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Article ; Online: Alemtuzumab and autoimmune polyglandular syndrome with type 1 diabetes mellitus.

García Estévez, D A / Pinal Osorio, I / Pato Pato, A

2024

Language	English
Publishing date	2024-02-20
Publishing country	Spain
Document type	Letter
ZDB-ID	2654369-2
ISSN	2173-5808 ; 2173-5808
ISSN (online)	2173-5808
ISSN	2173-5808
DOI	10.1016/j.nrleng.2024.02.006
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Double Dyson Index

Goulart, Cleverson A / Pato, Mauricio P

Entropy (Basel, Switzerland)

2023 Volume 25, Issue 6

Abstract: The Dyson index, β, plays an essential role in random matrix theory, as it labels the so-called "three-fold way" that refers to the symmetries satisfied by ensembles under unitary transformations. As is known, its 1, 2, and 4 values denote the orthogonal, ...

Abstract	The Dyson index, β, plays an essential role in random matrix theory, as it labels the so-called "three-fold way" that refers to the symmetries satisfied by ensembles under unitary transformations. As is known, its 1, 2, and 4 values denote the orthogonal, unitary, and symplectic classes, whose matrix elements are real, complex, and quaternion numbers, respectively. It functions, therefore, as a measure of the number of independent non-diagonal variables. On the other hand, in the case of β ensembles, which represent the tridiagonal form of the theory, it can assume any real positive value, thus losing that function. Our purpose, however, is to show that, when the Hermitian condition of the real matrices generated with a given value of β is removed, and, as a consequence, the number of non-diagonal independent variables doubles, non-Hermitian matrices exist that asymptotically behave as if they had been generated with a value 2β. Therefore, it is as if the β index were, in this way, again operative. It is shown that this effect happens for the three tridiagonal ensembles, namely, the β-Hermite, the β-Laguerre, and the β-Jacobi ensembles.
Language	English
Publishing date	2023-05-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2014734-X
ISSN	1099-4300 ; 1099-4300
ISSN (online)	1099-4300
ISSN	1099-4300
DOI	10.3390/e25060868
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Article ; Online: BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies.

Genovese, Giulio / Rockweiler, Nicole B / Gorman, Bryan R / Bigdeli, Tim B / Pato, Michelle T / Pato, Carlos N / Ichihara, Kiku / McCarroll, Steven A

Bioinformatics (Oxford, England)

2024 Volume 40, Issue 2

Abstract: Motivation: Many genetics studies report results tied to genomic coordinates of a legacy genome assembly. However, as assemblies are updated and improved, researchers are faced with either realigning raw sequence data using the updated coordinate system ...

Abstract	Motivation: Many genetics studies report results tied to genomic coordinates of a legacy genome assembly. However, as assemblies are updated and improved, researchers are faced with either realigning raw sequence data using the updated coordinate system or converting legacy datasets to the updated coordinate system to be able to combine results with newer datasets. Currently available tools to perform the conversion of genetic variants have numerous shortcomings, including poor support for indels and multi-allelic variants, that lead to a higher rate of variants being dropped or incorrectly converted. As a result, many researchers continue to work with and publish using legacy genomic coordinates. Results: Here we present BCFtools/liftover, a tool to convert genomic coordinates across genome assemblies for variants encoded in the variant call format with improved support for indels represented by different reference alleles across genome assemblies and full support for multi-allelic variants. It further supports variant annotation fields updates whenever the reference allele changes across genome assemblies. The tool has the lowest rate of variants being dropped with an order of magnitude less indels dropped or incorrectly converted and is an order of magnitude faster than other tools typically used for the same task. It is particularly suited for converting variant callsets from large cohorts to novel telomere-to-telomere assemblies as well as summary statistics from genome-wide association studies tied to legacy genome assemblies. Availability and implementation: The tool is written in C and freely available under the MIT open source license as a BCFtools plugin available at http://github.com/freeseek/score.
MeSH term(s)	Software ; Genome-Wide Association Study ; Genomics/methods ; Alleles ; INDEL Mutation
Language	English
Publishing date	2024-01-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btae038
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Article: What Have We Learned About the Genetics of Obsessive-Compulsive and Related Disorders in Recent Years?

Mattheisen, Manuel / Pato, Michele T / Pato, Carlos N / Knowles, James A

Focus (American Psychiatric Publishing)

2021 Volume 19, Issue 4, Page(s) 384–391

Abstract: Obsessive-compulsive disorder (OCD) is a complex, multifactorial disorder with onset in either childhood or early adulthood. Lifetime prevalence has been estimated to be around 2%-3%. ...

Abstract	Obsessive-compulsive disorder (OCD) is a complex, multifactorial disorder with onset in either childhood or early adulthood. Lifetime prevalence has been estimated to be around 2%-3%.
Language	English
Publishing date	2021-11-05
Publishing country	United States
Document type	Journal Article
ISSN	1541-4094
ISSN	1541-4094
DOI	10.1176/appi.focus.20210017
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Article ; Online: Pattern electroretinography response in amblyopic adults.

Fernandes, Andresa / Pinto, Nuno / Tuna, Ana Rita / Brardo, Francisco Miguel / Pato, Maria Vaz

International ophthalmology

2024 Volume 44, Issue 1, Page(s) 86

Abstract: Introduction: Amblyopia is generally a unilateral disorder, defined by at least a difference of two lines of visual acuity between both eyes with the best-corrected visual acuity, a decrease in contrast sensitivity, and a decrease in stereopsis. Pattern ...

Abstract	Introduction: Amblyopia is generally a unilateral disorder, defined by at least a difference of two lines of visual acuity between both eyes with the best-corrected visual acuity, a decrease in contrast sensitivity, and a decrease in stereopsis. Pattern electroretinogram (PERG) is a noninvasive technique that provides a retinal biopotential and is a highly sensitive indicator of changes in the macular area. Our aim was to evaluate if there are differences in the retinal response of an amblyopic eye compared with a normal eye (NE). Methods: We evaluated twenty-four adult volunteers, twelve amblyopes (mean 43.42 ± 12.72 years old), and twelve subjects with NE (mean 35.58 ± 12.85 years old). None of the subjects in the two groups had comorbidities. A complete optometric examination was performed including parameters such as visual acuity (VA) by far and near with ETDRS chart, eye alignment with cover test, and evaluation of retinal cells response with PERG. Results: The refractive error found in the NE group of subjects had a mean of - 0.95 ± 1.65D, while the amblyopic group showed a mean of - 2.03 ± 4.29D. The VA in amblyopic eyes had a mean of 0.38 ± 0.20 logMAR. Analyzing PERG data, we observed significant differences in the P50-N95 amplitudes of the amblyopic group compared with the NE group (p < 0.0001-amblyopic eye vs. NE; p = 0.039-fellow eye vs. NE). Discussion: These findings suggest that amblyopic patients may also present other impairments beyond the visual cortex. PERGs seem to be an important complementary examination in the diagnosis of other impairments in amblyopia.
MeSH term(s)	Adult ; Humans ; Middle Aged ; Young Adult ; Amblyopia/diagnosis ; Electroretinography ; Visual Acuity ; Retina/diagnostic imaging ; Refractive Errors
Language	English
Publishing date	2024-02-16
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	800087-6
ISSN	1573-2630 ; 0165-5701
ISSN (online)	1573-2630
ISSN	0165-5701
DOI	10.1007/s10792-024-03042-8
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Article: Comparison of Visual Field Measurements in Glaucomatous Eyes using Oculus and Metrovision Perimeters.

Daneshvar, Ramin / Ehsaei, Asieh / Moghadas Sharif, Nasrin / Pato, Zahra

Journal of current ophthalmology

2023 Volume 35, Issue 1, Page(s) 17–22

Abstract: Purpose: To investigate the agreement between the Oculus and Metrovision perimeters in the visual field evaluation of glaucoma patients.: Methods: In this cross-sectional study, 41 consecutive glaucoma patients were enrolled. After detailed clinical ... ...

Abstract	Purpose: To investigate the agreement between the Oculus and Metrovision perimeters in the visual field evaluation of glaucoma patients. Methods: In this cross-sectional study, 41 consecutive glaucoma patients were enrolled. After detailed clinical examinations, visual field testing was performed for all patients using the Oculus and Metrovision perimeters. The interval time between the two visual field examinations was 30 min. Results: A total of 22 participants were male (53.7%) and the mean ± standard deviation (SD) age was 58.6 ± 9.1 years. The absolute average of the mean deviation (MD) in the oculus perimeter (8.24 ± 4.92 dB) was higher compared to the Metrovision perimeter (4.02 ± 4.62; Conclusion: The Oculus and Metrovision perimeter devices have good agreement in lower MDs; however, they cannot be used interchangeably.
Language	English
Publishing date	2023-08-11
Publishing country	India
Document type	Journal Article
ISSN	2452-2325
ISSN	2452-2325
DOI	10.4103/joco.joco_197_22
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Article ; Online: TXNL1 has dual functions as a redox active thioredoxin-like protein as well as an ATP- and redox-independent chaperone.

Andor, Attila / Mohanraj, Mahendravarman / Pató, Zsuzsanna Anna / Úri, Katalin / Biri-Kovács, Beáta / Cheng, Qing / Arnér, Elias S J

Redox biology

2023 Volume 67, Page(s) 102897

Abstract: TXNL1 (also named TRP32, for thioredoxin related protein of 32 kDa) is a cytosolic thioredoxin-fold protein expressed in all cell types and conserved from yeast to mammals, but with yet poorly known function. Here, we expressed and purified human TXNL1 ... ...

Abstract	TXNL1 (also named TRP32, for thioredoxin related protein of 32 kDa) is a cytosolic thioredoxin-fold protein expressed in all cell types and conserved from yeast to mammals, but with yet poorly known function. Here, we expressed and purified human TXNL1 together with several Cys-to-Ser variants, characterizing their enzymatic properties. TXNL1 could reduce disulfides in insulin, cystine and glutathione disulfide (GSSG) in reactions coupled to thioredoxin reductase (TXNRD1, TrxR1) using NADPH, similarly to thioredoxin (TXN, Trx1), but with lower catalytic efficacy due to at least one order of magnitude higher K
MeSH term(s)	Animals ; Humans ; NADP/metabolism ; Oxidation-Reduction ; Cystine ; Thioredoxins/metabolism ; Thioredoxin-Disulfide Reductase/metabolism ; Insulins/metabolism ; Adenosine Triphosphate/metabolism ; Mammals/metabolism
Chemical Substances	NADP (53-59-8) ; Cystine (48TCX9A1VT) ; Thioredoxins (52500-60-4) ; Thioredoxin-Disulfide Reductase (EC 1.8.1.9) ; Insulins ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2023-09-26
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701011-9
ISSN	2213-2317 ; 2213-2317
ISSN (online)	2213-2317
ISSN	2213-2317
DOI	10.1016/j.redox.2023.102897
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Article: Cultured Mesenchymal Cells from Nasal Turbinate as a Cellular Model of the Neurodevelopmental Component of Schizophrenia Etiology.

Tung, Victoria Sook Keng / Mathews, Fasil / Boruk, Marina / Suppa, Gabrielle / Foronjy, Robert / Pato, Michele / Pato, Carlos / Knowles, James A / Evgrafov, Oleg V

bioRxiv : the preprint server for biology

2023

Abstract: Study of the neurodevelopmental molecular mechanisms of schizophrenia requires the development of adequate biological models such as patient-derived cells and their derivatives. We previously used cell lines with neural progenitor properties (CNON) ... ...

Abstract	Study of the neurodevelopmental molecular mechanisms of schizophrenia requires the development of adequate biological models such as patient-derived cells and their derivatives. We previously used cell lines with neural progenitor properties (CNON) derived from superior or middle turbinates of patients with schizophrenia and control groups to study gene expression specific to schizophrenia. In this study, we compared single cell-RNA seq data from two CNON cell lines, one derived from an individual with schizophrenia (SCZ) and the other from a control group, with two biopsy samples from the middle turbinate (MT), also from an individual with SCZ and a control. In addition, we compared our data with previously published data from olfactory neuroepithelium (1). Our data demonstrated that CNON originated from a single cell type which is present both in middle turbinate and olfactory neuroepithelium. CNON express multiple markers of mesenchymal cells. In order to define relatedness of CNON to the developing human brain, we also compared CNON datasets with scRNA-seq data of embryonic brain (2) and found that the expression profile of CNON very closely matched one of the cell types in the embryonic brain. Finally, we evaluated differences between SCZ and control samples to assess usability and potential benefits of using single cell RNA-seq of CNON to study etiology of schizophrenia.
Language	English
Publishing date	2023-03-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.28.534295
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Article ; Online: The Double Dyson Index β Effect in Non-Hermitian Tridiagonal Matrices

Cleverson A. Goulart / Mauricio P. Pato

Entropy, Vol 25, Iss 868, p

2023 Volume 868

Abstract: The Dyson index, ... β ... , plays an essential role in random matrix theory, as it labels the so-called “three-fold way” that refers to the symmetries satisfied by ensembles under unitary transformations. As is known, its ... 1 , ...

Abstract	The Dyson index, <semantics> β </semantics> , plays an essential role in random matrix theory, as it labels the so-called “three-fold way” that refers to the symmetries satisfied by ensembles under unitary transformations. As is known, its <semantics> 1 , </semantics> 2, and 4 values denote the orthogonal, unitary, and symplectic classes, whose matrix elements are real, complex, and quaternion numbers, respectively. It functions, therefore, as a measure of the number of independent non-diagonal variables. On the other hand, in the case of <semantics> β </semantics> ensembles, which represent the tridiagonal form of the theory, it can assume any real positive value, thus losing that function. Our purpose, however, is to show that, when the Hermitian condition of the real matrices generated with a given value of <semantics> β </semantics> is removed, and, as a consequence, the number of non-diagonal independent variables doubles, non-Hermitian matrices exist that asymptotically behave as if they had been generated with a value <semantics> 2 β . </semantics> Therefore, it is as if the <semantics> β </semantics> index were, in this way, again operative. It is shown that this effect happens for the three tridiagonal ensembles, namely, the <semantics> β </semantics> –Hermite, the <semantics> β </semantics> –Laguerre, and the <semantics> β </semantics> –Jacobi ensembles.
Keywords	random matrix theory ; β -ensembles ; pseudo-Hermitian ; PT-symmetry ; Science ; Q ; Astrophysics ; QB460-466 ; Physics ; QC1-999
Subject code	511
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Perceptions of the Sense of Security, Belonging, and Acculturative Stress among International Students in China during COVID-19 Outbreak-An Empirical Analysis.

Liu, Aijun / Sheng, Xiao / Pato, Innocensia Dickson / Mutinda, Gladys / Wu, Yanping

Healthcare (Basel, Switzerland)

2023 Volume 11, Issue 8

Abstract: Understanding the cross-cultural adaptation of students studying in foreign countries by exploring acculturative stress factors is crucial to ensure the smooth academic performance of the students and, in turn, to enhance the global reputation of their ... ...

Abstract	Understanding the cross-cultural adaptation of students studying in foreign countries by exploring acculturative stress factors is crucial to ensure the smooth academic performance of the students and, in turn, to enhance the global reputation of their universities. Therefore, it is an area of interest for the authorities (Ministry) and the corresponding management of universities. Using a random sample of 138 international students in China, descriptive and logistic regressions were conducted to assess the levels and influence of acculturative stress factors on cross-cultural adaptation, specifically on international students' sense of security and belonging during the COVID-19 pandemic outbreak. The results revealed that students were most concerned about homesickness, which obtained the highest mean score. The regression results indicated that the perception of fear and discrimination significantly impacted international students' sense of security. The perception of fear, guilt, and how long the student stayed in China also significantly affected the sense of belonging. We argue that the reflections provided herein are essential for universities to improve how they manage and handle international students to mitigate the effects of acculturative stress, particularly when additional stressful conditions are present, such as the COVID-19 pandemic.
Language	English
Publishing date	2023-04-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2721009-1
ISSN	2227-9032
ISSN	2227-9032
DOI	10.3390/healthcare11081202
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