21,531 results on '"Calixto A"'
Search Results
2. AnyMatch -- Efficient Zero-Shot Entity Matching with a Small Language Model
- Author
-
Zhang, Zeyu, Groth, Paul, Calixto, Iacer, and Schelter, Sebastian
- Subjects
Computer Science - Computation and Language ,Computer Science - Artificial Intelligence ,Computer Science - Databases - Abstract
Entity matching (EM) is the problem of determining whether two records refer to same real-world entity, which is crucial in data integration, e.g., for product catalogs or address databases. A major drawback of many EM approaches is their dependence on labelled examples. We thus focus on the challenging setting of zero-shot entity matching where no labelled examples are available for an unseen target dataset. Recently, large language models (LLMs) have shown promising results for zero-shot EM, but their low throughput and high deployment cost limit their applicability and scalability. We revisit the zero-shot EM problem with AnyMatch, a small language model fine-tuned in a transfer learning setup. We propose several novel data selection techniques to generate fine-tuning data for our model, e.g., by selecting difficult pairs to match via an AutoML filter, by generating additional attribute-level examples, and by controlling label imbalance in the data. We conduct an extensive evaluation of the prediction quality and deployment cost of our model, in a comparison to thirteen baselines on nine benchmark datasets. We find that AnyMatch provides competitive prediction quality despite its small parameter size: it achieves the second-highest F1 score overall, and outperforms several other approaches that employ models with hundreds of billions of parameters. Furthermore, our approach exhibits major cost benefits: the average prediction quality of AnyMatch is within 4.4% of the state-of-the-art method MatchGPT with the proprietary trillion-parameter model GPT-4, yet AnyMatch requires four orders of magnitude less parameters and incurs a 3,899 times lower inference cost (in dollars per 1,000 tokens)., Comment: 12 pages excluding references, 3 figures, and 5 tables
- Published
- 2024
3. Tumor de Krukenberg Associado a Virilização Durante a Gestação: Relato de um Caso e Revisão da Literatura
- Author
-
Cícero de Andrade Urban, Linei A. B. Dellê, Cíntia A. Cavalin, Júlio C. F. Batista, Claudinei de A. e Cruz, and Calixto A. Hakim Neto
- Subjects
Neoplasia de Ovário ,Câncer Gastro-Intestinal ,Tumor de Krukenberg ,Células em Anel de Sinete ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
O tumor de Krukenberg (TK) é uma entidade rara, caracterizada por neoplasia ovariana secundária a um tumor do trato gastrointestinal, freqüentemente bilateral, volumoso e assintomático. Afeta geralmente mulheres na quarta década de vida, correspondendo a l%-5% de todos os tumores ovarianos. Histologicamente são caracterizados por células neoplásicas em anel de sinete, com proliferação estromal não neoplásica e reativa. Poucos casos de TK funcionante são relatados, sendo a associação com virilização durante a gravidez rara. Os autores relatam o caso de uma paciente do sexo feminino, 35 anos de idade, que no segundo trimestre de gestação iniciou com hirsutismo, acne, voz grave e hipertensão arterial sistêmica. A ecografia pré-natal evidenciou volumoso tumor em ovário esquerdo. Foi submetida a cesariana, com nascimento de recém-nato masculino normal. Na evolução, a laparotomia para excisão do tumor em ovário esquerdo revelou carcinomatose peritoneal, metástase hepática e lesão infiltrativa em pequena curvatura gástrica. Exame histológico do tumor ovariano demonstrou adenocarcinoma pouco diferenciado, tipo anel de sinete. A biópsia da lesão gástrica também revelou adenocarcinoma pouco diferenciado, tipo anel de sinete. Foi conduzida com quimioterapia e radioterapia, sem resposta. Evoluiu a óbito oito meses após o diagnóstico.
- Published
- 2022
- Full Text
- View/download PDF
4. Neoplasia Endócrína Múltipla tipo 2b - Relato de três casos e revisão de Literatura
- Author
-
Cícero de Andrade Urban, Beatriz Garcia Sluminsky, Linei Augusta Brollini Dellê, Antônio Moris Cury, José Gastão Rocha de Carvalho, and Calixto Antonio Hakim Neto
- Subjects
Carcinoma Medular de Tireóide ,Feocromocitoma ,Neoplasia Endócrina Múltipla ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Neoplasia Endocrina Múltipla tipo 2B (NEM-2B) é uma síndrome incomum, herdada de forma autossômica dominante e com penetrância variável. Múltiplos órgãos são envolvidos, mas com uma tríade predominante de carcinoma medular de tireóide, feocromocitoma e ganglioneuromas do trato gastrointestinal. A maioria dos pacientes tem fácies característica, composta por eversão e alargamento dos lábios e eversão das pálpebras por neuromas mucosos. Os autores relatam três casos de NEM-2B, sendo dois do sexo masculino, com idade média de 15,9 anos. A manifestação clínica inicial em todos os casos foi crescimento de massa cervical em topografia de tireóide e hábito marfanóide. Foram submetidos a tireoidectomia total, com esvaziamento cervical bilateral por carcinoma medular de tireóide. Um paciente apresentou feocromocitoma quatro anos após o diagnóstico de tumor de tireóide, sendo submetido a laparotomia com excisão do tumor. Um paciente evoluiu a óbito 2,5 anos após o diagnóstico e os outros dois encontram-se livres de doença, com uma média de acompanhamento ambulatorial de um ano, apesar do teste de calcitonina positivo em um dos casos.
- Published
- 2022
- Full Text
- View/download PDF
5. MerlinS13 phosphorylation regulates meningioma Wnt signaling and magnetic resonance imaging features
- Author
-
Eaton, Charlotte D, Avalos, Lauro, Liu, S John, Chen, Zhenhong, Zakimi, Naomi, Casey-Clyde, Tim, Bisignano, Paola, Lucas, Calixto-Hope G, Stevenson, Erica, Choudhury, Abrar, Vasudevan, Harish N, Magill, Stephen T, Young, Jacob S, Krogan, Nevan J, Villanueva-Meyer, Javier E, Swaney, Danielle L, and Raleigh, David R
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Biomedical Imaging ,Clinical Trials and Supportive Activities ,Rare Diseases ,Cancer ,Clinical Research ,Brain Disorders ,Brain Cancer ,Neurosciences ,Meningioma ,Humans ,Phosphorylation ,Wnt Signaling Pathway ,Neurofibromin 2 ,Animals ,Magnetic Resonance Imaging ,Meningeal Neoplasms ,Mice ,Cell Line ,Tumor ,beta Catenin ,Female ,Serine ,Male ,Proteomics ,Biomarkers ,Tumor - Abstract
Meningiomas are associated with inactivation of NF2/Merlin, but approximately one-third of meningiomas with favorable clinical outcomes retain Merlin expression. Biochemical mechanisms underlying Merlin-intact meningioma growth are incompletely understood, and non-invasive biomarkers that may be used to guide treatment de-escalation or imaging surveillance are lacking. Here, we use single-cell RNA sequencing, proximity-labeling proteomic mass spectrometry, mechanistic and functional approaches, and magnetic resonance imaging (MRI) across meningioma xenografts and patients to define biochemical mechanisms and an imaging biomarker that underlie Merlin-intact meningiomas. We find Merlin serine 13 (S13) dephosphorylation drives meningioma Wnt signaling and tumor growth by attenuating inhibitory interactions with β-catenin and activating the Wnt pathway. MRI analyses show Merlin-intact meningiomas with S13 phosphorylation and favorable clinical outcomes are associated with high apparent diffusion coefficient (ADC). These results define mechanisms underlying a potential imaging biomarker that could be used to guide treatment de-escalation or imaging surveillance for patients with Merlin-intact meningiomas.
- Published
- 2024
6. Detailed delineation of the fetal brain in diffusion MRI via multi-task learning
- Author
-
Karimi, Davood, Calixto, Camilo, Snoussi, Haykel, Cortes-Albornoz, Maria Camila, Velasco-Annis, Clemente, Rollins, Caitlin, Jaimes, Camilo, Gholipour, Ali, and Warfield, Simon K.
- Subjects
Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning ,Quantitative Biology - Neurons and Cognition - Abstract
Diffusion-weighted MRI is increasingly used to study the normal and abnormal development of fetal brain in-utero. Recent studies have shown that dMRI can offer invaluable insights into the neurodevelopmental processes in the fetal stage. However, because of the low data quality and rapid brain development, reliable analysis of fetal dMRI data requires dedicated computational methods that are currently unavailable. The lack of automated methods for fast, accurate, and reproducible data analysis has seriously limited our ability to tap the potential of fetal brain dMRI for medical and scientific applications. In this work, we developed and validated a unified computational framework to (1) segment the brain tissue into white matter, cortical/subcortical gray matter, and cerebrospinal fluid, (2) segment 31 distinct white matter tracts, and (3) parcellate the brain's cortex and delineate the deep gray nuclei and white matter structures into 96 anatomically meaningful regions. We utilized a set of manual, semi-automatic, and automatic approaches to annotate 97 fetal brains. Using these labels, we developed and validated a multi-task deep learning method to perform the three computations. Our evaluations show that the new method can accurately carry out all three tasks, achieving a mean Dice similarity coefficient of 0.865 on tissue segmentation, 0.825 on white matter tract segmentation, and 0.819 on parcellation. The proposed method can greatly advance the field of fetal neuroimaging as it can lead to substantial improvements in fetal brain tractography, tract-specific analysis, and structural connectivity assessment.
- Published
- 2024
7. Streamline tractography of the fetal brain in utero with machine learning
- Author
-
Liu, Weide, Calixto, Camilo, Warfield, Simon K., and Karimi, Davood
- Subjects
Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,Quantitative Biology - Neurons and Cognition - Abstract
Diffusion-weighted magnetic resonance imaging (dMRI) is the only non-invasive tool for studying white matter tracts and structural connectivity of the brain. These assessments rely heavily on tractography techniques, which reconstruct virtual streamlines representing white matter fibers. Much effort has been devoted to improving tractography methodology for adult brains, while tractography of the fetal brain has been largely neglected. Fetal tractography faces unique difficulties due to low dMRI signal quality, immature and rapidly developing brain structures, and paucity of reference data. This work presents the first machine learning model for fetal tractography. The model input consists of five sources of information: (1) Fiber orientation, inferred from a diffusion tensor fit to the dMRI signal; (2) Directions of recent propagation steps; (3) Global spatial information, encoded as distances to keypoints in the brain cortex; (4) Tissue segmentation information; and (5) Prior information about the expected local fiber orientations supplied with an atlas. In order to mitigate the local tensor estimation error, a large spatial context around the current point in the diffusion tensor image is encoded using convolutional and attention neural network modules. Moreover, the diffusion tensor information at a hypothetical next point is included in the model input. Filtering rules based on anatomically constrained tractography are applied to prune implausible streamlines. We trained the model on manually-refined whole-brain fetal tractograms and validated the trained model on an independent set of 11 test scans with gestational ages between 23 and 36 weeks. Results show that our proposed method achieves superior performance across all evaluated tracts. The new method can significantly advance the capabilities of dMRI for studying normal and abnormal brain development in utero.
- Published
- 2024
8. White matter tract crossing and bottleneck regions in the fetal brain
- Author
-
Calixto, Camilo, Soldatelli, Matheus D., Li, Bo, Pierotich, Lana, Gholipour, Ali, Warfield, Simon K., and Karimi, Davood
- Subjects
Quantitative Biology - Neurons and Cognition - Abstract
There is a growing interest in using diffusion MRI to study the white matter tracts and structural connectivity of the fetal brain. Recent progress in data acquisition and processing suggests that this imaging modality has a unique role in elucidating the normal and abnormal patterns of neurodevelopment in utero. However, there have been no efforts to quantify the prevalence of crossing tracts and bottleneck regions, important issues that have been extensively researched for adult brains. In this work, we determined the brain regions with crossing tracts and bottlenecks between 23 and 36 gestational weeks. We performed probabilistic tractography on 59 fetal brain scans and extracted a set of 51 distinct white tracts, which we grouped into 10 major tract bundle groups. We analyzed the results to determine the patterns of tract crossings and bottlenecks. Our results showed that 20-25% of the white matter voxels included two or three crossing tracts. Bottlenecks were more prevalent. Between 75-80% of the voxels were characterized as bottlenecks, with more than 40% of the voxels involving four or more tracts. The results of this study highlight the challenge of fetal brain tractography and structural connectivity assessment and call for innovative image acquisition and analysis methods to mitigate these problems.
- Published
- 2024
9. Evaluating Linguistic Capabilities of Multimodal LLMs in the Lens of Few-Shot Learning
- Author
-
Dogan, Mustafa, Kesen, Ilker, Calixto, Iacer, Erdem, Aykut, and Erdem, Erkut
- Subjects
Computer Science - Computation and Language ,Computer Science - Computer Vision and Pattern Recognition - Abstract
The linguistic capabilities of Multimodal Large Language Models (MLLMs) are critical for their effective application across diverse tasks. This study aims to evaluate the performance of MLLMs on the VALSE benchmark, focusing on the efficacy of few-shot In-Context Learning (ICL), and Chain-of-Thought (CoT) prompting. We conducted a comprehensive assessment of state-of-the-art MLLMs, varying in model size and pretraining datasets. The experimental results reveal that ICL and CoT prompting significantly boost model performance, particularly in tasks requiring complex reasoning and contextual understanding. Models pretrained on captioning datasets show superior zero-shot performance, while those trained on interleaved image-text data benefit from few-shot learning. Our findings provide valuable insights into optimizing MLLMs for better grounding of language in visual contexts, highlighting the importance of the composition of pretraining data and the potential of few-shot learning strategies to improve the reasoning abilities of MLLMs., Comment: Preprint. 33 pages, 17 Figures, 3 Tables
- Published
- 2024
10. Inverse participation ratio and entanglement of edge states in HgTe quantum wells in a finite strip geometry
- Author
-
Calixto, Manuel and Castaños, Octavio
- Subjects
Condensed Matter - Mesoscale and Nanoscale Physics ,Quantum Physics - Abstract
Localization and entanglement properties of edge states of HgTe quantum wells in a finite strip geometry of width $L$ are studied under quantum information concepts such as: 1) inverse participation ratio (IPR), which measures localization, and 2) entropies of the reduced density matrix (RDM) for the spin sector, which measures quantum correlations due to the spin-orbit coupling (SOC). Qualitative and quantitative information on the edge states energies and wavefunctions is extracted from analytic and numerical Hamiltonian diagonalization approaches. The previously observed exponential decay of the energy gap with $L$ and its modulations is confirmed and nontrivial consequences of the strip width and Rashba terms on the charge conductance are also reviewed. Analysis of the structure of the edge-state wave functions in terms of spin, momentum $k_x$ in the $x$-direction and position $y$, evidences the spin polarization structure of edge states at the boundaries. An IPR analysis reveals that the valence edge states show maximum localization on the boundaries for certain values of the momenta $k_x$ in the vicinity of the $\Gamma$ point. The edge-state wave packets participate of less and less momenta as we approach to the boundaries $y=0,L$ (and also the center $y=L/2$, for some of them) of the strip. A study of the RDM to the spin sector of edge states sheds complementary information on the structure of spin probabilities in $(k_x,y)$ space, giving clear location of extremal values. The purity and entropies of the RDM inform on the regions $(k_x,y)$ where the spin sector is more and less entangled with the rest of the system, due to SOC., Comment: 10 pages, 11 figures
- Published
- 2024
11. Morphological structure, germination and vigor of Juglans jamaicensis c. dc. seeds in the Turquino National Park
- Author
-
José Luis Rodríguez Sosa and Calixto Aguilar Espinosa
- Subjects
cedro nogal ,juglans jamaicensis ,capacidad germinativa. ,Environmental sciences ,GE1-350 ,Ecology ,QH540-549.5 - Abstract
Seven groups of Juglans jamaicensis trees were selected in Turquino National Park to determine the morphological structure, germination power and vigor of Juglans jamaicensis seeds. To do this, the seeds were collected from the soil and subjected to pregerminative treatment, then 900 of them were placed in the germinator under a completely randomized design. The morphology of the seeds was evaluated from the parameters length of the major axis, diameter, weight and volume of the seed. The germination control started from the seventh day to 90 days. Germination capacity, germination dynamics, and seed vigor were determined through germination speed and Czabator indices. The morphological variation of seeds in relation to progenitor trees and sites, as well as the effect of parental origin on germination, germination dynamics and seed vigor was checked by means of a simple classification ANOVA, and the HSD-Tukey test. The structure of Juglans jamaicensis seeds is an adaptation of trees to the environment in which they develop in response to environmental variation and the establishment of Juglans jamaicensis regenerants in natural conditions, it is determined by high germination potential (73±16%), low germination speed (0.40±0.1) and vigor (0.38±0.3) as well as offspring anomalies, which are key elements leading to a potential decrease in the abundance of seedlings in the forest.
- Published
- 2019
12. Spatial genomic, biochemical and cellular mechanisms underlying meningioma heterogeneity and evolution
- Author
-
Lucas, Calixto-Hope G, Mirchia, Kanish, Seo, Kyounghee, Najem, Hinda, Chen, William C, Zakimi, Naomi, Foster, Kyla, Eaton, Charlotte D, Cady, Martha A, Choudhury, Abrar, Liu, S John, Phillips, Joanna J, Magill, Stephen T, Horbinski, Craig M, Solomon, David A, Perry, Arie, Vasudevan, Harish N, Heimberger, Amy B, and Raleigh, David R
- Subjects
Agricultural ,Veterinary and Food Sciences ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Agricultural Biotechnology ,Human Genome ,Cancer Genomics ,Brain Cancer ,Precision Medicine ,Biotechnology ,Cancer ,Brain Disorders ,Rare Diseases ,Good Health and Well Being ,Meningioma ,Humans ,Meningeal Neoplasms ,Genetic Heterogeneity ,DNA Copy Number Variations ,Gene Expression Regulation ,Neoplastic ,Genomics ,Single-Cell Analysis ,Cell Proliferation ,Neoplasm Recurrence ,Local ,Signal Transduction ,Cell Line ,Tumor ,Transcriptome ,Medical and Health Sciences ,Developmental Biology ,Agricultural biotechnology ,Bioinformatics and computational biology - Abstract
Intratumor heterogeneity underlies cancer evolution and treatment resistance, but targetable mechanisms driving intratumor heterogeneity are poorly understood. Meningiomas are the most common primary intracranial tumors and are resistant to all medical therapies, and high-grade meningiomas have significant intratumor heterogeneity. Here we use spatial approaches to identify genomic, biochemical and cellular mechanisms linking intratumor heterogeneity to the molecular, temporal and spatial evolution of high-grade meningiomas. We show that divergent intratumor gene and protein expression programs distinguish high-grade meningiomas that are otherwise grouped together by current classification systems. Analyses of matched pairs of primary and recurrent meningiomas reveal spatial expansion of subclonal copy number variants associated with treatment resistance. Multiplexed sequential immunofluorescence and deconvolution of meningioma spatial transcriptomes using cell types from single-cell RNA sequencing show decreased immune infiltration, decreased MAPK signaling, increased PI3K-AKT signaling and increased cell proliferation, which are associated with meningioma recurrence. To translate these findings to preclinical models, we use CRISPR interference and lineage tracing approaches to identify combination therapies that target intratumor heterogeneity in meningioma cell co-cultures.
- Published
- 2024
13. Construction of a comprehensive fetal monitoring database for the study of perinatal hypoxic ischemic encephalopathy.
- Author
-
Kearney, Robert, Wu, Yvonne, Vargas-Calixto, Johann, Forquer, Heather, Gerstley, Lawrence, Hamilton, Emily, Warrick, Philip, Kuzniewicz, Michael, and Cornet, Marie-Coralie
- Subjects
Childbirth ,Construction of a Comprehensive Fetal Monitoring Database for the Study of Perinatal Hypoxic Ischemic Encephalopathy ,Fetal heart rate ,Fetal monitoring ,Hypoxic-ischemic encephalopathy ,Labour ,Neonatal acidosis ,Neonatal encephalopathy ,Uterine pressure ,cardiotocography (CTG) - Abstract
This article describes the methods used to build a large-scale database of more than 250,000 electronic fetal monitoring (EFM) records linked to a comprehensive set of clinical information about the infant, the mother, the pregnancy, labor, and outcome. The database can be used to investigate how birth outcome is related to clinical and EFM features. The main steps involved in building the database were: (1) Acquiring the raw EFM recording and clinical records for each birth. (2) Assigning each birth to an objectively defined outcome class that included normal, acidosis, and hypoxic-ischemic encephalopathy. (3) Removing all personal health information from the EFM recordings and clinical records. (4) Preprocessing the deidentified EFM records to eliminate duplicates, reformat the signals, combine signals from different sensors, and bridge gaps to generate signals in a format that can be readily analyzed. (5) Post-processing the repaired EFM recordings to extract key features of the fetal heart rate, uterine activity, and their relations. (6) Populating a database that links the clinical information, EFM records, and EFM features to support easy querying and retrieval. •A multi-step process is required to build a comprehensive database linking electronic temporal fetal monitoring signals to a comprehensive set of clinical information about the infant, the mother, the pregnancy, labor, and outcome.•The current database documents more than 250,000 births including almost 4,000 acidosis and 400 HIE cases. This represents more than 80% of the births that occurred in 15 Northern California Kaiser Permanente Hospitals between 2011-2019. This is a valuable resource for studying the factors predictive of outcome.•The signal processing code and schemas for the database are freely available. The database will not be permitted to leave Kaiser firewalls, but a process is in place to allow interested investigators to access it.
- Published
- 2024
14. BraTS-Path Challenge: Assessing Heterogeneous Histopathologic Brain Tumor Sub-regions
- Author
-
Bakas, Spyridon, Thakur, Siddhesh P., Faghani, Shahriar, Moassefi, Mana, Baid, Ujjwal, Chung, Verena, Pati, Sarthak, Innani, Shubham, Baheti, Bhakti, Albrecht, Jake, Karargyris, Alexandros, Kassem, Hasan, Nasrallah, MacLean P., Ahrendsen, Jared T., Barresi, Valeria, Gubbiotti, Maria A., López, Giselle Y., Lucas, Calixto-Hope G., Miller, Michael L., Cooper, Lee A. D., Huse, Jason T., and Bell, William R.
- Subjects
Computer Science - Computer Vision and Pattern Recognition - Abstract
Glioblastoma is the most common primary adult brain tumor, with a grim prognosis - median survival of 12-18 months following treatment, and 4 months otherwise. Glioblastoma is widely infiltrative in the cerebral hemispheres and well-defined by heterogeneous molecular and micro-environmental histopathologic profiles, which pose a major obstacle in treatment. Correctly diagnosing these tumors and assessing their heterogeneity is crucial for choosing the precise treatment and potentially enhancing patient survival rates. In the gold-standard histopathology-based approach to tumor diagnosis, detecting various morpho-pathological features of distinct histology throughout digitized tissue sections is crucial. Such "features" include the presence of cellular tumor, geographic necrosis, pseudopalisading necrosis, areas abundant in microvascular proliferation, infiltration into the cortex, wide extension in subcortical white matter, leptomeningeal infiltration, regions dense with macrophages, and the presence of perivascular or scattered lymphocytes. With these features in mind and building upon the main aim of the BraTS Cluster of Challenges https://www.synapse.org/brats2024, the goal of the BraTS-Path challenge is to provide a systematically prepared comprehensive dataset and a benchmarking environment to develop and fairly compare deep-learning models capable of identifying tumor sub-regions of distinct histologic profile. These models aim to further our understanding of the disease and assist in the diagnosis and grading of conditions in a consistent manner.
- Published
- 2024
15. Anatomically Constrained Tractography of the Fetal Brain
- Author
-
Calixto, Camilo, Jaimes, Camilo, Soldatelli, Matheus D., Warfield, Simon K., Gholipour, Ali, and Karimi, Davood
- Subjects
Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
Diffusion-weighted Magnetic Resonance Imaging (dMRI) is increasingly used to study the fetal brain in utero. An important computation enabled by dMRI is streamline tractography, which has unique applications such as tract-specific analysis of the brain white matter and structural connectivity assessment. However, due to the low fetal dMRI data quality and the challenging nature of tractography, existing methods tend to produce highly inaccurate results. They generate many false streamlines while failing to reconstruct streamlines that constitute the major white matter tracts. In this paper, we advocate for anatomically constrained tractography based on an accurate segmentation of the fetal brain tissue directly in the dMRI space. We develop a deep learning method to compute the segmentation automatically. Experiments on independent test data show that this method can accurately segment the fetal brain tissue and drastically improve tractography results. It enables the reconstruction of highly curved tracts such as optic radiations. Importantly, our method infers the tissue segmentation and streamline propagation direction from a diffusion tensor fit to the dMRI data, making it applicable to routine fetal dMRI scans. The proposed method can lead to significant improvements in the accuracy and reproducibility of quantitative assessment of the fetal brain with dMRI.
- Published
- 2024
16. Consumption of food markers of a healthy diet according to racial groups of women in Brazil
- Author
-
Furtado de Figueiredo Neta, Joana, Calixto Gomes, Samara, Carneiro Alves de Oliveira, Bruno Luciano, Lima Sousa Henrique, Thayna de, Freire de Freitas, Roberto Wagner Junior, Gomes Guedes, Nirla, Bezerra Pinheiro, Ana Karina, and Coelho Damasceno, Marta Maria
- Published
- 2024
- Full Text
- View/download PDF
17. Implications of molecular classifications in glioma surgery
- Author
-
Kalluri, Anita L., Lee, Joyce H., Lucas, Calixto-Hope G., Rincon-Torroella, Jordina, and Bettegowda, Chetan
- Published
- 2024
- Full Text
- View/download PDF
18. Molecular characterization of gliosarcoma reveals prognostic biomarkers and clinical parallels with glioblastoma
- Author
-
Chen, Lucy, Rizk, Emanuelle, Sherief, Mohamed, Chang, Michael, Lucas, Calixto-Hope, Bettegowda, Chetan, Croog, Victoria, Mukherjee, Debraj, Rincon-Torroella, Jordina, Kamson, David Olayinka, Huang, Peng, Holdhoff, Matthias, and Schreck, Karisa
- Published
- 2024
- Full Text
- View/download PDF
19. Plant traits and seasonality shape coexistence and niche segregation patterns among spider species
- Author
-
da Silva Filho, Fábio Carlos, Stefani, Vanessa, and Calixto, Eduardo Soares
- Published
- 2024
- Full Text
- View/download PDF
20. Impact of upfront adjuvant chemoradiation on survival in patients with molecularly defined oligodendroglioma: the benefits of PCV over TMZ
- Author
-
Rincon-Torroella, Jordina, Rakovec, Maureen, Kalluri, Anita L., Jiang, Kelly, Weber-Levine, Carly, Parker, Megan, Raj, Divyaansh, Materi, Josh, Sepehri, Sadra, Ferres, Abel, Schreck, Karisa C., Aldecoa, Iban, Lucas, Calixto-Hope G., Sair, Haris I., Redmond, Kristin J., Holdhoff, Matthias, Weingart, Jon, Brem, Henry, Sánchez, Josep J. González, Ye, Xiaobu, and Bettegowda, Chetan
- Published
- 2024
- Full Text
- View/download PDF
21. Primary seed dispersal spatial patterns of Juglansjamaicensis C. DC. subsp. jamaicensis
- Author
-
José Luis Rodríguez Sosa, Calixto Aguilar Espinosa, and José Yulier Rodríguez Milanés
- Subjects
Juglans jamaicensis ,dispersión ,semillas ,sombra de semillas. ,Environmental sciences ,GE1-350 ,Ecology ,QH540-549.5 - Abstract
This work was carried out in two Zonal Units of Conservation of the Turquino National Park, with the seeds of seven trees in six locations, to characterize the dispersal of the seeds of Juglansjamaicensis subsp. jamaicensis in a protected area of national significance. For this, it was determined the dispersion of the seeds in parcels of 1 x 1 m located each 2 m along four 50-m length radial transects, guided toward the four cardinal points, from the base of the donating tree of seeds. Results revealed that the density of the seeds of Juglansjamaicensis dispersed on the surface of the ground, declined markedly with the distance from the plant. Maximum seed-dispersal distance was 23 m, and average distance was 13 m around the trees, comprising 84% of dispersed seeds. Seed dispersal varied among the cardinal points, resulting in an asymmetric distribution pattern biased toward the north, as consequence of the land slope. Seed density on the ground surface averages 12 seeds per m2, forming a small seed bank under natural conditions. These elements constitute indicators of fragility of the species in front of interferences and external factors as well as the contagious distribution pattern of the species in the forest.
- Published
- 2018
22. Quantum revivals in HgTe/CdTe quantum wells and topological phase transitions
- Author
-
Mayorgas, A., Calixto, M., Cordero, N. A., Romera, E., and Castaños, O.
- Subjects
Condensed Matter - Mesoscale and Nanoscale Physics ,Quantum Physics - Abstract
The time evolution of a wave packet is a tool to detect topological phase transitions in two-dimensional Dirac materials, such as graphene and silicene. Here we extend the analysis to HgTe/CdTe quantum wells and study the evolution of their electron current wave packet, using 2D effective Dirac Hamiltonians and different layer thicknesses. We show that the two different periodicities that appear in this temporal evolution reach a minimum near the critical thickness, where the system goes from normal to inverted regime. Moreover, the maximum of the electron current amplitude changes with the layer thickness, identifying that current maxima reach their higher value at the critical thickness. Thus, we can characterize the topological phase transitions in terms of the periodicity and amplitude of the electron currents., Comment: 10 pages, 10 figures, 1 table
- Published
- 2024
23. Relationship between morphology and dispersion of Juglansjamaicensis DC with the distance to the water course
- Author
-
José Luis Rodríguez Sosa, Calixto Aguilar Espinosa, and Yosmel Valdés Roblejo
- Subjects
Environmental sciences ,GE1-350 ,Ecology ,QH540-549.5 - Abstract
The study was conducted in the Turquino National Park in the Zonal Conservation Units Santo Domingo and La Platica, to establish the relationship between the shape of the seeds of Juglansjamaicensis and distance to waterways as an adaptive response to their dispersal mechanism 7 groups of trees were selected. Each player is taken tree seeds 50 which were performed measurements of height (H), width (L) and thickness (E) to determine the rate of roundness (R). The distance of each tree nearest the course of water was also measured. The relationship between the two variables was performed through a simple correlation analysis; however the comparison of means was through a simple ANOVA, while the distribution of the shape of the seeds in relation to the distance to the watercourse was analyzed through the Tukey test. Those trees closer to water courses had more round seeds, indicating that the mechanism of scattering by water influences the environment in which they live. The roundness index varied and seeds were identified with rates ranging from medium to high (0, 81 to 1, 12; mean = 1, 01). These results suggest that the shape of the seeds is an adaptation of trees J. jamaicensis the medium in response to dispersal mechanism for water.
- Published
- 2017
24. Analysis occupancy by lianas in the montane rain forest Turquino National Park
- Author
-
José Luis Rodríguez Sosa, Calixto Aguilar Espinosa, and José Yulier Rodríguez Milanés
- Subjects
bejucos, bosque pluvial montano, estructura de bosque, Parque Nacional Turquino ,Environmental sciences ,GE1-350 ,Ecology ,QH540-549.5 - Abstract
The study was conducted in the montane rain forest Turquino National Park in order to assess the occupation of the trees by vines. 70 plots of 10 x 10 m with a random sampling were established and individuals with more than 5 cm were recorded d 1,30 m. To establish the influence of lianas on forest structure, the occupancy rate was determined by lianas on trees recital 4 categories. The flora included 42 families, 66 genera, 74 species. The trees were distributed in 35 families, 58 genera and 65 species, while vines were grouped into seven families, genera and 9 8 species. Flora had a high percentage of involvement by lianas (74%), and 22% of its trees are busy with vines in the glass and around the tree, which limits flowering and fruiting. Gouania polygama and Cissus verticillata vines were most involved in the occupation of the trees. The greater involvement of lianas occurs in young trees from 6 to 10 cm in diameter, which affects forest management for forest conservation, as these trees are a clearing house for the vines reach the forest canopy. Threatened species Juglans jamaicensis and Magnolia cubensis subsp. cubensis showed involvement of its individuals between 33 and 81%, their risk by reducing their fertility potential.
- Published
- 2016
25. LA GESTIÓN DE LOS PROYECTOS CONSTRUCTIVOS MEDIANTE UNA VISIÓN HOLÍSTICA DE LA SOSTENIBILIDAD
- Author
-
Cely Calixto, Nelson Javier, Gallardo Amaya, Romel Jesús, and Zafra Mejia, Carlos Alfonso
- Published
- 2024
- Full Text
- View/download PDF
26. Coping with the COVID-19 Pandemic: Comparative Case Study of Coping and Resilience in Children from Different Educational Contexts in Colombia
- Author
-
Maria Fernanda Gonzalez-Puerto, Ingrid Anzelin, Sebastian Calixto, and Roberto Alvira
- Abstract
In 2020, humanity experienced one of the most complex situations in history: The COVID-19 pandemic, which caused significant social, economic, and educational consequences. Nevertheless, countries and people generally survived. Why? Resilience and the ability to cope are fundamental elements in human, community, and national survival. This study compared the situations experienced by six children from different social and educational backgrounds in Colombia during the COVID-19 pandemic using a collective analysis of cases. Interviews with children's families, as well as observations of the participants and a narrative instrument from the BASIC Ph resiliency model (Lahad, 2016) are used to describe the context, the promoting factors of resilience, and the so-called coping "channels" of each case. Results showed that (a) the difficulties perceived by families during the pandemic were different from those perceived by the children, and (b) the predominant coping channels had an important relationship with factors that promote resilience. Finally, although it is not clear from the present study whether the children developed resilience, they exhibited factors that determine their future development.
- Published
- 2023
27. Migraine aura discrimination using machine learning: an fMRI study during ictal and interictal periods
- Author
-
Fernandes, Jr, Orlando, Ramos, Lucas Rego, Acchar, Mariana Calixto, and Sanchez, Tiago Arruda
- Published
- 2024
- Full Text
- View/download PDF
28. How land use affects freshwater zooplankton communities: a global overview
- Author
-
Dos Santos, Natan Guilherme, Chiarelli, Laura Jardim, Morari, Pedro Henrique Ribeiro, de Souza, Maria Eduarda Turcato, Calixto, Guilherme, Kato, Brendown Eiji Dias, Del Pino Rodrigues, Gabriel Liboni, Figueira, Luana Cássia, and Castilho-Noll, Maria Stela Maioli
- Published
- 2024
- Full Text
- View/download PDF
29. A Machine Learning Approach for Analyzing Residual Stress Distribution in Cold Spray Coatings
- Author
-
Aparco, Rosa Huaraca, Tapia-Tadeo, Fidelia, Ascarza, Yajhayda Bellido, Ramírez, Alexis León, Huamán-Romaní, Yersi-Luis, and Otero, Calixto Cañari
- Published
- 2024
- Full Text
- View/download PDF
30. Association between ultra-processed food and snacking behavior in Brazil
- Author
-
Gombi-Vaca, Maria Fernanda, Martinez-Steele, Euridice, Andrade, Giovanna Calixto, Louzada, Maria Laura da Costa, and Levy, Renata Bertazzi
- Published
- 2024
- Full Text
- View/download PDF
31. LLM aided semi-supervision for Extractive Dialog Summarization
- Author
-
Mishra, Nishant, Sahu, Gaurav, Calixto, Iacer, Abu-Hanna, Ameen, and Laradji, Issam H.
- Subjects
Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
Generating high-quality summaries for chat dialogs often requires large labeled datasets. We propose a method to efficiently use unlabeled data for extractive summarization of customer-agent dialogs. In our method, we frame summarization as a question-answering problem and use state-of-the-art large language models (LLMs) to generate pseudo-labels for a dialog. We then use these pseudo-labels to fine-tune a chat summarization model, effectively transferring knowledge from the large LLM into a smaller specialized model. We demonstrate our method on the \tweetsumm dataset, and show that using 10% of the original labelled data set we can achieve 65.9/57.0/61.0 ROUGE-1/-2/-L, whereas the current state-of-the-art trained on the entire training data set obtains 65.16/55.81/64.37 ROUGE-1/-2/-L. In other words, in the worst case (i.e., ROUGE-L) we still effectively retain 94.7% of the performance while using only 10% of the data., Comment: to be published in EMNLP Findings
- Published
- 2023
32. ViLMA: A Zero-Shot Benchmark for Linguistic and Temporal Grounding in Video-Language Models
- Author
-
Kesen, Ilker, Pedrotti, Andrea, Dogan, Mustafa, Cafagna, Michele, Acikgoz, Emre Can, Parcalabescu, Letitia, Calixto, Iacer, Frank, Anette, Gatt, Albert, Erdem, Aykut, and Erdem, Erkut
- Subjects
Computer Science - Computation and Language ,Computer Science - Artificial Intelligence ,Computer Science - Computer Vision and Pattern Recognition - Abstract
With the ever-increasing popularity of pretrained Video-Language Models (VidLMs), there is a pressing need to develop robust evaluation methodologies that delve deeper into their visio-linguistic capabilities. To address this challenge, we present ViLMA (Video Language Model Assessment), a task-agnostic benchmark that places the assessment of fine-grained capabilities of these models on a firm footing. Task-based evaluations, while valuable, fail to capture the complexities and specific temporal aspects of moving images that VidLMs need to process. Through carefully curated counterfactuals, ViLMA offers a controlled evaluation suite that sheds light on the true potential of these models, as well as their performance gaps compared to human-level understanding. ViLMA also includes proficiency tests, which assess basic capabilities deemed essential to solving the main counterfactual tests. We show that current VidLMs' grounding abilities are no better than those of vision-language models which use static images. This is especially striking once the performance on proficiency tests is factored in. Our benchmark serves as a catalyst for future research on VidLMs, helping to highlight areas that still need to be explored., Comment: Preprint. 48 pages, 22 figures, 10 tables
- Published
- 2023
33. Explainable Artificial Intelligence for Drug Discovery and Development -- A Comprehensive Survey
- Author
-
Alizadehsani, Roohallah, Oyelere, Solomon Sunday, Hussain, Sadiq, Calixto, Rene Ripardo, de Albuquerque, Victor Hugo C., Roshanzamir, Mohamad, Rahouti, Mohamed, and Jagatheesaperumal, Senthil Kumar
- Subjects
Computer Science - Artificial Intelligence ,I.2.0 - Abstract
The field of drug discovery has experienced a remarkable transformation with the advent of artificial intelligence (AI) and machine learning (ML) technologies. However, as these AI and ML models are becoming more complex, there is a growing need for transparency and interpretability of the models. Explainable Artificial Intelligence (XAI) is a novel approach that addresses this issue and provides a more interpretable understanding of the predictions made by machine learning models. In recent years, there has been an increasing interest in the application of XAI techniques to drug discovery. This review article provides a comprehensive overview of the current state-of-the-art in XAI for drug discovery, including various XAI methods, their application in drug discovery, and the challenges and limitations of XAI techniques in drug discovery. The article also covers the application of XAI in drug discovery, including target identification, compound design, and toxicity prediction. Furthermore, the article suggests potential future research directions for the application of XAI in drug discovery. The aim of this review article is to provide a comprehensive understanding of the current state of XAI in drug discovery and its potential to transform the field., Comment: 13 pages, 3 figures
- Published
- 2023
34. Functional interactions between neurofibromatosis tumor suppressors underlie Schwann cell tumor de-differentiation and treatment resistance.
- Author
-
Vasudevan, Harish, Payne, Emily, Delley, Cyrille, John Liu, S, Mirchia, Kanish, Sale, Matthew, Lastella, Sydney, Nunez, Maria, Lucas, Calixto-Hope, Eaton, Charlotte, Casey-Clyde, Tim, Magill, Stephen, Chen, William, Braunstein, Steve, Perry, Arie, Jacques, Line, Reddy, Alyssa, Pekmezci, Melike, Abate, Adam, Mccormick, Frank, and Raleigh, David
- Subjects
Animals ,Humans ,Mice ,Mitogen-Activated Protein Kinase Kinases ,Neurilemmoma ,Neurofibromatoses ,Neurofibromatosis 1 ,Neurofibromatosis 2 ,Schwann Cells ,Drug Resistance ,Neoplasm - Abstract
Schwann cell tumors are the most common cancers of the peripheral nervous system and can arise in patients with neurofibromatosis type-1 (NF-1) or neurofibromatosis type-2 (NF-2). Functional interactions between NF1 and NF2 and broader mechanisms underlying malignant transformation of the Schwann lineage are unclear. Here we integrate bulk and single-cell genomics, biochemistry, and pharmacology across human samples, cell lines, and mouse allografts to identify cellular de-differentiation mechanisms driving malignant transformation and treatment resistance. We find DNA methylation groups of Schwann cell tumors can be distinguished by differentiation programs that correlate with response to the MEK inhibitor selumetinib. Functional genomic screening in NF1-mutant tumor cells reveals NF2 loss and PAK activation underlie selumetinib resistance, and we find that concurrent MEK and PAK inhibition is effective in vivo. These data support a de-differentiation paradigm underlying malignant transformation and treatment resistance of Schwann cell tumors and elucidate a functional link between NF1 and NF2.
- Published
- 2024
35. Maximal Integral Inequalities and Hausdorff–Young
- Author
-
Calderón, Calixto P. and Torchinsky, Alberto
- Published
- 2024
- Full Text
- View/download PDF
36. Novel SOX10 indel mutations drive schwannomas through impaired transactivation of myelination gene programs
- Author
-
Williams, Erik A, Ravindranathan, Ajay, Gupta, Rohit, Stevers, Nicholas O, Suwala, Abigail K, Hong, Chibo, Kim, Somang, Yuan, Jimmy Bo, Wu, Jasper, Barreto, Jairo, Lucas, Calixto-Hope G, Chan, Emily, Pekmezci, Melike, LeBoit, Philip E, Mully, Thaddeus, Perry, Arie, Bollen, Andrew, Van Ziffle, Jessica, Devine, W Patrick, Reddy, Alyssa T, Gupta, Nalin, Basnet, Kristen M, Macaulay, Robert JB, Malafronte, Patrick, Lee, Han, Yong, William H, Williams, Kevin Jon, Juratli, Tareq A, Mata, Douglas A, Huang, Richard SP, Hiemenz, Matthew C, Pavlick, Dean C, Frampton, Garrett M, Janovitz, Tyler, Ross, Jeffrey S, Chang, Susan M, Berger, Mitchel S, Jacques, Line, Song, Jun S, Costello, Joseph F, and Solomon, David A
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Pediatric ,Cancer ,Human Genome ,Neurosciences ,Biotechnology ,Genetics ,Rare Diseases ,Aetiology ,2.1 Biological and endogenous factors ,Humans ,INDEL Mutation ,Transcriptional Activation ,Neurilemmoma ,Neuroma ,Acoustic ,Mutation ,Nerve Sheath Neoplasms ,SOXE Transcription Factors ,myelination ,PMP2 ,Schwann cell ,schwannoma ,SOX10 ,Oncology and Carcinogenesis ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
BackgroundSchwannomas are common peripheral nerve sheath tumors that can cause severe morbidity given their stereotypic intracranial and paraspinal locations. Similar to many solid tumors, schwannomas and other nerve sheath tumors are primarily thought to arise due to aberrant hyperactivation of the RAS growth factor signaling pathway. Here, we sought to further define the molecular pathogenesis of schwannomas.MethodsWe performed comprehensive genomic profiling on a cohort of 96 human schwannomas, as well as DNA methylation profiling on a subset. Functional studies including RNA sequencing, chromatin immunoprecipitation-DNA sequencing, electrophoretic mobility shift assay, and luciferase reporter assays were performed in a fetal glial cell model following transduction with wildtype and tumor-derived mutant isoforms of SOX10.ResultsWe identified that nearly one-third of sporadic schwannomas lack alterations in known nerve sheath tumor genes and instead harbor novel recurrent in-frame insertion/deletion mutations in SOX10, which encodes a transcription factor responsible for controlling Schwann cell differentiation and myelination. SOX10 indel mutations were highly enriched in schwannomas arising from nonvestibular cranial nerves (eg facial, trigeminal, vagus) and were absent from vestibular nerve schwannomas driven by NF2 mutation. Functional studies revealed these SOX10 indel mutations have retained DNA binding capacity but impaired transactivation of glial differentiation and myelination gene programs.ConclusionsWe thus speculate that SOX10 indel mutations drive a unique subtype of schwannomas by impeding proper differentiation of immature Schwann cells.
- Published
- 2023
37. Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses
- Author
-
Chen, William C, Choudhury, Abrar, Youngblood, Mark W, Polley, Mei-Yin C, Lucas, Calixto-Hope G, Mirchia, Kanish, Maas, Sybren LN, Suwala, Abigail K, Won, Minhee, Bayley, James C, Harmanci, Akdes S, Harmanci, Arif O, Klisch, Tiemo J, Nguyen, Minh P, Vasudevan, Harish N, McCortney, Kathleen, Yu, Theresa J, Bhave, Varun, Lam, Tai-Chung, Pu, Jenny Kan-Suen, Li, Lai-Fung, Leung, Gilberto Ka-Kit, Chan, Jason W, Perlow, Haley K, Palmer, Joshua D, Haberler, Christine, Berghoff, Anna S, Preusser, Matthias, Nicolaides, Theodore P, Mawrin, Christian, Agnihotri, Sameer, Resnick, Adam, Rood, Brian R, Chew, Jessica, Young, Jacob S, Boreta, Lauren, Braunstein, Steve E, Schulte, Jessica, Butowski, Nicholas, Santagata, Sandro, Spetzler, David, Bush, Nancy Ann Oberheim, Villanueva-Meyer, Javier E, Chandler, James P, Solomon, David A, Rogers, C Leland, Pugh, Stephanie L, Mehta, Minesh P, Sneed, Penny K, Berger, Mitchel S, Horbinski, Craig M, McDermott, Michael W, Perry, Arie, Bi, Wenya Linda, Patel, Akash J, Sahm, Felix, Magill, Stephen T, and Raleigh, David R
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Cancer ,Clinical Research ,Brain Disorders ,Brain Cancer ,Rare Diseases ,4.2 Evaluation of markers and technologies ,Detection ,screening and diagnosis ,Humans ,Biomarkers ,Gene Expression Profiling ,Meningeal Neoplasms ,Meningioma ,Neoplasm Recurrence ,Local ,Prospective Studies ,Medical and Health Sciences ,Immunology ,Biomedical and clinical sciences ,Health sciences - Abstract
Surgery is the mainstay of treatment for meningioma, the most common primary intracranial tumor, but improvements in meningioma risk stratification are needed and indications for postoperative radiotherapy are controversial. Here we develop a targeted gene expression biomarker that predicts meningioma outcomes and radiotherapy responses. Using a discovery cohort of 173 meningiomas, we developed a 34-gene expression risk score and performed clinical and analytical validation of this biomarker on independent meningiomas from 12 institutions across 3 continents (N = 1,856), including 103 meningiomas from a prospective clinical trial. The gene expression biomarker improved discrimination of outcomes compared with all other systems tested (N = 9) in the clinical validation cohort for local recurrence (5-year area under the curve (AUC) 0.81) and overall survival (5-year AUC 0.80). The increase in AUC compared with the standard of care, World Health Organization 2021 grade, was 0.11 for local recurrence (95% confidence interval 0.07 to 0.17, P
- Published
- 2023
38. NF1 expression profiling in IDH-wildtype glioblastoma: genomic associations and survival outcomes
- Author
-
Michael Chang, Mohamed Sherief, Maria Ioannou, Viveka Chinnasamy, Lucy Chen, Michael Frost, Michelle Mattson-Hoss, Herb Sarnoff, David O. Kamson, Matthias Holdhoff, Debraj Mukherjee, Chetan Bettegowda, Jordina Rincon-Torroella, Victoria Croog, Peng Huang, Fausto J. Rodriguez, Calixto-Hope G. Lucas, and Karisa C. Schreck
- Subjects
Neurofibromin ,NF1 ,Biomarker ,Glioblastoma ,High-grade glioma ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Background NF1 inactivation is associated with sensitivity to MEK inhibitor targeted therapy in low-grade and some high-grade gliomas. NF1 loss may also be a harbinger of exploitable vulnerabilities in IDH-wildtype glioblastoma (GBM). Accurate and consistent detection of NF1 loss, however, is fraught given the large gene size, challenges with complete coverage and variant calling upon sequencing, and mechanisms of mRNA and protein regulation that result in early degradation in the absence of genomic alterations. Here, we seek to perform a composite analysis for NF1 loss accounting for genomic alterations and protein expression via immunohistochemistry. We also characterize the landscape of NF1 alterations in GBM. Methods We assembled a single-institution, retrospective cohort of 542 IDH-wildtype GBM with somatic next generation sequencing to investigate the frequency and nature of detected NF1 alterations. We selected 69 GBMs from which to build a tissue microarray (TMA) of 44 NF1-wildtype and 25 NF1-mutant cases. We performed NF1 immunohistochemistry using two different NF1 antibodies (NFC, Sigma-Aldrich; and iNF-07E, iNFixion Bioscience) and correlated results with clinical, genomic, and other immunohistochemical features. Results In our retrospective cohort, we identified 88 IDH-wildtype GBM with NF1 alterations (16%). NF1 alterations were mutually exclusive with EGFR and MDM2 alterations (p-adj
- Published
- 2024
- Full Text
- View/download PDF
39. Evaluation of efficacy and safety in the use of cytarabine for mobilization of hematopoietic stem cells in a reference hospital in northeastern Brazil
- Author
-
Kaio José Santos de Andrade, Luís Fábio Barbosa Botelho, Rodolfo Froes Calixto, Manuela Gomes de Oliveira, Leina Yukari Etto, and Luiz Victor Maia Loureiro
- Subjects
Hematopoietic stem cell transplantation ,Hematopoietic stem cell mobilization ,Ara-C ,Diseases of the blood and blood-forming organs ,RC633-647.5 - Abstract
Autologous hematopoietic stem cell transplantation (Auto-HSCT) is widely used in the treatment of patients with hematological neoplasms. Since these cells circulate in small quantities in the periphery, the use of regimens that promote their mobilization is essential. In this study, we retrospectively evaluated the efficacy and safety of using intermediate doses of cytarabine (1.6 g/m²) + filgrastim (10 mcg/kg/day) in the mobilization of stem cells in 157 patients treated by the Unified Health System at the Hematology and Bone Marrow Transplant Service of the Hospital Real Português de Beneficência, in Recife, Pernambuco. The sample included patients with multiple myeloma (MM) (58.6 %), lymphomas (29.9 %), and other neoplasms (11.5 %). The target of 2.0 × 10 6 CD34+ cells/kg was achieved by 148 (94.3 %) patients, in most cases (84.1 %) in a single apheresis and the median number of cells collected was 9.5 × 10 6 CD34+ cells/kg. No episode of febrile neutropenia was observed, however, 79 patients (50.3 %) required platelet transfusion (no cases attributed to bleeding). The median engraftment time was 11 days. Given these results, we suggest that the use of intermediate doses of cytarabine, combined with filgrastim, is safe and effective in mobilizing hematopoietic stem cells (HSCs).
- Published
- 2024
- Full Text
- View/download PDF
40. Salivary detection of Chikungunya virus infection using a portable and sustainable biophotonic platform coupled with artificial intelligence algorithms
- Author
-
Marco Guevara-Vega, Rafael Borges Rosa, Douglas Carvalho Caixeta, Mariana Araújo Costa, Rayany Cristina de Souza, Giulia Magalhães Ferreira, Anagê Calixto Mundim Filho, Murillo Guimarães Carneiro, Ana Carolina Gomes Jardim, and Robinson Sabino-Silva
- Subjects
ATR-FTIR ,Chikungunya virus ,Salivary diagnosis ,Machine learning algorithms ,Medicine ,Science - Abstract
Abstract The current detection method for Chikungunya Virus (CHIKV) involves an invasive and costly molecular biology procedure as the gold standard diagnostic method. Consequently, the search for a non-invasive, more cost-effective, reagent-free, and sustainable method for the detection of CHIKV infection is imperative for public health. The portable Fourier-transform infrared coupled with Attenuated Total Reflection (ATR-FTIR) platform was applied to discriminate systemic diseases using saliva, however, the salivary diagnostic application in viral diseases is less explored. The study aimed to identify unique vibrational modes of salivary infrared profiles to detect CHIKV infection using chemometrics and artificial intelligence algorithms. Thus, we intradermally challenged interferon-gamma gene knockout C57/BL6 mice with CHIKV (20 µl, 1 X 105 PFU/ml, n = 6) or vehicle (20 µl, n = 7). Saliva and serum samples were collected on day 3 (due to the peak of viremia). CHIKV infection was confirmed by Real-time PCR in the serum of CHIKV-infected mice. The best pattern classification showed a sensitivity of 83%, specificity of 86%, and accuracy of 85% using support vector machine (SVM) algorithms. Our results suggest that the salivary ATR-FTIR platform can discriminate CHIKV infection with the potential to be applied as a non-invasive, sustainable, and cost-effective detection tool for this emerging disease.
- Published
- 2024
- Full Text
- View/download PDF
41. Design, Construction and Finite Element Analysis of a Hexacopter for Precision Agriculture Applications
- Author
-
Miguel Ernesto Gutierrez-Rivera, Jesse Y. Rumbo-Morales, Gerardo Ortiz-Torres, Jose J. Gascon-Avalos, Felipe D. J. Sorcia-Vázquez, Carlos Alberto Torres-Cantero, Hector M. Buenabad-Arias, Iván Guillen-Escamilla, Maria A. López-Osorio, Manuel A. Zurita-Gil, Manuela Calixto-Rodriguez, Antonio Márquez Rosales, and Mario A. Juárez
- Subjects
UAV ,design ,finite element analysis ,ANSYS Workbench ,agriculture applications ,Engineering design ,TA174 - Abstract
Agriculture drones face important challenges regarding autonomy and construction, as flying time below the 9-minute mark is the norm, and their manufacture requires several tests and research before reaching proper flight dynamics. Therefore, correct design, analysis, and manufacture of the structure are imperative to address the aforementioned problems and ensure a robust build that withstands the tough environments of this application. In this work, the analysis and implementation of a Nylamid motor bracket, aluminum sandwich-type skeleton, and carbon fiber tube arm in a 30 kg agriculture drone is presented. The mechanical response of these components is evaluated using the finite element method in ANSYS Workbench, and the material behavior assumptions are assessed using a universal testing machine before their implementations. The general description of these models and the numerical results are presented. This early prediction of the behavior of the structure allows for mass optimization and cost reductions. The fast dynamics of drone applications set important restrictions in ductile materials such as this, requiring extensive structural analysis before manufacture. Experimental and numerical results showed a maximum variation of 8.7% for the carbon fiber composite and 13% for the Nylamid material. The mechanical properties of polyamide nylon allowed for a 51% mass reduction compared to a 6061 aluminum alloy structure optimized for the same load case in the motor brackets design. The low mechanical complexity of sandwich-type skeletons translated into fast implementation. Finally, the overall performance of the agriculture drone is evaluated through the data gathered during the flight test, showing the adequate design process.
- Published
- 2024
- Full Text
- View/download PDF
42. Self-Efficacy in Nursing Competencies during Students’ Clinical Practicum: The Development of a Self-Assessment Scale
- Author
-
Juan Arribas-Marín, Calixto Plumed-Moreno, and Vicente Hernández-Franco
- Subjects
nursing education ,clinical competence ,clinical practice ,latent class analysis ,questionnaire design ,validation study ,Nursing ,RT1-120 - Abstract
The evaluation of the competencies corresponding to the different professional profiles of future nursing graduates is fundamental to their training. In this regard, students’ self-evaluation must be part of their training. This study aimed to develop and psychometrically test the Perceived Self-Efficacy in Nursing Competencies (PSENC) Scale. This study was conducted in two phases: selecting and adjusting items and assessing the instrument’s psychometric properties. A sample of 1416 students completed the scale online. Exploratory factor and confirmatory factor analyses were conducted. Inferential analysis was carried out. The exploratory factor analysis of the PSENC scale with 20 items resulted in five factors (76.3% of variance). All factors showed Cronbach’s alpha coefficients > 0.70. The confirmatory factor analysis measurement model showed satisfactory and adequate goodness-of-fit indices. The developed scale showed the psychometric adequacy and usefulness to the self-assessment of nursing students regarding their self-efficacy expectations in competencies during their clinical practicum. This study was not registered.
- Published
- 2024
- Full Text
- View/download PDF
43. Neurological outcomes in neonates treated with therapeutic hypothermia: challenges in a developing country
- Author
-
Rita Farias Oliveira, Lucia Helena Wagner, Alexandre Sousa da Silva, Maura Calixto Cecherelli de Rodrigues, and Glenda Corrêa Borges de Lacerda
- Subjects
Hypoxia, Brain ,Hypothermia, Induced ,Neurologic Examination ,Developmental Disabilities ,Epilepsy ,Hipóxia Encefálica ,Hipotermia Induzida ,Exame Neurológico ,Deficiências do Desenvolvimento ,Epilepsia ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Background Hypoxic-ischemic encephalopathy (HIE) affects 1.5 newborns per 1 thousand term live births. Therapeutic hypothermia (TH) does not prevent all adverse outcomes. The experience with TH is still limited in Latin America. In Rio de Janeiro, Hospital Universitário Pedro Ernesto treats neonates with HIE since 2017 using the servo-controlled system.
- Published
- 2024
- Full Text
- View/download PDF
44. MerlinS13 phosphorylation regulates meningioma Wnt signaling and magnetic resonance imaging features
- Author
-
Charlotte D. Eaton, Lauro Avalos, S. John Liu, Zhenhong Chen, Naomi Zakimi, Tim Casey-Clyde, Paola Bisignano, Calixto-Hope G. Lucas, Erica Stevenson, Abrar Choudhury, Harish N. Vasudevan, Stephen T. Magill, Jacob S. Young, Nevan J. Krogan, Javier E. Villanueva-Meyer, Danielle L. Swaney, and David R. Raleigh
- Subjects
Science - Abstract
Abstract Meningiomas are associated with inactivation of NF2/Merlin, but approximately one-third of meningiomas with favorable clinical outcomes retain Merlin expression. Biochemical mechanisms underlying Merlin-intact meningioma growth are incompletely understood, and non-invasive biomarkers that may be used to guide treatment de-escalation or imaging surveillance are lacking. Here, we use single-cell RNA sequencing, proximity-labeling proteomic mass spectrometry, mechanistic and functional approaches, and magnetic resonance imaging (MRI) across meningioma xenografts and patients to define biochemical mechanisms and an imaging biomarker that underlie Merlin-intact meningiomas. We find Merlin serine 13 (S13) dephosphorylation drives meningioma Wnt signaling and tumor growth by attenuating inhibitory interactions with β-catenin and activating the Wnt pathway. MRI analyses show Merlin-intact meningiomas with S13 phosphorylation and favorable clinical outcomes are associated with high apparent diffusion coefficient (ADC). These results define mechanisms underlying a potential imaging biomarker that could be used to guide treatment de-escalation or imaging surveillance for patients with Merlin-intact meningiomas.
- Published
- 2024
- Full Text
- View/download PDF
45. Quality of life of families and siblings of children with cerebral palsy treated at a reference neurorehabilitation center in Brazil
- Author
-
Bruno Leonardo Scofano Dias, Maura Calixto Cecherelli de Rodrigues, and José Luiz Muniz Bandeira Duarte
- Subjects
Quality of life ,Family ,Siblings ,Cerebral palsy ,Pediatrics ,RJ1-570 - Abstract
Objectives: To investigate the associations between caregivers’ burden, family quality of life (QoL), and siblings’ QoL in Brazilian families of children with cerebral palsy, and to analyze siblings’ QoL using as a parameter the QoL of typically developed Brazilian children. Methods: It was a cross-sectional study. The 212 families, 212 caregivers and 131 siblings completed the Family Quality of Life Scale, Burden Interview, and KIDSCREEN-27 Child and Adolescent Version and Parents Version questionnaires at a neurorehabilitation center in southeast Brazil. Univariable and multivariable models were used. Results: Family QoL significantly worsened as caregivers’ burden increased (95 % CI -0.66 to -0.38). Caregivers’ burden was significantly lower with increasing family QoL scores (95 % CI -0.52 to -0.30). Self-reported siblings’ QoL was significantly worse than that of their typically developed peers (95 % CI -7.6 to -3.6). Self-reported siblings’ QoL was significantly lower as siblings’ age (95 % CI -2.52 to -0.59) and caregivers’ burden (95 % CI -0.35 to -0.05) increased. Parent-reported siblings’ QoL was significantly lower with increasing caregivers’ burden (95 % CI -0.45 to -0.16) and higher as family QoL increased (95 % CI 0.09 to 0.37). Conclusions: The cross-sectional nature of these data precludes any statement of causality. Family QoL worsened with higher caregivers’ burden levels. Lower caregivers’ burden scores were associated with a higher family QoL. Siblings’ QoL was impaired as compared to typically developed peers, worse among older siblings, and as caregivers’ burden increased and better with higher family QoL levels. Future multicenter studies may validate the generalizability of the present findings.
- Published
- 2024
- Full Text
- View/download PDF
46. The trajectory of head circumference and neurodevelopment in very preterm newborns during the first two years of life: a cohort study
- Author
-
Maria Luciana de Siqueira Mayrink, Letícia Duarte Villela, Maria Dalva Barbosa Baker Méio, Fernanda Valente Mendes Soares, Andrea Dunshee de Abranches, Sylvia Reis Gonçalves Nehab, Ana Beatriz Rodrigues Reis, Leticia Baptista de Paula Barros, Maura Calixto Cecherelli de Rodrigues, Saint-Clair Gomes Junior, and Maria Elisabeth Lopes Moreira
- Subjects
Head circumference ,Child development ,Preterm infants ,Follow-up ,Pediatrics ,RJ1-570 - Abstract
Objective: To evaluate the growth trajectory of head circumference and neurodevelopment, and to correlate head circumference with cognitive, language, and motor outcomes during the first two years. Method: Prospective cohort study in a tertiary hospital including 95 newborns under 32 weeks or 1500 g. Neonates who developed major neonatal morbidities were excluded. The head circumference was measured at birth, at discharge, and at term-equivalent age, 1, 3, 5, 12, 18, and 24 months of corrected age, and the Bayley Scales (Bayley-III) were applied at 12, 18 and 24 months of corrected age to assess cognitive, language and, motor domains. Scores below 85 were classified as mild/moderate deficits and scores below 70 as severe deficits. The association between head circumference Z score and Bayley scores was assessed using Pearson's correlation. The study considered a significance level of 0.05. Results: There was a decrease of -0.18 in the head circumference Z score between birth and discharge and the catch-up occurred between discharge and 1 month (an increase of 0.81 in the Z score). There was a positive correlation between head circumference and Bayley scores at 18 months. There was also a positive correlation between head circumference at discharge and at 5 months with the three domains of the Bayley. Conclusion: Serial measurements of head circumference provide knowledge of the trajectory of growth, with early catch-up between discharge and 1 month, as well as its association with neurodevelopment. Head circumference is therefore a valuable clinical marker for neurodevelopment, especially in very preterm newborns.
- Published
- 2024
- Full Text
- View/download PDF
47. Characterizing normal perinatal development of the human brain structural connectivity
- Author
-
Wu, Yihan, Vasung, Lana, Calixto, Camilo, Gholipour, Ali, and Karimi, Davood
- Subjects
Quantitative Biology - Neurons and Cognition ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
Early brain development is characterized by the formation of a highly organized structural connectome. The interconnected nature of this connectome underlies the brain's cognitive abilities and influences its response to diseases and environmental factors. Hence, quantitative assessment of structural connectivity in the perinatal stage is useful for studying normal and abnormal neurodevelopment. However, estimation of the connectome from diffusion MRI data involves complex computations. For the perinatal period, these computations are further challenged by the rapid brain development and imaging difficulties. Combined with high inter-subject variability, these factors make it difficult to chart the normal development of the structural connectome. As a result, there is a lack of reliable normative baselines of structural connectivity metrics at this critical stage in brain development. In this study, we developed a computational framework, based on spatio-temporal averaging, for determining such baselines. We used this framework to analyze the structural connectivity between 33 and 44 postmenstrual weeks using data from 166 subjects. Our results unveiled clear and strong trends in the development of structural connectivity in perinatal stage. Connection weighting based on fractional anisotropy and neurite density produced the most consistent results. We observed increases in global and local efficiency, a decrease in characteristic path length, and widespread strengthening of the connections within and across brain lobes and hemispheres. We also observed asymmetry patterns that were consistent between different connection weighting approaches. The new computational method and results are useful for assessing normal and abnormal development of the structural connectome early in life.
- Published
- 2023
48. Fixing confirmation bias in feature attribution methods via semantic match
- Author
-
Cinà, Giovanni, Fernandez-Llaneza, Daniel, Deponte, Ludovico, Mishra, Nishant, Röber, Tabea E., Pezzelle, Sandro, Calixto, Iacer, Goedhart, Rob, and Birbil, Ş. İlker
- Subjects
Computer Science - Machine Learning ,Computer Science - Artificial Intelligence - Abstract
Feature attribution methods have become a staple method to disentangle the complex behavior of black box models. Despite their success, some scholars have argued that such methods suffer from a serious flaw: they do not allow a reliable interpretation in terms of human concepts. Simply put, visualizing an array of feature contributions is not enough for humans to conclude something about a model's internal representations, and confirmation bias can trick users into false beliefs about model behavior. We argue that a structured approach is required to test whether our hypotheses on the model are confirmed by the feature attributions. This is what we call the "semantic match" between human concepts and (sub-symbolic) explanations. Building on the conceptual framework put forward in Cin\`a et al. [2023], we propose a structured approach to evaluate semantic match in practice. We showcase the procedure in a suite of experiments spanning tabular and image data, and show how the assessment of semantic match can give insight into both desirable (e.g., focusing on an object relevant for prediction) and undesirable model behaviors (e.g., focusing on a spurious correlation). We couple our experimental results with an analysis on the metrics to measure semantic match, and argue that this approach constitutes the first step towards resolving the issue of confirmation bias in XAI.
- Published
- 2023
49. Subcutaneous adipose tissue plays a beneficial effect on subclinical atherosclerosis in young survivors of acute lymphocytic leukemia
- Author
-
Siviero-Miachon AA, Spinola-Castro AM, Lee ML, Monteiro CM, Carvalho AC, Calixto AR, Geloneze B, and Guerra-Junior G
- Subjects
Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Adriana Aparecida Siviero-Miachon,1,2 Angela Maria Spinola-Castro,1,2 Maria Lucia de Martino Lee,2 Carlos Manoel de Castro Monteiro,3 Antonio Carlos de Camargo Carvalho,4 Antonio Ramos Calixto,5 Bruno Geloneze,5 Gil Guerra-Junior6 1Division of Pediatric Endocrinology, Department of Pediatrics, Federal University of Sao Paulo (UNIFESP/EPM), 2Pediatric Oncology Institute – IOP/GRAACC, Federal University of Sao Paulo (UNIFESP/EPM), 3Private Office, Castro Monteiro, Sao Paulo, 4Division of Cardiology, Federal University of Sao Paulo (UNIFESP/EPM), 5Laboratory of Investigation on Metabolism and Diabetes (LIMED), Faculty of Medical Sciences, State University of Campinas (UNICAMP), 6Division of Pediatric Endocrinology, Department of Pediatrics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Brazil Purpose: The aim of this study was to evaluate the relationship between body composition, metabolic profile, adipokines, and carotid intima-media thickness (cIMT) in young survivors of childhood acute lymphocytic leukemia (ALL). Patients and methods: This cross-sectional study compared 55 ALL survivors, of chronological age between 15 years and 24 years, assigned into two groups according to the exposure to cranial radiation therapy (CRT; 25 irradiated and 30 nonirradiated) with 24 leukemia-free controls, and assessed body fat mass (dual-energy X-ray absorptiometry), computed tomography scan-derived abdominal adipose tissue, lipid profile, blood pressure (BP), adipokines, and cIMT by a multiple regression analysis. Results: Treatment with CRT had an effect on all of the variables derived from the computed tomography scan: visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) (P
- Published
- 2015
50. Diametric and status structure, mortality and recruitment of Juglans jamaicensis C. DC., in the Turquino National Park
- Author
-
José Luis Rodríguez Sosa, Calixto Aguilar Espinosa, and José Yulier Rodríguez Milanés
- Subjects
Juglans jamaicensis, reclutamiento, estructura, plántula, mortalidad. ,Environmental sciences ,GE1-350 ,Ecology ,QH540-549.5 - Abstract
The work was done in the Turquino National Park in order to analyze the diametric structure, mortality and recruitment of Juglans jamaicensis C. DC., for the diagnosis of its condition. The diametric structure from 5 cm width classes and the taxon state structure was characterized. Dynamics of the species through the registration of all individuals for three consecutive years (2011-2013) was evaluated, and parameters determining the average annual death rate, annual rate of change and the finite rate of natural increase. In addition, the relationship between seedling abundance and exposure to light through a correspondence analysis was determined. It was found that Juglans jamaicensis presents an irregular diametric structure denoting a good reproduction and recruitment failure of its groups of trees in the forest, suggesting some imbalance between mortality and recruitment. The growth and retention of individuals are the parameters that have the greatest influence in maintaining Juglans jamaicensis in the forest since the rate indicators mean annual mortality rate of population change and finite natural growth rate reflect high mortality seedling stage as more vulnerable life cycle of the species phase, indicating a recruitment and population stability is not favorable. Tolerance of seedlings of Juglans jamaicensis in the first two years of life was confirmed.
- Published
- 2015
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.