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Background The underlying mechanisms and processes that prompt the colonisation of extreme environments, such as caves, constitute major research themes of evolutionary biology and biospeleology. The special adaptations required to survive in subterranean environments (low food availability, hypoxic waters, permanent darkness), and the geographical isolation of caves, nominate cave biodiversity as ideal subjects to answer long-standing questions concerning the interplay amongst adaptation, biogeography, and evolution. The present project aims to examine the phylogeographic patterns exhibited by two sympatric species of surface and cave-dwelling peracarid crustaceans ( Asellus aquaticus and Niphargus hrabei ), and in doing so elucidate the possible roles of isolation and exaptation in the colonisation and successful adaptation to the cave environment. Results Specimens of both species were sampled from freshwater hypogean (cave) and epigean (surface) habitats in Hungary, and additional data from neighbouring countries were sourced from Genbank. Sequencing of mitochondrial and nuclear loci revealed, through haplotype network reconstruction (TCS) and phylogenetic inference, the genetic structure, phylogeographic patterns, and divergence-time estimates of A. aquaticus and N. hrabei surface and cave populations. Contrasting phylogeographic patterns were found between species, with A. aquaticus showing strong genetic differentiation between cave and surface populations and N. hrabei lacking any evidence of genetic structure mediated by the cave environment. Furthermore, N. hrabei populations show very low levels of genetic differentiation throughout their range, which suggests the possibility of recent expansion events over the last few thousand years. Conclusions Isolation by cave environment, rather than distance, is likely to drive the genetic structuring observed between immediately adjacent cave and surface populations of A. aquaticus, a predominantly surface species with only moderate exaptations to subterranean life. For N. hrabei , in which populations exhibit a fully ‘cave-adapted’ (troglomorphic) phenotype, the lack of genetic structure suggests that subterranean environments do not pose a dispersal barrier for this surface-cave species.

Visual representation of material culture plays a crucial role in prehistoric archaeology, from academic research to public outreach and communication. Scientific illustration is a valuable tool for visualising lithic artefacts and refittings, where technical attributes must be drawn to enhance our understanding of their significance. However, the representation of lithic refittings, which involve dynamic and sequential transformations of a volume, requires an alternative approach to traditional two-dimensional models such as photography or illustration. Advances in imaging technologies have improved our ability to capture and communicate the multifaceted nature of archaeological artefacts. In this context, we present the ReViBE protocol (Refitting Visualisation using Blender Engine), which integrates photogrammetry, 3D modelling and the animation software Blender© for the virtual representation of lithic refittings. This protocol allows the sequential study of core reduction phases and their associated flakes, as well as other aspects related to knapping decision making (core rotations, surface modifications, and direction and position of impact points). Thus, this method allows the visualisation of techno-cognitive aspects involved in core reduction through a step-by-step animation process. In addition, the 3D models and virtual reconstructions generated by ReViBE can be accessed through open repositories, in line with the principles of open science and FAIR (Findable, Accessible, Interoperable, and Reusable) data. This accessibility ensures that data on lithic technology and human behaviour are widely available, promoting transparency and knowledge sharing, and enabling remote lithic analysis. This in turn breaks down geographical barriers and encourages scientific collaboration.

Methyl farnesoate (MF) is a sesquiterpenoid hormone that controls a variety of physiological processes in crustaceans, including morphogenesis, development, reproduction, and molting. MF action is mediated by a transcriptional signaling cascade consisting of Methoprene-tolerant (Met), Steroid receptor coactivator (Src), Krüppel homolog 1 (Kr-h1), and Ecdysone response gene 93 (E93) transcription factors (TFs), and transcriptional co-regulators CREB-binding protein (CBP) and C-terminal-binding protein (CtBP). Phylogenetic and sequence analyses revealed that these genes were highly conserved across pancrustacean species. Met and Src were characterized as basic helix-loop-helix, Period (Per)-Aryl Hydrocarbon Nuclear Translocator (ARNT)-Single-minded (Sim) protein (bHLH-PAS) TFs; Kr-h1 was characterized as a C2H2 zinc finger TF with seven zinc finger motifs; E93 was characterized as a helix-turn-helix, pipsqueak (HTH_Psq) TF. CBP was identified by several zinc finger-binding regions with Transcription Adaptor Zinc Finger 1 and 2, Really Interesting New Gene, Plant homeodomain, and Z-type zinc finger domains; the Kinase-inducible Domain Interacting-transcription factor docking site; the Bromodomain-acetylated lysine recognition and binding site; the histone acetyltransferase domain; and a C-terminal CREB-binding region containing a nuclear receptor co-activator-binding domain. CtBP had a dehydrogenase domain with arginine-glutamate-histidine catalytic triad. 81 Met contigs, 45 Src contigs, 136 Kr-h1 contigs, 66 E93 contigs, 60 CBP contigs, and 172 CtBP contigs were identified across pancrustacean taxa, including decapod crustaceans. Bioinformatic identification and annotation of these TFs and co-regulators in brachyuran Y-organ (YO) transcriptomes suggests that MF signaling influences YO ecdysteroidogenesis; functional tests in the YO are needed to establish causality.

The AGC kinases constitute a large and ancient gene superfamily with origins that coincided with the appearance of multicellularity. Three AGC kinase families—protein kinase A (PKA), protein kinase G (PKG), and protein kinase C (PKC)—mediate the actions of neuropeptide hormones, biogenic amines, and other ligands on various physiological processes in metazoans. Metazoans express two PKG types. Jawed vertebrates express three PKA catalytic (C) subunits, four regulatory (R) subunits, and twelve PKCs, organized into conventional, novel delta-like, novel epsilon-like, atypical, and protein kinase N (PKN) subfamilies. By contrast, invertebrate PKA and PKC sequences are not well characterized. Consequently, limited database resources can result in misidentification or mischaracterization of proteins and can lead to misinterpretation of experimental data. A broad phylogenetic and sequence analysis of CrusTome transcriptome and GenBank databases was used to characterize 640 PKA-C sequences, 1122 PKA-R sequences, and 1844 PKC sequences distributed among the Annelida, Arthropoda, Chordata, Cnidaria, Nematoda, Mollusca, Echinodermata, Porifera, Platyhelminthes, and Tardigrada. Phylogenetic analysis and multiple sequence alignments revealed conservation of certain PKA-C, PKA-R and PKC isoforms across metazoans, as well as diversification of additional taxon-specific isoforms. Decapods expressed four PKA-C isoforms, designated PKA-C1, -CD1, -CGLY1, and -CGLY2; five PKA-R isoforms, designated PKA-RI1, -RID1, -RIIGLY, and -RIID1; and five PKC isoforms, designated PKND1-3, conventional cPKCD1, novel nPKCD1δ and nPKCD1ε, and atypical aPKCD1. PKA-CGLY1, -CGLY2, and -RIIGLY had glycine-rich N-terminal sequences that were unique to crustaceans. These data suggest lineage-specific diversification that retained the core catalytic function of each kinase, while regions outside of the kinase domain may provide specialized regulatory mechanisms and/or spatiotemporal subcellular localization in invertebrate tissues.

Feedback from supermassive black holes is believed to be a critical driver of the observed color bimodality of galaxies above the Milky Way mass scale. Active galactic nuclei (AGN) feedback has been modeled in many galaxy formation simulations, but most implementations have involved simplified prescriptions or a coarse-grained interstellar medium (ISM). We present the first set of Feedback In Realistic Environments (FIRE)-3 cosmological zoom-in simulations with AGN feedback evolved to z ∼ 0, examining the impact of AGN feedback on a set of galaxies with halos in the mass range 1012–1013 M ⊙. These simulations combine detailed stellar and ISM physics with multichannel AGN feedback including radiative feedback, mechanical outflows, and, in some simulations, cosmic rays (CRs). We find that massive (>L*) galaxies in these simulations can match local scaling relations including the stellar mass–halo mass relation and the M BH–σ relation; in the stronger model with CRs, they also match the size–mass relation and the Faber–Jackson relation. Many of the massive galaxies in the simulations with AGN feedback have quenched star formation and elliptical morphologies, in qualitative agreement with observations. In contrast, simulations at the massive end without AGN feedback produce galaxies that are too massive and form stars too rapidly, are order-of-magnitude too compact, and have velocity dispersions well above Faber–Jackson. Despite these successes, the AGN models analyzed do not produce uniformly realistic galaxies when the feedback parameters are held constant: While the stronger model produces the most realistic massive galaxies, it tends to overquench the lower-mass galaxies. This indicates that further refinements of the AGN modeling are needed.

Learning effect occurs when the best performance is not achieved at the earliest trial of a repeated protocol of evaluation. The present study examined, within testing session, the intra-individual variation in an isokinetic strength protocol composed of five reciprocal concentric and eccentric contractions of knee extensors (KE) and knee flexors (KF) among male adolescent swimmers. Additionally, test-retest reliability was determined as intra-individual mean differences between two consecutive testing sessions. The sample included 38 swimmers aged 10.1–13.3 years. A subsample (n = 17) completed a second visit. Isokinetic dynamometry was used to assess concentric and eccentric contractions of KE and KF at an angular velocity of 60°.s -1 . The protocol included three preliminary repetitions that were not retained for analysis, a 60-second interval, and five reciprocal maximal concentric contractions (cc). The preceding sequence was repeated for eccentric contractions (ecc) of KE and KF. Multilevel regression confirmed intra-individual and inter-individual levels as significant sources of variance in peak torque (PT) values. Intra-class correlation (ICC) fluctuated between 0.582 and 0.834 and, in general, a substantial percentage of participants need more than three repetitions to attain their best PT: KEcc (36.8%), KEecc (23.7%), KFcc (39.5%), KFecc (18.4%). For the subsample of 17 swimmers who completed a second testing session, intra-individual mean differences of the best PT were trivial or small. In summary, the validity of shorter protocols may be compromised if swimmers do not attain their best peak torque in the first few attempts, and the reliability of a 5-repetition protocol seemed acceptable.

The use of image processing for the detection and classification of defects has been a reality for some time in science and industry. New methods are continually being presented to improve every aspect of this process. However, these new approaches are applied to a small, private collection of images, which makes a real comparative study of these methods very difficult. The objective of this paper was to compile a public annotated benchmark, that is, an extensive set of images with and without defects, and make these public, to enable the direct comparison of detection and classification methods. Moreover, different methods are reviewed and one of these is applied to the set of images; the results of which are also presented in this paper.

We employ the Feedback In Realistic Environments (FIRE-2) physics model to study how the properties of giant molecular clouds (GMCs) evolve during galaxy mergers. We conduct a pixel-by-pixel analysis of molecular gas properties in both the simulated control galaxies and galaxy major mergers. The simulated GMC pixels in the control galaxies follow a similar trend in a diagram of velocity dispersion (σ v ) versus gas surface density (Σmol) to the one observed in local spiral galaxies in the Physics at High Angular resolution in Nearby GalaxieS (PHANGS) survey. For GMC pixels in simulated mergers, we see a significant increase of a factor of 5–10 in both Σmol and σ v , which puts these pixels above the trend of PHANGS galaxies in the σ v versus Σmol diagram. This deviation may indicate that GMCs in the simulated mergers are much less gravitationally bound compared with simulated control galaxies with virial parameters (α vir) reaching 10–100. Furthermore, we find that the increase in α vir happens at the same time as the increase in global star formation rate, which suggests that stellar feedback is responsible for dispersing the gas. We also find that the gas depletion time is significantly lower for high-α vir GMCs during a starburst event. This is in contrast to the simple physical picture that low-α vir GMCs are easier to collapse and form stars on shorter depletion times. This might suggest that some other physical mechanisms besides self-gravity are helping the GMCs in starbursting mergers collapse and form stars.

Transcriptomes from nontraditional model organisms often harbor a wealth of unexplored data. Examining these data sets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption, access to genomic and transcriptomic resources for nontraditional model organisms remains limited. Crustaceans, for example, being among the most numerous, diverse, and widely distributed taxa on the planet, often serve as excellent systems to address ecological, evolutionary, and organismal questions. While they are ubiquitously present across environments, and of economic and food security importance, they remain severely underrepresented in publicly available sequence databases. Here, we present CrusTome, a multispecies, multitissue, transcriptome database of 201 assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoans for phylogenetic context) as an evolving and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ genomic/transcriptomic techniques and data sets. CrusTome is presented in BLAST and DIAMOND formats, providing robust data sets for sequence similarity searches, orthology assignments, phylogenetic inference, etc. and thus allowing for straightforward incorporation into existing custom pipelines for high-throughput analyses. In addition, to illustrate the use and potential of CrusTome, we conducted phylogenetic analyses elucidating the identity and evolution of the cryptochrome/photolyase family of proteins across crustaceans.

In this review, we summarize the latest research pertaining to MicroRNAs (miRs) related to cardiovascular diseases. In today’s molecular age, the key clinical aspects of diagnosing and treating these type of diseases are crucial, and miRs play an important role. Therefore, we have made a thorough analysis discussing the most important candidate protagonists of many pathways relating to such conditions as atherosclerosis, heart failure, myocardial infarction, and congenital heart disorders. We approach miRs initially from the fundamental molecular aspects and look at their role in developmental pathways, as well as regulatory mechanisms dysregulated under specific cardiovascular conditions. By doing so, we can better understand their functional roles. Next, we look at therapeutic aspects, including delivery and inhibition techniques. We conclude that a personal approach for treatment is paramount, and so understanding miRs is strategic for cardiovascular health.