G. Montero González

University of California, Davis

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Javier Arsuaga

University of California, Davis

Tyler Borrman

University of Massachusetts Chan Medical School

Mirna Alvarenga

National Autonomous University of Honduras

Stella R. Hartono

University of California, Davis

Morgan Martin

Harvard University

N.I. Núñez Morales

Loma Linda University

A.M. González Pinto Arrillaga

Hospital Universitario Araba

Manda Riehl

Rose–Hulman Institute of Technology

Jon Gaviña Arenaza

Hospital Universitario Araba

Catherine Park

University of California, San Francisco

Cooperative Institutions

Hospital Universitario Araba

University of California, Davis

Osakidetza

Consejo Superior de Investigaciones Científicas

Marqués de Valdecilla University Hospital

University of California, San Francisco

Universidad de Ciencias Médicas de Cienfuegos

Universidad de Valladolid

Forest Science and Technology Centre of Catalonia

Instituto de Ciencias Forestales

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Modelos dinámicos dependientes e independientes de la edad: crecimiento en diámetro de Quercus ilex L. en dehesas

Cuadernos de la Sociedad Española de Ciencias Forestales (2007)

Guillermo Gea Izquierdo Isabel Cañellas E. Garriga García G. Montero González

Quercus ilex (encina) es la especie arborea mas representada en las dehesas y la frondosa mas extendida en Espana. Pese a ello, no existen modelos de crecimiento publicados para esta especie en el oeste peninsular que nos permitan simular el crecimiento de estas masas asi como predecir estructuras y producciones futuras. En este trabajo se estudia el crecimiento en diametro de la encina en las dehesas, comparando modelos dinamicos dependientes e independientes de la edad y discutiendo su aplicabilidad y la distribucion del error medio. En los modelos independientes de la edad el error aumento respecto a los modelos dependientes de la edad, aunque se mantuvo menor del 15% en las clases diametricas entre 15 y 50 cm. Por ello consideramos que su uso puede resultar muy interesante cuando no se conozca la edad de los arboles estudiados (la practica totalidad de los casos), aceptando que el error cometido es mayor que en modelos que incluyen la edad como covariable. Se muestra ademas como resulta indispensable analizar el error con los parametros ajustados teniendo en cuenta la autocorrelacion serial, pero sin incluir el termino autoregresivo. En estructuras de datos tan autocorrelacionados como las que se usan en analisis de crecimiento en diametro cuando se analizan secciones del fuste, la influencia del termino autoregresivo enmascara el comportamiento predictivo, pudiendo falsear la seleccion de los modelos.

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Alzheimer’s & Neurodegenerative Diseases (2017)

Julio López Argüelles Julio López Argüelles Aleima Rodríguez Carvajal G. Montero González M Leydi

Introduction:Parkinson Disease (PD) although described initially by James Parkinson as a disease with motor disorder it has been demonstrated that the cognitive disorders in the form of disejecutive syndrome are frequent worsening with the evolution.Objective: To characterize the Frontal Dysfunction (FD) in the patients with PD and to determine the factors related with frontal dysfunction in early stages. Method:We studied 125 patients with diagnosis of idiopathic PD and Hoehn and Yahr Stages <2, to those which it was carried to them out survey with demographic, clinical and neuropsychological data studies included the Frontal Assessment Battery (FAB). Results:The mean age was of 68.1±8.6, the onset age was of 62.6±10.5, the diestrums predominated and those which initiated with tremor.Of the 125 patients 71.4% presented FD, with an average of the FAB of 11.82±3.7.The age (R=-0.45;p<0.001) and onset age (R=-0.33;p=0.02) showed inversely proportional correlation with the FD.Other related variables were the schooling up to second level (p=0.003) and the rural origin with significance <0.001. Conclusion:The age and onset age higher than 60 years, the lower schooling than second level of teaching, rural origin and the presence of cognitive dysfunction are related to FD in early stages of PD.

10.24966/and-9608/vol3iss2

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Benzodiazepines abstinence syndrome with psychotic symptoms: Case report

European Psychiatry (2017)

N.I. Núñez Morales Marcos Gómez‐Revuelta Brígida Hernández M. Laborde Zufiaurre A. Aranzabal Itoiz

Introduction Several studies point to the importance that the complex formed by GABA and the benzodiazepine receptor play for cerebral dopaminergic transmission and, hence, to the pathophysiology of psychotic symptoms. The decrease in GABA neuratransmisión or the hypofunction of the system in the hippocampus, cortex and other limbic prefrontal or subcortical regions has consequences as emotional dysregulation, cognitive impairment and development of positive psychotic symptoms. Objectives We intended to show an additional practical example to the limited literature available based on a case linking the emergence of psychotic symptoms due to acute benzodiazepine withdrawal. Methods We present the case of a 21 year old man who was sent to the emergency room of our hospital after an episode of aggressiveness on the street. The patient showed a psychotic schizophrenic syndrome with significant emotional and behavioural impact with aggressive and bizarre movements. In parallel, restlessness, sweating, tremor, increased blood pressure and tachycardia were observed. Symptoms had started abruptly two hours earlier. The patient companion explained that he usually took Alprazolam at an of over 40 mg per day. He had decided to give up this consumption abruptly four days earlier. Discussion GABAergic deficits cause the imbalance between excitatory and inhibitory neurotransmission that may relate the pathophysiology of psychotic symptoms. The dysfunction of the GABAergic cortical interneurons could affect to the modulating response from the association cortex, which, could also relate with the appearance of these symptoms. Conclusion This case could relate a decrease in GABAergic transmission with the appearance of psychotic symptoms. Disclosure of interest The authors have not supplied their declaration of competing interest.

Pathophysiology

10.1016/j.eurpsy.2017.01.568

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The R-loop Grammar predicts R-loop formation under different topological constraints

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Margherita Maria Ferrari Svetlana Poznanović Manda Riehl Jacob Lusk Stella R. Hartono

R-loops are transient three-stranded nucleic acids that form during transcription when the nascent RNA hybridizes with the template DNA, freeing the DNA non-template strand. There is growing evidence that R-loops play important roles in physiological processes such as control of gene expression, and that they contribute to chromosomal instability and disease. It is known that R-loop formation is influenced by both the sequence and the topology of the DNA substrate, but many questions remain about how R-loops form and the 3-dimensional structures that they adopt. Here we represent an R-loop as a word in a formal grammar called the R-loop grammar and predict R-loop formation. We train the R-loop grammar on experimental data obtained by single-molecule R-loop footprinting and sequencing (SMRF-seq). Despite not containing explicit topological information, the R-loop grammar accurately predicts R-loop formation on plasmids with varying starting topologies and outperforms previous methods in R-loop prediction.

Loop fusion

Loop fission

Footprinting

10.1101/2024.12.03.626533

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Topological Analysis of Amplicon Structure in Comparative Genomic Hybridization (CGH) Data: An Application to ERBB2/HER2/NEU Amplified Tumors

Lecture notes in computer science (2016)

Sergio Ardanza-Trevijano G. Montero González Tyler Borrman Juan Luis Garcı́a Javier Arsuaga

Amplicon

Comparative genomic hybridization

Homology

10.1007/978-3-319-39441-1_11

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APLICACIÓN DE LOS MODELOS MIXTOS A UN CASO PRÁCTICO DE MODELIZACIÓN DEL CRECIMIENTO Y PRODUCCIÓN DE LAS MASAS FORESTALES

Cuadernos de la Sociedad Española de Ciencias Forestales (2004)

R. Calama Sainz G. Montero González

Los modelos mixtos conforman una herramienta de interes para la modelizacion del crecimiento y la produccion de variables de interes forestal, al permitir el ajuste de funciones lineales sobre observaciones que no verifiquen el supuesto de independencia. En el presente trabajo se presenta una aproximacion teorica a los modelos mixtos y se muestra un caso practico de aplicacion para la modelizacion de la relacion diametro-altura.

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Patrón de crecimiento en altura dominante en masas naturales y artificiales de "pinus pinea L.": Comparación a través de modelos dinámicos

Cuadernos de la Sociedad Española de Ciencias Forestales (2007)

G. Madrigal Casanueva Rafael Alonso Ponce Jaime Valverde G. Montero González R. Calama Saínz

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CATEGORIZACION DE PATOLOGIA DE MAMA SEGÚN SISTEMA BIRADS

Revista Científica de la Escuela Universitaria de las Ciencias de la Salud (2019)

G. Montero González Mirna Alvarenga Eliza Funes Lizandro Guillen M.J. Delgado González

El sistema de datos y reporte de imagen de mama (BIRADS) es una herramienta que establece una estandarización en los informes mamográficos, para reducir la confusión en la interpretación del diagnóstico en la patología mamaria. Objetivo: Categorizar la patología mamaria detectada por el sistema BIRADS. Pacientes y Métodos: Estudio descriptivo y prospectivo, realizado a 1537 pacientes que acudieron a Mediscan para estudio de mamografía de tamizaje (mamografía de control/ anual) en el período comprendido entre enero 2014 a marzo 2015. Resultados: 560(36.2%) de los pacientes tenian edades entre 40 y 49 años, 1098(71.4%) de los pacientes presentaron factores de riesgo para cáncer de mama y los que más prevalecieron fueron biopsia previa de mama, carga genética para cáncer de mama y secreción por el pezón. El 2% fueron clasificados como BIRADS IV y V con el estudio de biopsia complementario solicitado, 10 pacientes fueron diagnosticados con Carcinoma Ductal Infiltrante. Conclusión: La relación entre los resultados mamográficos con el sistema BIRADS nos facilita el manejo de los mismos bajo recomendaciones precisas que mejoran la detección del cáncer de mama. Recomendación: Sensibilizar a las pacientes que la detección precoz es la mejor herramienta para el diagnóstico temprano. Palabras clave Determinación, Enfermedades Genéticas Congénitas, Neoplasias de la mama, Neoplasias

10.5377/rceucs.v3i1.7023

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Identification of Copy Number Aberrations in Breast Cancer Subtypes Using Persistence Topology

Microarrays (2015)

Javier Arsuaga Tyler Borrman Raymond G. Cavalcante G. Montero González Catherine Park

DNA copy number aberrations (CNAs) are of biological and medical interest because they help identify regulatory mechanisms underlying tumor initiation and evolution. Identification of tumor-driving CNAs (driver CNAs) however remains a challenging task, because they are frequently hidden by CNAs that are the product of random events that take place during tumor evolution. Experimental detection of CNAs is commonly accomplished through array comparative genomic hybridization (aCGH) assays followed by supervised and/or unsupervised statistical methods that combine the segmented profiles of all patients to identify driver CNAs. Here, we extend a previously-presented supervised algorithm for the identification of CNAs that is based on a topological representation of the data. Our method associates a two-dimensional (2D) point cloud with each aCGH profile and generates a sequence of simplicial complexes, mathematical objects that generalize the concept of a graph. This representation of the data permits segmenting the data at different resolutions and identifying CNAs by interrogating the topological properties of these simplicial complexes. We tested our approach on a published dataset with the goal of identifying specific breast cancer CNAs associated with specific molecular subtypes. Identification of CNAs associated with each subtype was performed by analyzing each subtype separately from the others and by taking the rest of the subtypes as the control. Our results found a new amplification in 11q at the location of the progesterone receptor in the Luminal A subtype. Aberrations in the Luminal B subtype were found only upon removal of the basal-like subtype from the control set. Under those conditions, all regions found in the original publication, except for 17q, were confirmed; all aberrations, except those in chromosome arms 8q and 12q were confirmed in the basal-like subtype. These two chromosome arms, however, were detected only upon removal of three patients with exceedingly large copy number values. More importantly, we detected 10 and 21 additional regions in the Luminal B and basal-like subtypes, respectively. Most of the additional regions were either validated on an independent dataset and/or using GISTIC. Furthermore, we found three new CNAs in the basal-like subtype: a combination of gains and losses in 1p, a gain in 2p and a loss in 14q. Based on these results, we suggest that topological approaches that incorporate multiresolution analyses and that interrogate topological properties of the data can help in the identification of copy number changes in cancer.

Topological data analysis

Identification

Persistent Homology

10.3390/microarrays4030339

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Prediction in Cancer Genomics Using Topological Signatures and Machine Learning

Abel symposia (2020)

G. Montero González Arina Ushakova Radmila Sazdanović Javier Arsuaga

Comparative genomic hybridization

10.1007/978-3-030-43408-3_10

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