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Neves, I.

Publications and source records attributed to Neves, I..

3 recordsLinked to original sources

Big-team science reveals that patterns of inhibitory control variation in teleost fishes differ from those in mammals and birds

Understanding the evolution of cognition is fundamental to understanding the origins and nature of our own cognitive abilities, with cross-species comparisons providing a cornerstone of this endeavor. Yet, comparative cognition so far has largely focused on endothermic vertebrates, particularly mammals and birds, while ectotherms--representing a substantial proportion of vertebrate diversity--remain relatively understudied. Moreover, variation in experimental methods makes existing data difficult to compare across species. Big-team science offers a way to overcome these limitations by enabling standardized cognitive testing across broad taxonomic scales. Here, we apply this approach to fishes, using inhibitory control as a proof of concept for standardized comparative testing in 444 individuals across 22 teleost species spanning 19 genera. We demonstrate that standardized cognitive testing across such diversity is feasible, while also revealing substantial heterogeneity in the sample. Performance varied markedly among species, but, strikingly, showed only a weak phylogenetic signal, contrasting with patterns previously reported in mammals and birds. In addition, we detected great within-species variation, including differences across research groups, suggesting that performance may reflect not only species-level evolutionary history but also ontogenetic experience and the capacity to adjust decision rules to local conditions. Together, our findings highlight the importance of both evolutionary and environmental sources of cognitive variation and demonstrate that extending standardized comparative approaches beyond traditionally studied endotherms can reveal a more dynamic and complex picture of cognitive evolution across the vertebrate lineage.

animal behavior and cognition↗

Identification of an epigenetically and phenotypically distinct peritumoral glioblastoma cell population linked to inferior patient outcome

Glioblastoma (GB) is an aggressive and therapy-resistant primary brain tumor with dismal prognosis. Lethality is in most patients caused by a local peritumoral (Edge) relapse near the resection cavity. This region is insufficiently studied and experimental models are scarce. We have analyzed matched tissue samples and cell cultures from bulk tumors and Edge regions of 11 GB patients. Genomic profiling displayed similar genetic alterations and subclonal distributions of matched bulk and Edge regions. Functional, phenotypic and combined single nucleus (sn) RNA-seq and ATAC-seq analyses showed distinct differences between bulk and Edge GB cells with similar shifts across patients. Sn multiomics uncovered a subset of Edge cells defined by unique chromatin accessibility signatures and elevated mesenchymal and immune gene expression. Integrated computational and functional investigations converged on microglia-derived Oncostatin-M as a driver of the Edge-unique phenotype, and high expression of Edge-related signatures correlated with inferior patient outcome in independent GB cohorts.

cancer biology↗

Real-time identification of carbapenemase-producing Klebsiella pneumoniae lineages and outbreak detection using FT-IR ATR

Expansion of carbapenemase-producing Klebsiella pneumoniae (CP-Kp) is driven by nosocomial dissemination, and effective infection control depends on timely and reliable typing data. Here, we evaluated our previously developed Fourier-transform infrared spectroscopy (FT-IR) with attenuated total reflectance (ATR) workflow for real-time typing of Kp capsular (KL)-types and lineages to support infection control. FT-IR spectra were acquired from Columbia agar with 5% sheep blood cultures of all CP-Kp infection isolates (n=136) from hospitalized patients at a northern Portugal hospital (April 2022 - March 2023), and analyzed using automated machine-learning (ML) classification models. Typing results were confirmed by wzi sequencing, MLST and/or WGS. FT-IR typing on Columbia agar plates showed 73% sensitivity, 79% specificity and 74% accuracy. Our method correctly typed 94% of typeable isolates (78/83), from which 87% were comunicated in <24h. Sixty percent of non-typeable isolates were considered false negatives, but the majority (66%) was correctly predicted when re-tested in Mueller-Hinton agar, improving sensitivity (92%), specificity (76%) and accuracy (89%) of Kp typing. Three Kp lineages (ST147-KL64, ST15-KL19, ST268-KL20) represented 74% of the sample, with ST268-KL20 causing an outbreak in Neonatal Intensive Care unit, quickly recognized by FT-IR enabling immediate infection control measures. Epidemiological links between patiens were mostly found on medical, surgical and urology units, using EpiLinx software. Most isolates (98%) produced KPC-3. Our FT-IR ATR ML-based typing workflow demonstrated high performance standards in real-time and high adaptability to clonal dynamics. The unprecedent time-to-response (same day of species identification) represents an opportunity to implement timely and effective infection control measures. ImportanceThis study represents the first prospective and real-time evaluation of FT-IR spectroscopy to type multidrug resistant Klebsiella pneumoniae to support surveillance and infection control. We demonstrate a high sensitivity, specificity and accuracy of a previously developed workflow that allows precise identification of K. pneumoniae lineages. The adaptability to changes in clonal dynamics and bacterial typing in <24h offer significant advantages in both high- and low-income countries for a timely infection control and improvement of antimicrobial resistance management.

microbiology↗