, Zurlo, Francesco, Series Editor, Jinyi, Zhi, Series Editor, Pozzatti Amadori, Marilaine, Series Editor, Caon, Maurizio, Series Editor, Ródenas-López, Manuel A., editor, Calvo-López, José, editor, and Salcedo-Galera, Macarena, editor

Published
2022
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32. Proposal for a Digital Information Model to Manage the Archaeological Site of Itálica

Author

Guerrero Vega, José María, Fornos, Roque Angulo, Román, Manuel Castellano, Tosi, Francesca, Editor-in-Chief, Germak, Claudio, Series Editor, Zurlo, Francesco, Series Editor, Jinyi, Zhi, Series Editor, Pozzatti Amadori, Marilaine, Series Editor, Caon, Maurizio, Series Editor, Ródenas-López, Manuel A., editor, Calvo-López, José, editor, and Salcedo-Galera, Macarena, editor

Published
2022
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33. The Innovation in Manufacturing Areas of Electronics Industry of Mexicali Using PLC

Author

Hernández, Roberto Carlos Valdés, Villanueva, Adelaida Figueroa, Vega, José Luis Arcos, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Zhang, Yu-Dong, editor, Senjyu, Tomonobu, editor, So-In, Chakchai, editor, and Joshi, Amit, editor

Published
2022
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34. Analysis of Cellular Feature Differences of Astrocytomas with Distinct Mutational Profiles Using Digitized Histopathology Images

Author

Roy, Mousumi, Wang, Fusheng, Teodoro, George, Vega, Jose Velazqeuz, Brat, Daniel, and Kong, Jun

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Cellular phenotypic features derived from histopathology images are the basis of pathologic diagnosis and are thought to be related to underlying molecular profiles. Due to overwhelming cell numbers and population heterogeneity, it remains challenging to quantitatively compute and compare features of cells with distinct molecular signatures. In this study, we propose a self-reliant and efficient analysis framework that supports quantitative analysis of cellular phenotypic difference across distinct molecular groups. To demonstrate efficacy, we quantitatively analyze astrocytomas that are molecularly characterized as either Isocitrate Dehydrogenase (IDH) mutant (MUT) or wildtype (WT) using imaging data from The Cancer Genome Atlas database. Representative cell instances that are phenotypically different between these two groups are retrieved after segmentation, feature computation, data pruning, dimensionality reduction, and unsupervised clustering. Our analysis is generic and can be applied to a wide set of cell-based biomedical research.

Published
2018

35. Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Author

Mitros, Therese, Session, Adam M, James, Brandon T, Wu, Guohong Albert, Belaffif, Mohammad B, Clark, Lindsay V, Shu, Shengqiang, Dong, Hongxu, Barling, Adam, Holmes, Jessica R, Mattick, Jessica E, Bredeson, Jessen V, Liu, Siyao, Farrar, Kerrie, Głowacka, Katarzyna, Jeżowski, Stanisław, Barry, Kerrie, Chae, Won Byoung, Juvik, John A, Gifford, Justin, Oladeinde, Adebosola, Yamada, Toshihiko, Grimwood, Jane, Putnam, Nicholas H, De Vega, Jose, Barth, Susanne, Klaas, Manfred, Hodkinson, Trevor, Li, Laigeng, Jin, Xiaoli, Peng, Junhua, Yu, Chang Yeon, Heo, Kweon, Yoo, Ji Hye, Ghimire, Bimal Kumar, Donnison, Iain S, Schmutz, Jeremy, Hudson, Matthew E, Sacks, Erik J, Moose, Stephen P, Swaminathan, Kankshita, and Rokhsar, Daniel S

Subjects
Biotechnology, Human Genome, Genetics, Affordable and Clean Energy, Biomass, Chromosomes, Plant, DNA Transposable Elements, Diploidy, Evolution, Molecular, Gene Expression Regulation, Plant, Genetic Variation, Genome, Plant, Genomics, Models, Genetic, Phylogeny, Poaceae, Polyploidy, Saccharum, Seasons, Sorghum
Abstract

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

Published
2020

36. High-grade neuroepithelial tumor with BCOR exon 15 internal tandem duplication-a comprehensive clinical, radiographic, pathologic, and genomic analysis.

Author

Ferris, Sean P, Velazquez Vega, Jose, Aboian, Mariam, Lee, Julieann C, Van Ziffle, Jessica, Onodera, Courtney, Grenert, James P, Saunders, Tara, Chen, Yunn-Yi, Banerjee, Anu, Kline, Cassie N, Gupta, Nalin, Raffel, Corey, Samuel, David, Ruiz-Diaz, Irune, Magaki, Shino, Wilson, Dianne, Neltner, Janna, Al-Hajri, Zahra, Phillips, Joanna J, Pekmezci, Melike, Bollen, Andrew W, Tihan, Tarik, Schniederjan, Matthew, Cha, Soonmee, Perry, Arie, and Solomon, David A

Subjects
Humans, Neoplasms, Neuroepithelial, Glioma, Central Nervous System Neoplasms, Brain Neoplasms, Telomerase, Proto-Oncogene Proteins, Transcription Factors, Repressor Proteins, Genomics, Exons, Adolescent, Child, Child, Preschool, Infant, Female, Male, Cyclin-Dependent Kinase Inhibitor p16, E1A-Associated p300 Protein, Kaplan-Meier Estimate, Biomarkers, Tumor, Oligodendrocyte Transcription Factor 2, BCOR exon 15 internal tandem duplication, HGNET, brain tumor, high-grade neuroepithelial tumor, molecular neuro-oncology, molecular neuropathology, molecular neurooncology, Neurology & Neurosurgery, Clinical Sciences, Neurosciences
Abstract

High-grade neuroepithelial tumor with BCOR exon 15 internal tandem duplication (HGNET BCOR ex15 ITD) is a recently proposed tumor entity of the central nervous system (CNS) with a distinct methylation profile and characteristic genetic alteration. The complete spectrum of histologic features, accompanying genetic alterations, clinical outcomes, and optimal treatment for this new tumor entity are largely unknown. Here, we performed a comprehensive assessment of 10 new cases of HGNET BCOR ex15 ITD. The tumors mostly occurred in young children and were located in the cerebral or cerebellar hemispheres. On imaging all tumors were large, well-circumscribed, heterogeneous masses with variable enhancement and reduced diffusion. They were histologically characterized by predominantly solid growth, glioma-like fibrillarity, perivascular pseudorosettes, and palisading necrosis, but absence of microvascular proliferation. They demonstrated sparse to absent GFAP expression, no synaptophysin expression, variable OLIG2 and NeuN positivity, and diffuse strong BCOR nuclear positivity. While BCOR exon 15 internal tandem duplication was the solitary pathogenic alteration identified in six cases, four cases contained additional alterations including CDKN2A/B homozygous deletion, TERT amplification or promoter hotspot mutation, and damaging mutations in TP53, BCORL1, EP300, SMARCA2 and STAG2. While the limited clinical follow-up in prior reports had indicated a uniformly dismal prognosis for this tumor entity, this cohort includes multiple long-term survivors. Our study further supports inclusion of HGNET BCOR ex15 ITD as a distinct CNS tumor entity and expands the known clinicopathologic, radiographic, and genetic features.

Published
2020

45. DFT study of ionic liquids adsorption on circumcoronene shaped graphene

Author

Ruzanov, Anton, Lembinen, Meeri, Ers, Heigo, de la Vega, José M. García, Lage-Estebanez, Isabel, Lust, Enn, and Ivaništšev, Vladislav B.

Subjects
Condensed Matter - Soft Condensed Matter, Physics - Chemical Physics
Abstract

Carbon materials have a range of properties such as high electrical conductivity, high specific surface area, and mechanical flexibility are relevant for electrochemical applications. Carbon materials are utilised in energy conversion-and-storage devices along with electrolytes of complementary properties. In this work, we study the interaction of highly concentrated electrolytes (ionic liquids) at a model carbon surface (circumcoronene) using density functional theory methods. Our results indicate the decisive role of the dispersion interactions that noticeably strengthen the circumcoronene-ion interaction. Also, we focus on the adsorption of halide anions as the electrolytes containing these ions are promising for practical use in supercapacitors and solar cells.

Published
2017
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46. Plastic Injection Molding Process Analysis: Data Integration and Modeling for Improved Production Efficiency.

Author

Hernández-Vega, Jose Isidro, Reynoso-Guajardo, Luis Alejandro, Gallardo-Morales, Mario Carlos, Macias-Arias, María Ernestina, Hernández, Amadeo, de la Cruz, Nain, Soto-Soto, Jesús E., and Hernández-Santos, Carlos

Subjects
INJECTION molding of plastics, RANDOM forest algorithms, MANUFACTURING processes, PLASTIC analysis (Engineering), STATISTICAL decision making
Abstract

This paper presents a comprehensive analysis of the plastic injection molding process through the integration of data acquisition technologies and classification models. In collaboration with a company specializing in plastic injection, data were extracted directly from the machine during a specific period at the beginning of a shift change. These data were subjected to exploratory analysis to identify correlations between important variables, such as injection time, cycle time, and mold pressures. Additionally, classification models, including Random Forest and Logistic Regression, were constructed to predict and classify the process state based on these variables. The model results demonstrated high predictive performance, with 99.5% accuracy for Random Forest and 97% for Logistic Regression. These results provide a strong foundation for the early identification of potential problems and informed decision making to improve the efficiency of the plastic injection molding process. This study contributes to the advancement of the integration of intelligent technologies in industrial process optimization, aligned with the principles of Industry 4.0. [ABSTRACT FROM AUTHOR]

Published
2024
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47. The origin and collapse of rock glaciers during the Bølling-Allerød interstadial: A new study case from the Cantabrian Mountains (Spain)

Author

Santos-González, Javier, González-Gutiérrez, Rosa Blanca, Redondo-Vega, José María, Gómez-Villar, Amelia, Jomelli, Vincent, Fernández-Fernández, José M., Andrés, Nuria, García-Ruiz, José M., Peña-Pérez, Sergio Alberto, Melón-Nava, Adrián, Oliva, Marc, Álvarez-Martínez, Javier, Charton, Joanna, and Palacios, David

Published
2022
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