Human coronaviruses (HCoVs), including SARS-CoV and MERS-CoV, are zoonotic pathogens that originated in wild animals. HCoVs have large genomes that encode a fixed array of structural and nonstructural components, as well as a variety of accessory proteins that differ in number and sequence even among closely related CoVs. Thus, in addition to recombination and mutation, HCoV genomes evolve through gene gains and losses. In this review we summarize recent findings on the molecular evolution of HCoV genomes, with special attention to recombination and adaptive events that generated new viral species and contributed to host shifts and to HCoV emergence. Video Abstract
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
Abstract m6A is a prevalent internal modification in mRNAs and has been linked to the diverse effects on mRNA fate. To explore the landscape and evolution of human m6A, we generated 27 m6A methylomes across major adult tissues. These data reveal dynamic m6A methylation across tissue types, uncover both broadly or tissue-specifically methylated sites, and identify an unexpected enrichment of m6A methylation at non-canonical cleavage sites. A comparison of fetal and adult m6A methylomes reveals that m6A preferentially occupies CDS regions in fetal tissues. Moreover, the m6A sub-motifs vary between fetal and adult tissues or across tissue types. From the evolutionary perspective, we uncover that the selection pressure on m6A sites varies and depends on their genic locations. Unexpectedly, we found that ∼40% of the 3′UTR m6A sites are under negative selection, which is higher than the evolutionary constraint on miRNA binding sites, and much higher than that on A-to-I RNA modification. Moreover, the recently gained m6A sites in human populations are clearly under positive selection and associated with traits or diseases. Our work provides a resource of human m6A profile for future studies of m6A functions, and suggests a role of m6A modification in human evolutionary adaptation and disease susceptibility.
Most video-based action recognition approaches choose to extract features from the whole video to recognize actions. The cluttered background and non-action motions limit the performances of these methods, since they lack the explicit modeling of human body movements. With recent advances of human pose estimation, this work presents a novel method to recognize human action as the evolution of pose estimation maps. Instead of relying on the inaccurate human poses estimated from videos, we observe that pose estimation maps, the byproduct of pose estimation, preserve richer cues of human body to benefit action recognition. Specifically, the evolution of pose estimation maps can be decomposed as an evolution of heatmaps, e.g., probabilistic maps, and an evolution of estimated 2D human poses, which denote the changes of body shape and body pose, respectively. Considering the sparse property of heatmap, we develop spatial rank pooling to aggregate the evolution of heatmaps as a body shape evolution image. As body shape evolution image does not differentiate body parts, we design body guided sampling to aggregate the evolution of poses as a body pose evolution image. The complementary properties between both types of images are explored by deep convolutional neural networks to predict action label. Experiments on NTU RGB+D, UTD-MHAD and PennAction datasets verify the effectiveness of our method, which outperforms most state-of-the-art methods.
The evolutionary process leading to human brain globularity was gradual and paralleled the emergence of behavioral modernity. Modern humans have large and globular brains that distinguish them from their extinct Homo relatives. The characteristic globularity develops during a prenatal and early postnatal period of rapid brain growth critical for neural wiring and cognitive development. However, it remains unknown when and how brain globularity evolved and how it relates to evolutionary brain size increase. On the basis of computed tomographic scans and geometric morphometric analyses, we analyzed endocranial casts of Homo sapiens fossils (N = 20) from different time periods. Our data show that, 300,000 years ago, brain size in early H. sapiens already fell within the range of present-day humans. Brain shape, however, evolved gradually within the H. sapiens lineage, reaching present-day human variation between about 100,000 and 35,000 years ago. This process started only after other key features of craniofacial morphology appeared modern and paralleled the emergence of behavioral modernity as seen from the archeological record. Our findings are consistent with important genetic changes affecting early brain development within the H. sapiens lineage since the origin of the species and before the transition to the Later Stone Age and the Upper Paleolithic that mark full behavioral modernity.
Larissa Leão F. de Sousa, Mariana Dias Guilardi, Junior Olimpio Martins
et al.
Abstract Background Rabies, a lethal viral zoonotic disease, remains a significant global public health concern. In northeastern Brazil, in particular, its epidemiology is complex and dynamic, characterized by the presence of several reservoirs associated with human rabies infection. Methods This study, conducted from June 2022 to July 2023, was part of a passive epidemiological surveillance initiative under Brazil’s National Rabies Surveillance Program. It investigated the presence of Rhabdovirus (RhabV) in 356 postmortem chiropteran brain samples using three diagnostic techniques for rabies and conducted an evolutionary study on both pan-RhabV- and pan-LYSSAV-positive PCR samples. The samples were collected from 20 bat species and different locations in the State of Ceará, an endemic region for the rabies virus (RABV). Rabies-positive samples were further explored through Bayesian, genetic distance mapping and recombination analyses. Results From a total of 356 samples collected, 43 (12.07%) were positive for direct immunofluorescence (DIF) and 40 (11.23%) for mouse intracerebral inoculation (MIT) tests. Among the positive results, 40 samples were confirmed by both DIF and MIT, while 13 (3.65%) had inconclusive results for one or both techniques. Molecular assays identified 38 rabies-positive samples (10.67%). Members of the Molossidae and Phyllostomidae families had the highest prevalence, highlighting the role of insectivorous and frugivorous bats in the cycle and dynamics of rabies transmission. Phylogenetic reconstructions revealed three distinct and well-supported clusters and clades, indicating the cocirculation of different RABV lineages in the region and shedding light on both intra- and interhost diversity. We also demonstrated genetic distance among the RABV clusters and inferred that their common ancestor originated in Europe, later diversifying across continents. No recombination breakpoints were identified. Conclusions This study highlights the dynamic nature of RABV evolution within individual bat hosts, contributing to the understanding of the genetic diversity of RABV variants found in several bat species in northeastern Brazil. This study provides crucial insights into viral transmission dynamics within and between different host species and is essential for designing effective rabies control and prevention strategies tailored to endemic regions.
Environmental sciences, Public aspects of medicine
Elizabeth Anne Watkins, Emanuel Moss, Ramesh Manuvinakurike
et al.
In this short paper we address issues related to building multimodal AI systems for human performance support in manufacturing domains. We make two contributions: we first identify challenges of participatory design and training of such systems, and secondly, to address such challenges, we propose the ACE paradigm: "Action and Control via Explanations". Specifically, we suggest that LLMs can be used to produce explanations in the form of human interpretable "semantic frames", which in turn enable end users to provide data the AI system needs to align its multimodal models and representations, including computer vision, automatic speech recognition, and document inputs. ACE, by using LLMs to "explain" using semantic frames, will help the human and the AI system to collaborate, together building a more accurate model of humans activities and behaviors, and ultimately more accurate predictive outputs for better task support, and better outcomes for human users performing manual tasks.
Alexander Whitehead, Anthony Sinclair, Christopher Scott
The pathogenic environment has been a constant shaping presence in human evolution. Despite its importance, this factor has been given little consideration and research. Here, we use experimental archaeology and microscopic analysis to present and support a novel hypothesis on the pathogenic properties of bifacial butchery tools during the Middle Pleistocene. Use-wear evidence from the Acheulean site of Boxgrove, Sussex suggests that a sample of flint bifaces were used for butchery tasks for a remarkably limited duration. Circumstantial evidence from other Acheulean sites, such as the apparent discard of bifaces at single-episode butchery sites, and biface caching sites, also suggest limited-use, and extend this interpretation beyond Boxgrove. There is no current utilitarian explanation for why such an apparently over-engineered tool would be discarded after such a limited duration of use. This pilot study demonstrates, via experimental investigation, that residual animal tissue from performing butchery tasks cannot be completely removed from the flake scars of flint bifaces using prehistorically available cleaning methods. It is argued that the animal tissue is likely to begin spoiling within hours of butchery, which poses a significant risk of introducing pathogens into foodstuffs if the biface is reused, resulting in foodborne illness. Subsequently, hominins likely learned to minimise this risk by discarding each flint bifacial tool after a single episode of butchery.
Abstract Background Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species. Results E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans. Conclusions Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.
Steering models (such as the generalized two-point model) predict human steering behavior well when the human is in direct control of a vehicle. In vehicles under autonomous control, human control inputs are not used; rather, an autonomous controller applies steering and acceleration commands to the vehicle. For example, human steering input may be used for state estimation rather than direct control. We show that human steering behavior changes when the human no longer directly controls the vehicle and the two are instead working in a shared autonomy paradigm. Thus, when a vehicle is not under direct human control, steering models like the generalized two-point model do not predict human steering behavior. We also show that the error between predicted human steering behavior and actual human steering behavior reflects a fundamental difference when the human directly controls the vehicle compared to when the vehicle is autonomously controlled. Moreover, we show that a single distribution describes the error between predicted human steering behavior and actual human steering behavior when the human's steering inputs are used for state estimation and the vehicle is autonomously controlled, indicating there may be a underlying model for human steering behavior under this type of shared autonomous control. Future work includes determining this shared autonomous human steering model and demonstrating its performance.
Yasemin Göksu, Antonio De Almeida Correia, Vignesh Prasad
et al.
Bimanual handovers are crucial for transferring large, deformable or delicate objects. This paper proposes a framework for generating kinematically constrained human-like bimanual robot motions to ensure seamless and natural robot-to-human object handovers. We use a Hidden Semi-Markov Model (HSMM) to reactively generate suitable response trajectories for a robot based on the observed human partner's motion. The trajectories are adapted with task space constraints to ensure accurate handovers. Results from a pilot study show that our approach is perceived as more human--like compared to a baseline Inverse Kinematics approach.
Eike Schneiders, Christopher Fourie, Stanley Celestin
et al.
Successful entrainment during collaboration positively affects trust, willingness to collaborate, and likeability towards collaborators. In this paper, we present a mixed-method study to investigate characteristics of successful entrainment leading to pair and group-based synchronisation. Drawing inspiration from industrial settings, we designed a fast-paced, short-cycle repetitive task. Using motion tracking, we investigated entrainment in both dyadic and triadic task completion. Furthermore, we utilise audio-video recordings and semi-structured interviews to contextualise participants' experiences. This paper contributes to the Human-Computer/Robot Interaction (HCI/HRI) literature using a human-centred approach to identify characteristics of entrainment during pair- and group-based collaboration. We present five characteristics related to successful entrainment. These are related to the occurrence of entrainment, leader-follower patterns, interpersonal communication, the importance of the point-of-assembly, and the value of acoustic feedback. Finally, we present three design considerations for future research and design on collaboration with robots.