Publications by authors named "Lilian Salinas"

7 Publications

  • Page 1 of 1

Finding the fixed points of a boolean network from a positive feedback vertex set.

Bioinformatics 2020 Nov 2. Epub 2020 Nov 2.

Departamento de Ing. Informática y Cs. de la Computación and CI2MA, Universidad de Concepción, Concepción, Chile.

Motivation: In the modeling of biological systems by Boolean networks a key problem is finding the set of fixed points of a given network. Some constructed algorithms consider certain structural properties of the regulatory graph like those proposed by Akutsu et al. (1998b); Zhang et al. (2007) which consider a feedback vertex set of the graph. However, these methods do not take into account the type of action (activation, inhibition) between its components.

Results: In this paper we propose a new algorithm for finding the set of fixed points of a Boolean network, based on a positive feedback vertex set P of its regulatory graph and which works, by applying a sequential update schedule, in time O(2 |P| · n2+k), where n is the number of components and the regulatory functions of the network can be evaluated in time O(nk), k ≥ 0. The theoretical foundation of this algorithm is due a nice characterization, that we give, of the dynamical behavior of the Boolean networks without positive cycles and with a fixed point.

Availability And Implementation: An executable file of FixedPoint algorithm made in Java and some examples of input files are available at: www.inf.udec.cl/~lilian/FPCollector/.

Supplementary Information: Supplementary material is available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btaa922DOI Listing
November 2020

The use of the MSVT in children and adolescents with epilepsy.

Appl Neuropsychol Child 2020 Oct-Dec;9(4):323-328. Epub 2020 Apr 16.

Neuropsychology Service, Alberta Children's Hospital, Calgary, Canada.

Pediatric neuropsychologists are increasingly recognizing the importance of performance validity testing during evaluations. The use of such measures to detect insufficient effort is of particular importance in pediatric epilepsy evaluations, where test results are often used to guide surgical decisions and failure to detect poor task engagement can result in postsurgical cognitive decline. The present investigation assesses the utility of the Medical Symptom Validity Test (MSVT) in 104 clinically referred children and adolescents with epilepsy. Though the overall failure rate was 15.4% of the total group, children with 2nd grade or higher reading skills (a requirement of the task) passed at a very high rate (96.6%). Of the three failures, two were unequivocally deemed true positives, while the third failed due to extreme somnolence during testing. Notably, for those with ≥2nd grade reading levels, MSVT validity indices were unrelated to patient age, intellectual functioning, or age of epilepsy onset, while modest relations were seen with specific memory measures, number of epilepsy medications, and seizure frequency. Despite these associations, however, this did not result in more failures in this population of children and adolescents with substantial neurologic involvement, as pass rates exceeded 92% for those with intellectual disability, high seizure frequency, high medication burden, and even prior surgical resection of critical memory structures.
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http://dx.doi.org/10.1080/21622965.2020.1750127DOI Listing
April 2020

Memory in children with epilepsy: Utility of the WRAML-2 in generalized and focal epilepsy syndromes.

Epilepsy Behav 2018 12 26;89:30-36. Epub 2018 Oct 26.

Neuropsychology Service, Alberta Children's Hospital, Alberta Children's Hospital Research Institute, University of Calgary, Canada.

The material-specific model for memory impairment predicts that verbal memory deficits are seen with left temporal seizures, and visual memory deficits are seen with right temporal seizures (Henkin et al., 2005). In pediatric epilepsy, seizure pathology has not always yielded the expected material-specific memory profiles. This study used the Wide Range Assessment of Memory and Learning-Second Edition (WRAML-2) to assess memory functioning among pediatric patients with epilepsy. The WRAML-2 was administered to 180 youth with epilepsy during their neuropsychological evaluations. Memory and recognition scores correlated significantly with epilepsy severity variables. There were no significant differences in verbal and visual memory and recognition index scores among patients with generalized epilepsy or among those with lateralized or localized electroencephalography (EEG) patterns and lesions on imaging. However, clinically meaningful verbal versus visual discrepancy scores were significantly related to lateralized abnormalities on EEG and magnetic resonance imaging (MRI) results. Most patients with right hemisphere pathology showed the expected material-specific visual memory deficits, while fewer than 15% of the left hemisphere cases showed the expected verbal memory deficits. Over one-third of those with identified left-sided pathology showed clinically significant deficits in visual memory. Findings are incongruent with the material-specific memory model and reflect the fact that early developmental neurological insults can lead to functional reorganization/crowding effects in children with left hemisphere epilepsy. On exploratory analyses, there were no significant differences in discrepancy scores among participants with left, right, and bilateral languages on Wada and functional MRI (fMRI). However, those with right and bilateral language dominance were more likely to show discrepancies that were incongruent with the material-specific model.
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http://dx.doi.org/10.1016/j.yebeh.2018.10.002DOI Listing
December 2018

WHO-AVLT recognition trial: Initial validation for a new malingering index for Spanish-speaking patients.

Appl Neuropsychol Adult 2019 Nov-Dec;26(6):564-572. Epub 2018 Sep 5.

Neuropsychology Division, Department of Neurology, NYU School of Medicine , New York , New York , USA.

Several methods for identifying suboptimal effort on Spanish neuropsychological assessment have been established. The purpose of this retrospective study was to determine whether recognition data from the WHO-AVLT could be employed for determination of malingering in a Spanish-speaking sample. Sixteen subjects in litigation, 25 neurological patients, and 14 healthy controls completed neuropsychological testing. All subjects completed the Test of Memory Malingering (TOMM). Inclusion criteria for neurological patients and controls included performance above the standard TOMM cutoff. Subjects in litigation were classified as probable malingering, through lower than cutoff performance on the TOMM and at least one other performance validity measure. Cut-off scores for classification of malingering were determined based on the number of recognition hits on the WHO-AVLT. The probable malingering group performed significantly worse than both groups on recognition hits. A score <10 was determined to be the optimal group cutoff, with 56.25% sensitivity and specificity greater than 92%. A combination score of 14 increased sensitivity to 68.75%. These findings provide initial validation of a new malingering index, based on the number of hits on the WHO-AVLT recognition trial. This index will provide valuable information to neuropsychologists conducting forensic or clinical evaluations on Spanish-speaking individuals.
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http://dx.doi.org/10.1080/23279095.2018.1470974DOI Listing
February 2020

Spectrum of CFTR gene mutations in Ecuadorian cystic fibrosis patients: the second report of the p.H609R mutation.

Mol Genet Genomic Med 2017 11 11;5(6):751-757. Epub 2017 Oct 11.

Área de Biología Molecular, NETLAB Laboratorios Especializados, Quito, Ecuador.

Background: High heterogeneity in the CFTR gene mutations disturbs the molecular diagnosis of cystic fibrosis (CF). In order to improve the diagnosis of CF in our country, the present study aims to define a panel of common CFTR gene mutations by sequencing 27 exons of the gene in Ecuadorian Cystic Fibrosis patients.

Methods: Forty-eight Ecuadorian individuals with suspected/confirmed CF diagnosis were included. Twenty-seven exons of CFTR gene were sequenced to find sequence variations. Prevalence of pathogenic variations were determined and compared with other countries' data.

Results: We found 70 sequence variations. Eight of these are CF-causing mutations: p.F508del, p.G85E, p.G330E, p.A455E, p.G970S, W1098X, R1162X, and N1303K. Also this study is the second report of p.H609R in Ecuadorian population. Mutation prevalence differences between Ecuadorian population and other Latin America countries were found.

Conclusion: The panel of mutations suggested as an initial screening for the Ecuadorian population with cystic fibrosis should contain the mutations: p.F508del, p.G85E, p.G330E, p.A455E, p.G970S, W1098X, R1162X, and N1303K.
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http://dx.doi.org/10.1002/mgg3.337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702561PMC
November 2017

Impact of depressive symptoms and hepatic encephalopathy on health-related quality of life in cirrhotic hepatitis C patients.

Metab Brain Dis 2016 08 31;31(4):869-80. Epub 2016 Mar 31.

Division of Gastroenterology, Department of Medicine, New York University Langone Medical Center, New York City, NY, USA.

Depression, common in chronic medical conditions, and hepatic encephalopathy (HE), a reversible neuropsychiatric syndrome due to liver dysfunction, are associated with impaired health-related quality of life (HRQOL) in cirrhosis and hepatitis C (HCV). This study investigated the impact of depression and HE on HRQOL in cirrhotic patients with HCV. A convenience sample of 43 ambulatory patients, with varying degrees of cirrhosis secondary to HCV, was prospectively enrolled in this study. Participants were assessed for any current depressive, fatigue, and daytime sleepiness symptoms and underwent a psychometric evaluation to determine the presence of HE symptoms. Participants reported current HRQOL on general health and liver disease-specific questionnaires. Diagnosis and current health status were confirmed via medical records. The associations between disease severity, depressive symptoms, HE, fatigue, and daytime sleepiness were measured. Predictors of HRQOL in this sample were determined. Depressive symptoms (70 %) and HE (77 %) were highly prevalent in this sample, with 58 % actively experiencing both conditions at the time of study participation. A significant positive association was found between depressive symptoms and HE severity (P = .05). Depressive symptoms were significantly associated with fatigue (P < .001), daytime sleepiness (P < .001), general HRQOL (P < .001), and disease-specific HRQOL (P < .001). HE was significantly associated with fatigue (P = .02), general HRQOL (P < .001), and disease-specific HRQOL (P < .001). Depressive symptoms and HE were significant predictors of reduced HRQOL (P < .001), with depressive symptoms alone accounting for 58.8 % of the variance. Depressive symptoms and HE accounted for 68.0 % of the variance. Findings suggest a possible pathophysiological link between depression and HE in cirrhosis, and potentially a wider-reaching benefit of treating minimal and overt HE than previously appreciated.
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http://dx.doi.org/10.1007/s11011-016-9817-yDOI Listing
August 2016

Enumeration and extension of non-equivalent deterministic update schedules in Boolean networks.

Bioinformatics 2016 03 31;32(5):722-9. Epub 2015 Oct 31.

Departamento de Ingeniería Matemática, Universidad de Concepción, Casilla 160-C, Concepción, Chile and Centro de Investigación en Ingeniería Matemática, CIMA, Casilla 160-C, Concepción, Chile.

Motivation: Boolean networks (BNs) are commonly used to model genetic regulatory networks (GRNs). Due to the sensibility of the dynamical behavior to changes in the updating scheme (order in which the nodes of a network update their state values), it is increasingly common to use different updating rules in the modeling of GRNs to better capture an observed biological phenomenon and thus to obtain more realistic models.In Aracena et al. equivalence classes of deterministic update schedules in BNs, that yield exactly the same dynamical behavior of the network, were defined according to a certain label function on the arcs of the interaction digraph defined for each scheme. Thus, the interaction digraph so labeled (update digraphs) encode the non-equivalent schemes.

Results: We address the problem of enumerating all non-equivalent deterministic update schedules of a given BN. First, we show that it is an intractable problem in general. To solve it, we first construct an algorithm that determines the set of update digraphs of a BN. For that, we use divide and conquer methodology based on the structural characteristics of the interaction digraph. Next, for each update digraph we determine a scheme associated. This algorithm also works in the case where there is a partial knowledge about the relative order of the updating of the states of the nodes. We exhibit some examples of how the algorithm works on some GRNs published in the literature.

Availability And Implementation: An executable file of the UpdateLabel algorithm made in Java and the files with the outputs of the algorithms used with the GRNs are available at: www.inf.udec.cl/ ∼lilian/UDE/ CONTACT: lilisalinas@udec.cl

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btv628DOI Listing
March 2016