Biology subjects

Araujo, E.

Publications and source records attributed to Araujo, E..

6 recordsLinked to original sources

bioRxiv2025

Spontaneous eye movements reveal that premotor cortex is involved in human thinking

Non-visual saccades (NVS) are spontaneous eye movements humans make while thinking. Their role is puzzling and there is no framework to explain them in terms of underlying neural systems. Here we studied neural activity preceding NVS when subjects performed standardized abstract thinking tasks. We used high-density EEG and focused on frontal and parietal channels representing oculomotor cortical areas. We found that NVS are distinctively preceded by neural activity changes in frontal and parietal EEG channels qualitatively different to that for voluntary saccades. However, only the ERP amplitude changes in frontal channels, but not in parietal channels, were different from saccadic preparation. A source reconstruction analysis additionally revealed that presaccadic neural activity originated mainly in the premotor cortex. Frequency spectrum analyses showed increased synchronization in alpha to low gamma bands suggesting complex top-down and bottom-up processing. We propose that this presaccadic activity while thinking represents evidence accumulation and attentional shifts, as shown before in the premotor cortex during sensorimotor tasks. Our findings suggest that human thinking appears to function similarly to human actions and engages premotor areas responsible for evaluating and manipulating objects also when evaluating and manipulating concepts.

neuroscience↗

bioRxiv2024

Automatic crystal identification for crystallography: a comparison between direct methods and artificial intelligence strategies

Crystallography is an important, and well-established technique for assessing crystalline atomic structure of a wide variety of materials. An auxiliary optical microscope instrument is used to perform the data acquisition at the manaca beamline, a crystallography experimental station from sirius (the 4th generation Brazilian synchrotron). The importance of detecting these crystals in the auxiliary image is to define the best order in which each crystal will be measured by the incident beam since each one of them must be measured only once; improving beamtime and maximizing user experience at the facility. Detecting rough crystal positions from these auxiliary images is a scientific computing task, which could benefit from some open artificial intelligence tools. This manuscript compares a real-time object detection interface (Yolo) with a new, simple and effective strategy obtained from a particular partial differential equation.

bioinformatics↗

bioRxiv2024

The De Bruijn Mapping Problem with Changes in the Graph

In computational biology, mapping a sequence s onto a sequence graph G poses a significant challenge. One possible approach to tackling this problem is to find a walk p in G that spells a sequence most similar to s. This challenge is formally known as the Graph Sequence Mapping Problem (GSMP). In this paper, we delve into an alternative problem formulation known as the De Bruijn Graph Sequence Mapping Problem (BSMP). Both problems have three variants: changes only in the sequence, changes in the graph, and changes in both the sequence and the graph. We concentrate on addressing the variant involving changes in the graph. In the literature, when this problem does not allow the De Bruijn graph to induce new arcs after changes, it becomes NP-complete, as proven by Gibney et. al [4]. However, we reformulate the problem by considering the characteristics of the arcs induced in the De Bruijn graph. This reformulation alters the problem definition, thereby enabling the application of a polynomial-time algorithm for its resolution. Approaching the problem with this arc-inducing characteristic is new, and the algorithm proposed in this work is new in the literature.

bioinformatics↗

bioRxiv2024

CXCR3-expressing myeloid cells recruited to the hypothalamus protect against diet-induced body mass gain and metabolic dysfunction

Microgliosis is an important component of diet-induced hypothalamic inflammation in obesity. A few hours after the introduction of a high-fat diet, the mediobasal hypothalamus resident microglia undergo morphological and functional changes toward an inflammatory phenotype. If the consumption of large amounts of dietary fats persists for long periods, bone marrow- derived myeloid cells are recruited and integrated into a new landscape of hypothalamic microglia. However, it is currently unknown what are the transcriptional signatures and specific functions exerted by either resident or recruited subsets of hypothalamic microglia. Here, the elucidation of the transcriptional signatures revealed that resident microglia undergo only minor changes in response to dietary fats; however, under the consumption of a high-fat diet, there are major transcriptional differences between resident and recruited immune cells with major impact on chemotaxis. In addition, in CCR2+ recruited peripheral immune cells, there are major transcriptional differences between females and males with important impact on transcripts involved in neurodegeneration and thermogenesis. The chemokine receptor CXCR3 emerged as one of the components of chemotaxis with the greatest difference between recruited and resident microglia, and thus, was elected for further intervention. The hypothalamic immunoneutralization of CXCL10, one of the ligands for CXCR3, resulted in increased body mass gain and reduced energy expenditure, particularly in females. Furthermore, the chemical inhibition of CXCR3 resulted in a much greater change in phenotype with increased body mass gain, reduced energy expenditure, increased blood leptin, glucose intolerance, and reduced insulin. Thus, this study has elucidated the transcriptional differences between resident microglia and recruited immune cells in diet-induced obesity, identifying chemokines as a relevant subset of genes undergoing regulation. In addition, we showed that a subset of recruited immune cells expressing CXCR3 has a protective, rather than a detrimental role in the metabolic outcomes promoted by the consumption of a high-fat diet, thus, establishing a new concept in obesity-associated hypothalamic inflammation.

neuroscience↗

bioRxiv2023

Heuristics for the De Bruijn Graph Sequence Mapping Problem

In computational biology, mapping a sequence s onto a sequence graph G is a significant challenge. One possible approach to addressing this problem is to identify a walk p in G that spells a sequence which is most similar to s. This problem is known as the Graph Sequence Mapping Problem (GSMP). In this paper, we study an alternative problem formulation, namely the De Bruijn Graph Sequence Mapping Problem (BSMP), which can be stated as follows: given a sequence s and a De Bruijn graph Gk (where k[≥] 2), find a walk p in Gk that spells a sequence which is most similar to s according to a distance metric. We present both exact algorithms and approximate distance heuristics for solving this problem, using edit distance as a criterion for measuring similarity.

bioinformatics↗

bioRxiv2021

Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil

The Northeast region of Brazil registered the second highest incidence proportion of chikungunya fever in 2019. In that year an outbreak consisting of patients presented with febrile disease associated with joint pain were reported by the public primary health care service in the city of Natal, Rio Grande do Norte state, in March 2019. At first, the aetiological agent of the disease was undetermined. Since much is still unknown about chikungunya virus (CHIKV) genomic diversity and evolutionary history in this northeasternmost state, we used a combination of portable whole genome sequencing, molecular clock, and epidemiological analyses that revealed the re-introduction of the CHIKV East-Central-South-African (ECSA) lineage into Rio Grande do Norte. We estimated CHIKV ECSA lineage was first introduced into Rio Grande do Norte in early June 2014, while the 2019 outbreak clade diverged around April 2018 during a period of increased chikungunya incidence in the Southeast region, which might have acted as a source of virus dispersion towards the Northeast region. Together, these results confirm the ECSA lineage continues to spread across the country through interregional importation events likely mediated by human mobility. HIGHLIGHTSCHIKV ECSA lineage introduction into Rio Grande do Norte state, Northeast Brazil, was estimated to early June 2014 At least two CHIKV importation events occurred in Rio Grande do Norte state, Brazil The 2019 chikungunya outbreak in Rio Grande do Norte was likely caused by a second event of CHIKV introduction imported from Rio de Janeiro state.

genomics↗