Biology subjects

Oana, S.

Publications and source records attributed to Oana, S..

3 recordsLinked to original sources

bioRxiv2023

PyHFO: Lightweight Deep Learning-poweredEnd-to-End High-Frequency Oscillations AnalysisApplication

In the context of epilepsy studies, intracranially-recorded interictal high-frequency oscillations (HFOs) in EEG signals are emerging as promising spatial neurophysiological biomarkers for epileptogenic zones. While significant efforts have been made in identifying and understanding these biomarkers, deep learning is carving novel avenues for biomarker detection and analysis. Yet, transitioning such methodologies to clinical environments is difficult due to the rigorous computational needs of processing EEG data via deep learning. This paper presents our development of an advanced end to end software platform, PyHFO, aimed at bridging this gap. PyHFO provides an integrated and user-friendly platform that includes time-efficient HFO detection algorithms such as short-term energy (STE) and Montreal Neurological Institute and Hospital (MNI) detectors and deep learning models for artifact and HFO with spike classification. This application functions seamlessly on conventional computer hardware. Our platform has been validated to adeptly handle datasets from 10-minute EEG recordings captured via grid/strip electrodes in 19 patients. Through implementation optimization, PyHFO achieves speeds up to 50 times faster than the standard HFO detection method. Users can either employ our pre-trained deep learning model for their analyses or use their EEG data to train their model. As such, PyHFO holds great promise for facilitating the use of advanced EEG data analysis tools in clinical practice and large-scale research collaborations.

neuroscience↗

bioRxiv2022

Cloning of Nine Glucocorticoid Receptor Isoforms from the Slender African lungfish (Protopterus dolloi)

We wanted to clone the glucocorticoid receptor (GR) from slender African lungfish (Protopterus dolloi) for comparison to P. dolloi MR, which we had cloned and were characterizing, as well as for comparison to the GRs from humans, elephant shark and zebrafish. However, although sequencing of the genome of the Australian lungfish (Neoceratodus forsteri), as well as, that of the West African lungfish (Protopterus annectens) were reported in the first three months of 2021, we could not retrieve a GR sequence with a BLAST search of GenBank, when we submitted our research for publication in July 2021. Moreover, we were unsuccessful in cloning the GR from slender African lungfish using a cDNA from the ovary of P. dolloi and PCR primers that had successfully cloned a GR from elephant shark, Xenopus and gar GRs. On October 21, 2021 the nucleotide sequence of West African lungfish (P. annectens) GR was deposited in GenBank. We used this GR sequence to construct PCR primers that successfully cloned the GR from the slender spotted lungfish. Here, we report the sequences of nine P. dolloi GR isoforms and explain the basis for the previous failure to clone a GR from slender African lungfish using PCR primers that cloned the GR from elephant shark, Xenopus and gar. Studies are underway to determine corticosteroid activation of these slender African lungfish GRs.

evolutionary biology↗

bioRxiv2021

Aldosterone, Dexamethasone and Triamcinolone Activate African Lungfish Mineralocorticoid Receptor: Increased Activation After Removal of the Amino-Terminal Domain

Aldosterone, the main physiological mineralocorticoid in humans and other terrestrial vertebrates, first appears in lungfish, which are lobe-finned fish that are forerunners of terrestrial vertebrates. Aldosterone activation of the MR regulates internal homeostasis of water, sodium and potassium, which was critical in the conquest of land by vertebrates. We studied transcriptional activation of the slender African lungfish MR by aldosterone, other corticosteroids and progesterone and find that aldosterone, 11-deoxycorticosterone, 11-deoxycortisol and progesterone have half-maximal responses (EC50s) below 1 nM and are potential physiological mineralocorticoids. In contrast, EC50s for corticosterone and cortisol were 23 nM and 66 nM, respectively. Unexpectedly, truncated lungfish MR, consisting of the DNA-binding, hinge and steroid-binding domains, had a stronger response to corticosteroids and progesterone than full-length lungfish MR, indicating that the N-terminal domain represses steroid activation of lungfish MR, unlike human MR in which the N-terminal domain contains an activation function. BLAST searches of GenBank did not retrieve a GR ortholog, leading us to test dexamethasone and triamcinolone for activation of lungfish MR. At 10 nM, both synthetic glucocorticoids are about 4-fold stronger than 10 nM aldosterone in activating full-length lungfish MR, leading us to propose that lungfish MR also functions as a GR.

physiology↗