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Article: Expression of tumoral GSK3-β, PD-L1, and CD8 cell density in urothelial carcinomas, association with tumor grade and overall survival.

Almeida Rodrigues, Aline Kimberly / Silva, Paulo Goberlanio / Nogueira, Cleto / Ferreira, Samuel S / Cordeiro, Juliana / Carneiro, Benedito / Tavora, Fabio

American journal of clinical and experimental immunology

2023 Volume 12, Issue 5, Page(s) 87–97

Abstract: Bladder cancer is the most common malignancy in the urinary tract, and is biologically and clinically quite heterogeneous. Around 90% of diagnoses are made in the 6: Objective: To investigate the protein expression of PD-L1 and GSK-3β and the CD8- ... ...

Abstract	Bladder cancer is the most common malignancy in the urinary tract, and is biologically and clinically quite heterogeneous. Around 90% of diagnoses are made in the 6 Objective: To investigate the protein expression of PD-L1 and GSK-3β and the CD8-positive immune infiltrates in bladder carcinomas. Materials and methods: This was a cross-sectional study of 140 samples of urothelial carcinomas from 2015 to 2018. Automated digitally assisted scoring and conventional analyses of the markers of GSK-3β (27C10), CD8 (7103β) and PDL-1 (22c3), were reviewed by two pathologists independently and a histologic score was calculated. The density of CD8 was also measured. Results: The immunoexpression of GSK-3β (91%) was presented in most samples, PD-L1 in 62.9% and CD8 cells present in 46.3% of cases. When analyzed in conjunction, the levels of GSK-3β and PD-L1 (P = 0.033), and CD8 and PD-L1 (P<0.002) showed significant correlations. No significant associations were observed between GSK-3β and CD8. The positivity of GSK-3β and PD-L1 was predominant in high-grade tumors. Conclusion: Despite the tumor microenvironment heterogeneity, the expression of CD8, GSK-3β and PDL1 could be valuable and GSK-3β could be a potential target in advanced bladder cancer, especially in the context of immunotherapy.
Language	English
Publishing date	2023-10-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2695562-3
ISSN	2164-7712
ISSN	2164-7712
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Article ; Online: Comparison of glass and digital slides for cervical cytopathology screening and interpretation.

de Velozo, Guilherme / Cordeiro, Juliana / Sousa, Jefferson / Holanda, Ana Cláudia / Pessoa, Giovanni / Porfírio, Mônica / Távora, Fábio

Diagnostic cytopathology

2023 Volume 51, Issue 12, Page(s) 735–743

Abstract: Cervical cancer is the second most common form of cancer and a leading cause of premature death among women aged 15 to 44 worldwide. In Brazil, there is a high prevalence of infection by the human papillomavirus - HPV. Digital pathology optimizes time ... ...

Abstract	Cervical cancer is the second most common form of cancer and a leading cause of premature death among women aged 15 to 44 worldwide. In Brazil, there is a high prevalence of infection by the human papillomavirus - HPV. Digital pathology optimizes time and space for reading cervicovaginal cytology slides. We evaluated the feasibility of using whole slide images (WSI) for the routine interpretation of cytology exams. A total of 99 cases of vaginal cytology were selected from a reference laboratory in Northeastern Brazil. Three cytotechnicians participated in the study. Cellular atypia was the one that most presented concordance values. Two observers almost perfectly agreed (k = 0.86 and k = 0.84, respectively) on the negative diagnoses. The performance of the evaluators for NILM (negative for intraepithelial lesion and malignancy) showed high reproducibility and sensitivity in the digital slides, mainly between evaluators A and C. In contrast, the microbiology group showed disagreement between the diagnoses by digital slides and the standard- gold. The concordance between the digital diagnoses and the gold standard for ASCUS was 89%. In the inflammatory category, Spearman's test showed similar results between raters A, B, and C (rs = 0.47, rs = 0.41, and rs = 0.47, respectively). This study reports the diagnostic validation using digital slides in view of the need to optimize the cytology visualization process. Our experience shows good diagnostic agreement between digital and optical microscopy in several analyzed categories, but mainly in relation to cellular atypia and inflammatory processes.
MeSH term(s)	Female ; Humans ; Reproducibility of Results ; Image Processing, Computer-Assisted/methods ; Cervix Uteri/pathology ; Cytodiagnosis/methods ; Uterine Cervical Neoplasms/diagnosis ; Uterine Cervical Neoplasms/pathology ; Human Papillomavirus Viruses ; Vaginal Smears/methods
Language	English
Publishing date	2023-08-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	632710-2
ISSN	1097-0339 ; 8755-1039
ISSN (online)	1097-0339
ISSN	8755-1039
DOI	10.1002/dc.25209
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Article ; Online: Horizontal Transposon Transfer and Their Ecological Drivers: The Case of Flower-breeding Drosophila.

Carvalho, Tuane L / Cordeiro, Juliana / Vizentin-Bugoni, Jeferson / Fonseca, Pedro M / Loreto, Elgion L S / Robe, Lizandra J

Genome biology and evolution

2023 Volume 15, Issue 5

Abstract: Understanding the mechanisms that shape the architecture, diversity, and adaptations of genomes and their ecological and genetic interfaces is of utmost importance to understand biological evolution. Transposable elements (TEs) play an important role in ... ...

Abstract	Understanding the mechanisms that shape the architecture, diversity, and adaptations of genomes and their ecological and genetic interfaces is of utmost importance to understand biological evolution. Transposable elements (TEs) play an important role in genome evolution, due to their ability to transpose within and between genomes, providing sites of nonallelic recombination. Here we investigate patterns and processes of TE-driven genome evolution associated with niche diversification. Specifically, we compared TE content, TE landscapes, and frequency of horizontal transposon transfers (HTTs) across genomes of flower-breeding Drosophila (FBD) with different levels of specialization on flowers. Further, we investigated whether niche breadth and ecological and geographical overlaps are associated with a potential for HTT rates. Landscape analysis evidenced a general phylogenetic pattern, in which species of the D. bromeliae group presented L-shaped curves, indicating recent transposition bursts, whereas D. lutzii showed a bimodal pattern. The great frequency of highly similar sequences recovered for all FBD suggests that these species probably experienced similar ecological pressures and evolutionary histories that contributed to the diversification of their mobilomes. Likewise, the richness of TEs superfamilies also appears to be associated with ecological traits. Furthermore, the two more widespread species, the specialist D. incompta and the generalist D. lutzii, presented the highest frequency of HTT events. Our analyses also revealed that HTT opportunities are positively influenced by abiotic niche overlap but are not associated with phylogenetic relationships or niche breadth. This suggests the existence of intermediate vectors promoting HTTs between species that do not necessarily present overlapping biotic niches.
MeSH term(s)	Animals ; Phylogeny ; Drosophila/genetics ; Plant Breeding ; DNA Transposable Elements/genetics ; Flowers
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2023-05-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evad068
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Article ; Online: Comparison of glass and digital slides for cervical cytopathology screening and interpretation.

de Sousa Velozo, Guilherme / Cordeiro, Juliana / Sousa, Jefferson / Holanda, Ana Cláudia / Pessoa, Giovanni / Porfírio, Mônica Modesto Araújo E / Távora, Fábio

Diagnostic cytopathology

2023 Volume 51, Issue 12, Page(s) 790

MeSH term(s)	Female ; Humans ; Cytology ; Cervix Uteri/pathology ; Uterine Cervical Neoplasms/diagnosis ; Uterine Cervical Neoplasms/pathology
Language	English
Publishing date	2023-10-12
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	632710-2
ISSN	1097-0339 ; 8755-1039
ISSN (online)	1097-0339
ISSN	8755-1039
DOI	10.1002/dc.25240
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Article ; Online: COVID-19: clinical factors associated with functional capacity of hospitalized patients at admission and discharge.

Guimarães, Raiany Franca / Barbalho-Moulim, Marcela Cangussu / Wittmer, Veronica Lourenço / Serafim, Lais Mello / Kuster, Elizângela / Emiliano, Jenaine Rosa Godinho / Cordeiro, Juliana Baroni / Silva, Michele Coutinho Maia da / Lima, Rozy Tozetti / Zangirolami-Raimundo, Juliana / Raimundo, Rodrigo Daminello / Abreu, Luiz Carlos / Paro, Flavia Marini

Jornal brasileiro de pneumologia : publicacao oficial da Sociedade Brasileira de Pneumologia e Tisilogia

2024 Volume 49, Issue 6, Page(s) e20230121

MeSH term(s)	Humans ; Patient Discharge ; COVID-19 ; Hospitalization
Language	Portuguese
Publishing date	2024-01-05
Publishing country	Brazil
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	2223157-2
ISSN	1806-3756 ; 1806-3713
ISSN (online)	1806-3756
ISSN	1806-3713
DOI	10.36416/1806-3756/e20230121
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Article: Effects of landscape heterogeneity on population genetic structure and demography of Amazonian phyllostomid bats

Silva, Sofia Marques / Ferreira, Gilmax / Pamplona, Hanna / Carvalho, Tuane Letícia / Cordeiro, Juliana / Trevelin, Leonardo Carreira

Mammal research. 2021 Jan., v. 66, no. 1

2021

Abstract: Anthropogenic landscape changes resulting in habitat degradation, loss and fragmentation might decrease connectivity and effective sizes of wild populations, threatening local biodiversity. Assumed large distributions of both species and habitats have ... ...

Abstract	Anthropogenic landscape changes resulting in habitat degradation, loss and fragmentation might decrease connectivity and effective sizes of wild populations, threatening local biodiversity. Assumed large distributions of both species and habitats have probably discouraged studies correlating altered landscapes’ structure and composition to patterns of genetic diversity in the Neotropics. Yet, considering the increasingly high rates of deforestation and habitat conversion in Amazonia, investigating local and regional-scale effects of habitat conversion on Amazonian mammals is of paramount importance. Here, we use widespread, non-threatened, phyllostomid bats to understand how current forest dynamics are influencing genetic diversity patterns and functional connectivity of eastern Amazonian volant mammals. Four frugivorous species, Carollia perspicillata, Rhinophylla pumilio, Dermanura gnoma and Artibeus obscurus, were sampled across a heterogeneously fragmented region. Twelve more or less isolated rainforest remnants surrounded by urban areas, pastures, crops, secondary forests and other land uses comprise the studied landscapes, and are compared using a landscape genetics approach applied to mitochondrial DNA loci. Here, we report species-specific consequences of habitat fragmentation. Although the overall levels of genetic diversity were high, our data show that (i) population structure is heterogeneous across the altered landscapes; (ii) landscapes with higher habitat availability harbour populations with higher genetic diversity; and (iii) the populations assessed might be demographically declining.
Keywords	Artibeus ; Carollia ; Neotropics ; biodiversity ; deforestation ; demography ; forest dynamics ; frugivores ; genetic structure ; genetic variation ; habitat destruction ; habitat fragmentation ; habitats ; landscape genetics ; landscapes ; mammals ; mitochondrial DNA ; population genetics ; population structure ; rain forests ; research ; Amazonia
Language	English
Dates of publication	2021-01
Size	p. 217-225.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	NAL-light
ZDB-ID	2808353-2
ISSN	2199-241X ; 2199-2401
ISSN (online)	2199-241X
ISSN	2199-2401
DOI	10.1007/s13364-020-00546-3
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Article: First molecular phylogeny of Paralucilia Brauer & Bergenstamm, 1891 (Insecta, Diptera, Calliphoridae): A preliminary approach

Madeira-Ott, Taís / Marinho, Marco A.T / Cordeiro, Juliana / Thyssen, Patricia J

Acta tropica. 2019 Oct., v. 198

2019

Abstract: Paralucilia Brauer & Bergenstamm, 1891 (Diptera, Oestroidea, Calliphoridae) is a small genus of blowflies restricted to the Neotropical region, which is commonly reported on decaying corpses and vertebrate carcasses. The number of species currently ... ...

Abstract	Paralucilia Brauer & Bergenstamm, 1891 (Diptera, Oestroidea, Calliphoridae) is a small genus of blowflies restricted to the Neotropical region, which is commonly reported on decaying corpses and vertebrate carcasses. The number of species currently assigned to this genus and their denominations are contentious, with either three or five species recognized by different authors. This taxonomic instability results in a lack of consensus in species determination, making it impossible to compare results from different studies as well as to elaborate confident taxonomic keys. In order to solve some of the most commonly reported taxonomic conflicts within this genus, to the best of our knowledge, this study presents the first phylogenetic hypothesis for the relationships among Paralucilia species, based on molecular analysis of the COI, ITS2, 28S, and 16S genes. Maximum parsimony, maximum likelihood, and Bayesian inference analyses were used for phylogenetic reconstruction and divergence time estimation analyses. Intra- and interspecific genetic distances were calculated among species using the COI dataset. The results showed that at least three of the five currently accepted species are well defined: P. fulvinota, P. pseudolyrcea, and P. paraensis, however, a significant level of intraspecific variation was observed in P. fulvinota. These findings will assist future revisions of the description, classification, and distribution of species of Paralucilia, as well as in the elaboration of taxonomic keys. Additionally, we show that it is possible to clarify the evolutionary history of this Neotropical genus using supplementary evidence such as morphology and molecular data.
Keywords	Bayesian theory ; Calliphoridae ; Neotropics ; data collection ; genes ; genetic distance ; internal transcribed spacers ; intraspecific variation ; phylogeny ; ribosomal DNA ; statistical analysis ; taxonomic keys ; vertebrates
Language	English
Dates of publication	2019-10
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	210415-5
ISSN	1873-6254 ; 0001-706X
ISSN (online)	1873-6254
ISSN	0001-706X
DOI	10.1016/j.actatropica.2019.105096
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Evolutionary history and classification of Micropia retroelements in Drosophilidae species.

Cordeiro, Juliana / Carvalho, Tuane Letícia / Valente, Vera Lúcia da Silva / Robe, Lizandra Jaqueline

PloS one

2019 Volume 14, Issue 10, Page(s) e0220539

Abstract: Transposable elements (TEs) have the main role in shaping the evolution of genomes and host species, contributing to the creation of new genes and promoting rearrangements frequently associated with new regulatory networks. Support for these hypotheses ... ...

Abstract	Transposable elements (TEs) have the main role in shaping the evolution of genomes and host species, contributing to the creation of new genes and promoting rearrangements frequently associated with new regulatory networks. Support for these hypotheses frequently results from studies with model species, and Drosophila provides a great model organism to the study of TEs. Micropia belongs to the Ty3/Gypsy group of long terminal repeats (LTR) retroelements and comprises one of the least studied Drosophila transposable elements. In this study, we assessed the evolutionary history of Micropia within Drosophilidae, while trying to assist in the classification of this TE. At first, we performed searches of Micropia presence in the genome of natural populations from several species. Then, based on searches within online genomic databases, we retrieved Micropia-like sequences from the genomes of distinct Drosophilidae species. We expanded the knowledge of Micropia distribution within Drosophila species. The Micropia retroelements we detected consist of an array of divergent sequences, which we subdivided into 20 subfamilies. Even so, a patchy distribution of Micropia sequences within the Drosophilidae phylogeny could be identified, with incongruences between the species phylogeny and the Micropia phylogeny. Comparing the pairwise synonymous distance (dS) values between Micropia and three host nuclear sequences, we found several cases of unexpectedly high levels of similarity between Micropia sequences in divergent species. All these findings provide a hypothesis to the evolution of Micropia within Drosophilidae, which include several events of vertical and horizontal transposon transmission, associated with ancestral polymorphisms and recurrent Micropia sequences diversification.
MeSH term(s)	Animals ; Databases, Nucleic Acid ; Drosophilidae/classification ; Drosophilidae/genetics ; Evolution, Molecular ; Genome, Insect ; Retroelements
Chemical Substances	Retroelements
Language	English
Publishing date	2019-10-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0220539
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Article ; Online: First molecular phylogeny of Paralucilia Brauer & Bergenstamm, 1891 (Insecta, Diptera, Calliphoridae): A preliminary approach.

Madeira-Ott, Taís / Marinho, Marco A T / Cordeiro, Juliana / Thyssen, Patricia J

Acta tropica

2019 Volume 198, Page(s) 105096

Abstract	Paralucilia Brauer & Bergenstamm, 1891 (Diptera, Oestroidea, Calliphoridae) is a small genus of blowflies restricted to the Neotropical region, which is commonly reported on decaying corpses and vertebrate carcasses. The number of species currently assigned to this genus and their denominations are contentious, with either three or five species recognized by different authors. This taxonomic instability results in a lack of consensus in species determination, making it impossible to compare results from different studies as well as to elaborate confident taxonomic keys. In order to solve some of the most commonly reported taxonomic conflicts within this genus, to the best of our knowledge, this study presents the first phylogenetic hypothesis for the relationships among Paralucilia species, based on molecular analysis of the COI, ITS2, 28S, and 16S genes. Maximum parsimony, maximum likelihood, and Bayesian inference analyses were used for phylogenetic reconstruction and divergence time estimation analyses. Intra- and interspecific genetic distances were calculated among species using the COI dataset. The results showed that at least three of the five currently accepted species are well defined: P. fulvinota, P. pseudolyrcea, and P. paraensis, however, a significant level of intraspecific variation was observed in P. fulvinota. These findings will assist future revisions of the description, classification, and distribution of species of Paralucilia, as well as in the elaboration of taxonomic keys. Additionally, we show that it is possible to clarify the evolutionary history of this Neotropical genus using supplementary evidence such as morphology and molecular data.
MeSH term(s)	Animals ; Bayes Theorem ; DNA/genetics ; Diptera/classification ; Diptera/genetics ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2019-07-16
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	210415-5
ISSN	1873-6254 ; 0001-706X
ISSN (online)	1873-6254
ISSN	0001-706X
DOI	10.1016/j.actatropica.2019.105096
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Article ; Online: The use of DNA barcode for identifying species of Oxysarcodexia Townsend (Diptera: Sarcophagidae): A preliminary survey.

Madeira, Tais / Souza, Carina M / Cordeiro, Juliana / Thyssen, Patricia J

Acta tropica

2016 Volume 161, Page(s) 73–78

Abstract: Oxysarcodexia is one of the Neotropical richest genera within the Sarcophagidae family. Medical, veterinary and forensic importance of these flies are due to their association with corpses, cases of myiasis in humans and domestic animals, and being ... ...

Abstract	Oxysarcodexia is one of the Neotropical richest genera within the Sarcophagidae family. Medical, veterinary and forensic importance of these flies are due to their association with corpses, cases of myiasis in humans and domestic animals, and being pathogen carriers. Regarding morphological identification, molecular techniques, especially the DNA-based ones, arise as useful alternatives or complementary methodologies for species identification. Thus, in this study we aimed to investigate the potential of the COI marker (barcode region) to delimit Oxysarcodexia species in comparison with the morphological identification criteria. A COI fragment was amplified and the length of the sequences after alignment were of 648bp (149 parsimoniously informative variable sites). According to the Neighbor-Joining phylogenetic tree, specimens of the same morphological species were clustered in monophyletic clades (82-100% bootstrap branch support). Species-level resolution thus achieved was successful, despite low interspecific divergence (1.8-2.3%) and since interspecific variation was higher than intraspecific divergence (0.1-1.2%). Therefore, the use of COI barcode sequences supports differentiation and identification of the Oxysarcodexia species studied.
MeSH term(s)	Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genome, Insect ; Humans ; Phylogeny ; Sarcophagidae/classification ; Sarcophagidae/genetics ; Sequence Analysis, DNA ; Surveys and Questionnaires
Chemical Substances	Electron Transport Complex IV (EC 1.9.3.1)
Language	English
Publishing date	2016-09
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article
ZDB-ID	210415-5
ISSN	1873-6254 ; 0001-706X
ISSN (online)	1873-6254
ISSN	0001-706X
DOI	10.1016/j.actatropica.2016.05.017
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