The role of astro- and microglial cells in the pathogenesis of epilepsy is currently under active in-vestigation. It is proposed that the activity of these cells may be regulated by agonists of peroxi-some proliferator-activated nuclear receptors (PPARs). The objective of this study was to investi-gate the effects of the PPAR β/δ agonist GW0742 (Fitorine) on the behavior and gene expression of astro- and microglial proteins involved in the regulation of epileptogenesis in rat brain in a lithi-um-pilocarpine model of temporal lobe epilepsy (TLE). A seven-day administration of GW0742 at a dose of 5 mg/kg/day has been shown to suppress TLE-related behavioral hyperactivity in the Open Field test and to attenuate the TLE-induced increase in gene expression and protein levels of astro- and microglial activation markers Gfap and Aif1 in the dorsal hippocampus and temporal cortex. Furthermore, GW0742 reversed the TLE-related increase in Lcn2 gene expression (a marker of the A1 phenotype of astrocytes) in the temporal cortex, the increase in the ratio of Nos2/Arg1 gene expression (markers of the M1/M2 phenotypes of microglia), and the decrease in Arg1 gene ex-pression in the dorsal hippocampus. The results suggest that GW0742 may mitigate behavioral and biochemical abnormalities in a lithium-pilocarpine model of TLE.

Epilepsy is known to cause alterations in neural networks. However, many details of these changes remain poorly understood. The objective of this study was to investigate changes in the properties of hippocampal CA1 pyramidal neurons and their synaptic inputs in a rat lithium-pilocarpine model of epilepsy. In the chronic phase of the model, we found a marked loss of pyramidal neurons in the CA1 area. However, the membrane properties of the neurons remained essentially unal-tered. The results of the electrophysiological and morphological studies indicate that the direct pathway from the entorhinal cortex to CA1 neurons is reinforced in epileptic animals, whereas the inputs to them from CA3 are either unaltered or even diminished. In particular, the dendritic spine density in the str. lacunosum moleculare, where the direct pathway from the entorhinal cortex ter-minates, was found to be 2.5 times higher in epileptic rats than in control rats. Furthermore, the summation of responses upon stimulation of the temporoammonic pathway was enhanced by approximately twofold in epileptic rats. This enhancement is believed to be a significant con-tributing factor to the heightened epileptic activity observed in the entorhinal cortex of epileptic rats using an ex vivo 4-aminopyridine model.

The study of the pathogenesis of febrile seizures and their consequences frequently necessitates gene expression analysis. The primary methodology employed for such analysis is reverse transcription with quantitative polymerase chain reaction (RT-qPCR). To guarantee the accuracy of data obtained by RT-qPCR, it is crucial to utilize stably expressed reference genes. The objective of this study was to identify the most suitable reference genes for use in the analysis of mRNA production in various brain regions of rats following prolonged neonatal febrile seizures. The expression stability of eight housekeeping genes was evaluated using the online tool RefFinder in the dorsal and ventral hippocampal regions and in the temporal and medial prefrontal cortex of the brain. The Ppia gene exhibited the greatest stability of expression. Conversely, the genes with the least stable expression level are Actb and Ywhaz; thus, it is not recommended to use them for normalization in a febrile seizure model. Additionally, the majority of housekeeping genes demonstrate age-related, region-specific fluctuations. Therefore, it is crucial to employ the appropriate housekeeping genes for each brain structure under investigation when examining the expression dynamics of genes of interest in a febrile seizure model.

The existence of multiple copies of genes is a well-known phenomenon. A gene family is a set of sufficiently similar genes, formed by gene duplication. In earlier works conducted on limited number of completely sequenced and annotated genomes it was found that size of gene family and size of genome are positively correlated. Additionally, it was found that several atypical microbes deviated from the observed general trend. In this study, we reexamined these associations on a larger dataset consisting of 1484 prokaryotic genomes and using several ranking approaches. We applied ranking methods in such a way that genomes with lower number of paralogs would have lower rank. Until now only simple ranking methods were used; we applied the Kemeny optimal aggregation approach as well. Regression and correlation analysis were utilized in order to accurately quantify and characterize the relationships between measures of paralog indices and genome size. In addition, boxplot analysis was employed as a method for outlier detection. We found that, in general, all paralog indexes positively correlate with an increase of genome size. As expected, different groups of atypical prokaryotic genomes were found for different types of paralog quantities.

Two welcome extensions of evolutionary thinking have come to prominence over the last thirty years: the so-called “extended evolutionary synthesis” (EES) and debate about biological kinds and individuals. These two agendas have, however, remained orthogonal to one another. The EES has mostly restricted itself to widening the explanations of adaptation offered by the preceding “modern evolutionary synthesis” by including additional mechanisms of inheritance and variation; while discussion of biological kinds has turned toward philosophical questions of essential vs. contingent properties of life forms and realist vs. epistemological approaches to categorization and classification. Here we attempt to broaden the explanatory scope of evolutionary theory by linking these two agendas. We expand on the mechanistic orientation of the EES, using new understandings of networked systems of components in order to engage the distinct intellectual challenge of the origination of historical kinds. With this phrase we designate a subset of natural kinds that acquires, through evolutionary processes, a quasi-independent lineage-history. Such kinds emerge in both biology and culture, and we enlarge the limited number of historical kinds that have thus far been recognized in evolutionary biology in a series of paradigmatic exemplars, from genes and cell types to rituals and music. For each exemplar we discern specific mechanisms by which it arose and persists; comparing these, we suggest a general unity in the ways in which diverse historical kinds originate.

Since its inception, evolutionary theory has experienced a number of extensions. The most important of these took the forms of the Modern Evolutionary Synthesis (MES), embracing genetics and population biology in the early 20^th century, and the Extended Evolutionary Synthesis (EES) of the last thirty years, embracing, among other factors, non-genetic forms of inheritance. While we appreciate the motivation for this recent extension, we argue that it does not go far enough, since it restricts itself to widening explanations of adaptation by adding mechanisms of inheritance and variation. A more thoroughgoing extension is needed, one that widens the explanatory scope of evolutionary theory. In addition to adaptation and its various mechanisms, evolutionary theory must recognize as a distinct intellectual challenge the origin of what we call “historical kinds.” Under historical kinds we include any process that acquires a quasi-independent and traceable lineage-history in biological and cultural evolution. We develop the notion of a historical kind in a series of paradigmatic exemplars, from genes and homologues to rituals and music, and we propose a preliminary characterization.

The binomial nomenclature system, introduced by Carl Linnaeus in the 18th century, has been fundamental for scientific communication and data management. Despite its utility, some scientific names reflect historical biases and ethical issues, including colonial legacies, racism, sexism, and derogatory terms. Recent debates highlight the need to address these injustices, with arguments both for and against revising such names. Critics argue that extensive revisions could disrupt scientific stability, while proponents emphasize the moral imperative to correct these issues. In this opinion paper, we advocate for the establishment of a dedicated committee within international nomenclature bodies to revise taxonomic names with clear ethical concerns and recommend the use of persistent identifiers to effectively manage and track name changes, mitigating potential disruptions to taxonomy and the science that depends on it. By adopting transparent revision processes and making use of digital technology, we can address ethical issues without remarkable upheaval. Science should not perpetuate historical injustices, and it is vital for the scientific community to proactively address social injustices in nomenclature to mitigate ongoing debates and resistance.

The COVID 19 pandemic saw the emergence of various Variants of Concern (VOCs) that took the world by storm, often replacing the ones that preceded them. The characteristic mutant constellations of these VOCs increased viral transmissibility and infectivity. Their origin and evolution remain puzzling. With the help of data mining efforts and the GISAID database, a chronology of 22 haplotypes described viral evolution up until July 23, 2023. Since the 3-dimensional atomic structures of proteins corresponding to the identified haplotypes are not available, ab initio methods were here utilized. Regions of intrinsic disorder proved to be important for viral evolution, as evidenced by the targeted change to the nucleocapsid (N) protein at the sequence, structure, and biochemical levels. The linker region of the N-protein, which binds to the RNA genome and self-oligomerizes for efficient genome packaging, was greatly impacted by mutations throughout the pandemic, followed by changes in structure and intrinsic disorder. Remarkably, VOC constellations acted cooperatively to balance the more extreme effects of individual haplotypes. Our strategy of mapping the dynamic evolutionary landscape of genetically linked mutations to the N-protein structure demonstrates the utility of ab initio modeling and deep learning tools for therapeutic intervention.

Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. Virus species are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by phylogenetic analysis of aligned genomic or metagenomic sequences. Taxonomic units are assumed independent organizational, functional and evolutionary units that follow a ‘natural’ historical rationale. Here, I use phylogenomic and other arguments to show that viruses are not self-standing genetically-driven biological systems. Instead, they are crucial components of holobionts, units of biological organization that dynamically integrate the genetics, epigenetic, physiological and functional properties of their co-evolving members. Remarkably, phylogenomic analyses show viruses share protein domain and loop structures with cells throughout history via massive processes of reticulate evolution, helping spread evolutionary innovations across a wider taxonomic spectrum. Thus, viruses are not merely MGEs or microbes. Instead, their genomes and proteomes conduct cellularly integrated processes akin to those cataloged by the GO Consortium. This prompts the generation of compositional hierarchies that replace the ‘is-a-kind-of’ by a ‘is-a-part-of’ logic to better describe the mereology of integrated cellular and viral makeup. My analysis demands a new paradigm that integrates virus taxonomy into a modern evolutionarily centered taxonomy of organisms.

Relationships of the three bryophyte lineages (liverworts, mosses, and hornworts) to vascular plants is a pivotal question in the study of origin and evolution of land plants. In recent decades, this question has been subject to intense phylogenetic analyses using morphological characters, multigene DNA sequences, and genome structural characters. A tentative consensus reached ten years ago suggested that bryophytes are a paraphyletic group, with liverworts being sister to all other land plants and hornworts being sister to vascular plants. However, several more recent nuclear phylogenomic studies have concluded that bryophytes represent a monophyletic group that is sister to vascular plants. A discussion is presented here on strengths and weaknesses of different types of characters (morphological traits, nucleotide sequences, and genome structural arrangements), and their suitability for resolving deep phylogenetic relationships. Moreover, several criteria for credible phylogenetic reconstruction are proposed. Strong statistical support for reconstructed relationships should be derived from high quality, independent characters selected for suitability to the particular question being addressed. The relationships inferred in a study should be congruent with those from as many other lines of phylogenetic evidence as possible. Any incongruities should be explicable by well-understood biological mechanisms. It is concluded that the relationships of the three bryophyte lineages to vascular plants should currently be viewed as unresolved. This is a difficult phylogenetic problem; the land plants underwent a rapid radiation a long time ago. Yet, further exploration of analytical methods and careful choice of characters should lead to eventual elucidation of diversification patterns among early land plants.

Multiple sequence alignments and phylogenetic trees are rich in biological information and are fundamental to research in biology. PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for diverse analyses, including (i) constructing a phylogenomic supermatrix, (ii) detecting errors in orthology inference, (iii) quantifying biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution-based screens to facilitate gene function prediction. Several PhyKIT functions that streamline multiple sequence alignment and phylogenetic processing—such as renaming FASTA entries or tree tips—are also discussed. These protocols demonstrate how simple command-line operations in the unified framework of PhyKIT facilitate diverse phylogenomic data analysis and processing, from supermatrix construction and diagnosis to gene function prediction.

Under the development mode of deep blending of emerging technologies, major projects are important for enhancing China's comprehensive national strength and independent innovation capability. Based on the social benefits of major projects, and considering the influence of reputation factors, an evolutionary game model composed of a general contractor and subcontractor of major projects is established. This paper studies the influence of various factors including the income distribution coefficient of collaborative innovation, and MATLAB simulation software is analyzed the influence of factors on an evolutionary path. The results show that a reasonable income distribution coefficient can promote the game behavior of both parties to the direction of active collaborative innovation; The reduction of innovation cost and the improvement of spillover technology absorption capacity can make innovation subjects tend to choose active collaborative innovation strategies. In addition, reputation loss above a specific threshold can effectively inhibit free-riding behavior and encourage innovation subjects to choose active collaborative innovation strategies. The research results provide reference for promoting major projects' technology innovation.

Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and serve crucial regulatory functions in both animals and plants. Nevertheless, there is limited understanding of lncRNAs and their patterns of expression and roles in sharks. In the current study, we systematically identified and characterized lncRNAs in the blue shark Prionace glauca from four tissues (liver, spleen, muscle, and kidney) using high-throughput sequencing and bioinformatics tools. A total of 21,932 high confidence lncRNAs were identified with 8,984 and 3,067 stably and tissue-specific expressed lncRNAs, respectively. In addition, a total of 45,007 differentially expressed (DE) lncRNAs were obtained among tissues, with kidney versus muscle having the largest numbers across tissues. DE lncRNAs trans target protein-coding genes were predicted, and functional gene ontology enrichment of these genes showed GO terms such as muscle system processes, cellular/metabolic processes, and stress and immune responses, all of which correspond with the specific biological functions of each tissue analyzed. These results advance our knowledge of lncRNAs in sharks and present novel data on tissue-specific lncRNAs, providing key information to support future functional shark investigations.

Understanding the evolutionary role of environmentally-induced phenotypic variation (i.e., environmental plasticity) is an important issue in developmental evolution. One of the major physiological responses to environmental changes is cellular stress, which is counteracted by a generic stress reaction that detoxifies the cell, refolds proteins, and repairs DNA damage. In this paper, we elaborate on a previous finding suggesting that the cell differentiation cascade of human decidual stromal cells, a cell type critical for embryo implantation and the maintenance of pregnancy, evolved from a cellular stress reaction. We hypothesize that the stress reaction in these cells was elicited ancestrally through the inflammation caused by embryo attachment and invasion. We describe a model, Stress-Induced Evolutionary Innovation (SIEI), whereby ancestral stress reactions and their corresponding pathways can be transformed into novel structural components of body plans, such as new cell types. After reviewing similarities and differences between SIEI and the “plasticity first hypothesis” (PFH) of evolution, we argue that SIEI is a distinct form of plasticity-based evolutionary change because it leads to the origin of novel structures rather than the adaptive transformation of a pre-existing character.

Objective: To explore the hot spots and development trends of community public health research. Methods: The literature related to this topic was searched in CNKI and PubMed databases, and the trend map of the number of articles was drawn according to the obtained data. The included literature were analyzed with Vosviewer software for keyword and author co-occurrence, and CiteSpace 6.3.R1 Basic software was used for mechanism co-occurrence, key emergence and clustering analysis, and timeline distribution map drawing. Results: 189 Chinese literature and 77 English literature were selected. The Chinese literature focused on “community public health service, emergency management, and community governance”, and the research trend was “community public health emergency management and community governance”; English literature focuses on “nursing education, health education, human qualitative research”. Conclusion: Although the Chinese and English literature shows that scholars in this field have different emphases, the primary community health is the key and difficult point to realize the national public health service project, and improving the basic public health service in the primary community is related to the health of all the people, so it is very important.

The history of life on Earth has been shaped by a series of major evolutionary innovations. While some of these innovations occur repeatedly, some of the most important innovations are evolutionary singularities, arising only once. This fact has often been interpreted to mean that singularities are particularly difficult, low-probability evolutionary events, implying the long-term course of life on Earth is highly contingent. Alternatively, singularities could arise from evolutionary priority effects, where first-movers suppress subsequent independent origins. Here, we disentangle these hypotheses by examining the origins of phototrophy. The ability to use light for energy evolved independently twice, preserving information about their origins that is lost when examining singularities. We show that the two forms of phototrophy occupy opposite ends of key trade-offs: most importantly efficiency of light capture vs. return on investment. Our results suggest that the dual singularity of phototrophy exists due to evolutionary interactions between nascent phototrophs, within a phototrophic niche space too large for a single first mover to fill all niches and fully suppress all future innovation. While often ignored over geological time scales, ecological interactions and evolutionary priority effects may play a fundamental role in the tempo and mode of major evolutionary innovations.

Quill mites of the family Syringophilidae are widely distributed parasites of birds inhabiting the interior of feather quills. In this paper, we provide detailed information on the host spectrum and distribution for six previously described species of syringophilines associated with starlings with new host and locality records. Additionally, we describe three new species, Aulonastus indonesianus Marcisova, Skoracki and Patan sp. n. from the Common Hill Myna Gracula religiosa Linnaeus in Indonesia (Java) and the White-necked Myna Streptocitta albicollis (Vieillot) in Indonesia (Celebes), Aulonastus anais Skoracki and Patan sp. n. from the Golden Myna Mino anais (Lesson) in Papua New Guinea, and Syringophiloidus poeopterus Skoracki and Patan sp. n. from the Abbott's Starling Poeoptera femoralis (Richmond) in Tanzania. Finally, we explore the host-parasite interactions within the system comprising starlings and syringophiline mites.

The diversification of life-histories is mediated by cooperation, innovations of biological information, modularity, and heterochrony in developmental processes. These processes are defined, contextualized, and exemplified, studying the evolution of coloniality (i.e. life-history involving modularization of the multicellular individual) in the family of benthic tunicates Styelidae. This study proposes that in these colonial tunicates there is an inter-generational division of labor, where one generation is feeding, a second is developing by morphogenetic processes, and a third is aging by programmed cell death and phagocytosis. The communication system developed in these colonies is mediated, by changes in proportion, location, and gene expression of specialized blood cells. Colonial life-history in animals is related to the reduction of individual size; development of extra-corporeal tissues to interconnect zooids; the inter-generational division of labor; and the reduction of zooid’s individuality. Processes analogous with the widely accepted major evolutionary transitions (METs), suggesting that coloniality could be studied as a MET. The understanding of colonial life-histories could provide information about key mechanisms for life diversification.

Phytochemicals have a long and successful history in drug discovery. With recent advancements in analytical techniques and methodologies, discovering bioactive leads from natural compounds has become easier. Computational techniques like molecular docking, QSAR modelling and machine learning, and network pharmacology are among the most promising new tools that allow researchers to make predictions concerning natural products' potential targets, thereby guiding experimental validation efforts. Additionally, approaches like LC-MS or LC-NMR speed up compound identification by streamlining analytical processes. Integrating structural and computational biology aids in lead identification, thus providing invaluable information to understand how phytochemicals interact with potential targets in the body. Emerging computational approach is machine learning involving QSAR modelling and deep neural networks that interrelate phytochemical properties with diverse physiological activities such as antimicrobial or anticancer effects.

As a manifestation of technological innovation achievements, patents reflect the frontier of technological development in the field. This paper constructs a multi-entity patent collaboration network and analyzes its evolution patterns to provide a reference for innovation organizations to grasp the general direction of innovation development and select partners. Based on the data of collaboration patents of two and three organizations in China's new energy vehicles (NEV) industry from 2008 to 2021, this paper constructs higher-order interaction collaboration innovation networks in different periods to analyze the spatial evolution of networks and patent cooperation activities. The results show that the generalized degree distribution of nodes and edges conforms to the power-law distribution. The two-dimensional simplex networks gradually form triangle groups centered on the core nodes, and the importance of key edges is beginning to emerge. Key organizations and partners, including State Grid Corporation of China, Tsinghua University, and China Electric Power Research Institute, will largely determine the direction for the future development of cooperation innovation. The study also reveals that Beijing, Jiangsu, Zhejiang, Guangzhou, and Shanghai are in central positions in the cooperative innovation network, based on their cooperation breadth and depth measures. Additionally, key links formed by Beijing as hubs are not only the center of information exchange but also function as bridges that connect to other regions.

A review of the concept of "fitness" as it is used in evolutionary theory.

The subfamily Picobiinae (Acariformes: Syringophilidae) comprises obligate and permanent parasites of birds found exclusively in the quills of contour feathers. In this paper, we studied associations of picobiine mites with birds of the family Sturnidae (Aves: Passeriformes). Among the 414 examined bird individuals belonging to 44 species (35.2% of all sturnids), 103 individuals from 24 species (54.5% of examined species) were parasitised by quill mites. The diversity of mites was represented by five species, including one newly described, Picobia malayi Patan and Skoracki sp. n. Statistical analysis of the Picobiinae-Sturnidae bipartite network demonstrated a low connectance value (Con = 0.20) and high modularity, with significant differences in the H2' specialisation index compared to null model values. The network structure, characterised by four distinct modules, highlighted the specificity and narrow oligoxenous to mesostenoxenous nature of the mite-host associations. The distribution of Picobia species was congruent with the phylogeny of their starling hosts, with different mites parasitising specific clades of starlings. The findings suggest that the social and breeding behaviours of starlings influence quite a high prevalence. Finally, our studies support the validity of museum collections to study these parasitic interactions.

With the rapid evolution of SARS-CoV-2, the emergence of new strains is an intriguing question. This paper presents an evolutionary theory to analyze the mutations of the virus and identify the conditions that lead to the generation of new strains. We represent the virus variants using a 4-letter sequence based on amino acid mutations on the spike protein and employ an n-distance algorithm to derive a variant phylogenetic tree. We show that the theoretically-derived tree aligns with experimental data on virus evolution. Additionally, we propose an A-X model, utilizing the set of existing mutation sites (A) and a set of randomly generated sites (X), to calculate the emergence of new strains. Our findings demonstrate that a sufficient number of random iterations can predict the generation of new macro-lineages when the number of sites in X is large enough. These results provide a crucial theoretical basis for understanding the evolution of SARS-CoV-2.

This study aims to investigate the psychological cognitive mechanisms of rural residents amidst the renewal of suburban historical and cultural villages by examining the interplay between nostalgia, collective memory, subjective well-being and place identity in rural tourism destinations. Using Naobao Village as a case study—a suburban historical and cultural village in Hohhot, Inner Mongolia, this research employs a comprehensive approach integrating experimental methods and questionnaire surveys. The findings demonstrate that analyzing the interaction among the four emotions can elucidate the psychological cognitive mechanism of residents. Moreover, it uncovers that tourism effects significantly influence residents' perception of their living environment with positive effects on collective memory, subjective well-being and place identity. In the theoretical model for generating psychological cognition among residents in suburban historical and cultural villages, subjective well-being and collective memory play crucial mediating roles. This study provides a theoretical foundation and practical guidance for spatial reconstruction and cultural evolution of tourist landscapes in suburban rural tourist destinations.

A new evolutionary game is introduced which incorporates states and actions into the strategies of the organisms of the evolving populations. The game centrally features actions that result in demographic flow between states that may not conserve organism numbers. It is by this feature that the game encapsulate a range of other evolutionary games, and can encode almost very complex interactions between organisms, species and populations. The game's formalism is expounded and the nature of the game's equilibrium is discussed. This discussion leads to an algorithm for numerically determining the stable equilibrium points which is exemplified in the context of a modified Hawk-Dove game. The game's flexibility for modeling population dynamics is evaluated and compared with other evolutionary games.

Rice has become the second major food among rural people. It is one of the most nutrient and low-cost food available in Asia. Rice is composed of two major subspecies as Japonica and Indica and it belongs to the Poaceae family. The World Bank predicts that rice demand will grow 51% faster than population growth in 2025. It is high time to develop a model which predicts the type of infected paddy leaf and avoids the loss of grains. In this paper, the proposed hybrid CNN model, three CNN networks with different layer properties are trained parallel. The extracted feature from these CNN networks is combined to provide the classification of the type of infected leaf. Fieldwork was carried and about 340 samples are collected from five different types of classes. The proposed hybrid model was tested with both the fieldwork dataset and also with an available dataset on the internet. The experimental results show that the proposed model outperforms the other CNN network and yields an accuracy value of 98%, a precision value of 95%, and a misclassification rate of 4% respectively.

REDD+ (Reducing Emissions from Deforestation and Forest Degradation) aims to achieve its purpose by working across multiple sectors and involving multi-level actors in reducing deforestation and forest degradation in tropical countries. By contrast, the European Union (EU) Action Plan on Forest Law Enforcement, Governance and Trade (FLEGT) and its Voluntary Partnership Agreements (VPAs) focus on forestry and functions at bilateral state level. The FLEGT Action Plan specifically aims to tackle illegal logging, legalise timber production and trade improve forest governance in countries exporting tropical timber to the EU. Since illegal logging is just one driver of deforestation and forest degeneration, and legalisation of logging does not necessarily reduce deforestation and forest degradation, the two instruments differ in scale and scope. However, by addressing the causes of deforestation and forest degradation and their underlying governance issues, the EU FLEGT and REDD+ share many functional linkages at higher levels of forest policy and forest governance. The contribution and participation of civil society organisations (CSOs) and other actors is imperative to both processes. Our study is based on a survey of key actors (national and international) in REDD+ and FLEGT VPA processes in the Lao People’s Democratic Republic. Our analysis was guided by the theoretical perspectives of the policy arrangement approach and examination of two specific dimensions of this approach, namely resources and rules of the game. This paper argues that participation of CSOs in both processes is crucial as it facilitates and nurtures the very much needed cooperation between other national and international actors. The paper also argues that participation of CSOs feeds valuable information and knowledge into REDD+ and FLEGT VPA processes, thus contributing to increased legitimacy, justice and transparency.

The rapid evolution of drug resistance is one of the greatest health issues of the 21st century. There is an alarming situation to find new therapeutic strategies or candidate drugs to tackle ongoing multi-drug resistance development. The marine environment is one of the prime natural ecosystems on Earth, the majority of which is still unexplored, especially when it comes to the microbes. A wide variety of bioactive compounds have been obtained from a varied range of marine organisms, however, marine bacteria-produced bacteriocins are still undermined. Owing to the distinct environmental stresses that marine bacterial communities encounter, their bioactive compounds frequently undergo distinct adaptations that confer on them a variety of shapes and functions, setting them apart from their terrestrial counterparts. The ribosomally-synthesized and posttranslationally modified peptides (RiPPs), bacteriocins are of special interest because of their variety in structure and diverse potential biological activities. Additionally, the gut microbiome of marine creatures are largely unexplored source of new bacteriocins with promising activities. There is a huge possibility of novel bacteriocins from marine bacterial communities that might come out as efficient candidates to fight against antibiotic resistance, especially in light of the growing pressure from antibiotic-resistant diseases and industrial desire for innovative treatments. The present review summarizes known bacteriocins from marine bacteria, evolutionary aspects, challenges, and huge possibilities of unexplored bacteriocins from marine bacterial communities.

Attempts to find and quantify the supposed low entropy of organisms and its preservation are revised. Absolute entropy of the mixed components of non-living biomass (around -1.6 x 103 J K-1 L-1) is the reference to which other entropy decreases would be ascribed to life. Compartmentation of metabolites and departure from the equilibrium of metabolic reactions account for 1 and 40-50 J K-1 L-1, respectively, decreases of entropy and, though small, are distinctive features of living tissues. DNA and proteins do not supply significant decreases of thermodynamic entropy, but their low informational entropy is relevant for life and its evolution. No other living feature contributes significantly to the low entropy associated to life. The photosynthetic conversion of radiant energy to biomass energy accounts for the most of entropy (2.8 x 105 J K-1 carbon kg-1) produced by living beings. The comparative very low entropy produced in other processes (around 4.8 x102 J K-1 L-1 day-1 in human body) must be rapidly exported outside as heat to preserve the low entropy decreases due to compartmentation and non-equilibrium metabolism. Enzymes and genes are described whose control minimize the rate of production of entropy and could explain selective pressures in biological evolution and the rapid proliferation of cancer cells.

In the field of Natural Language Processing (NLP), Large Language Models (LLMs) have shown great potential in document-level event extraction tasks, but existing methods face challenges in the design of prompts. To address this issue, we propose an optimization strategy called "Definition-driven Document-level Event Extraction (DDEE)." By adjusting the length of the prompt and enhancing the clarity of heuristics, we have significantly improved the event extraction performance of LLMs. We used data balancing techniques to solve the long-tail effect problem, enhancing the model's generalization ability for event types. At the same time, we refined the prompt to ensure it is both concise and comprehensive, adapting to the sensitivity of LLMs to the style of prompts. In addition, the introduction of structured heuristic methods and strict limiting conditions has improved the precision of event and argument role extraction. These strategies not only solve the prompt engineering problems of LLMs in document-level event extraction but also promote the development of event extraction technology, providing new research perspectives for other tasks in the NLP field.

The apicomplexan parasite, Sarcocystis neurona causes the degenerative neurological equine protozoal myeloencephalitis (EPM) disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions such as host cell invasion, cell cycle progression and host immune responses evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans. Further, three-dimensional (3D) homology models for selected S. neurona putative PKs were constructed and evaluated for inhibitor docking. We identified 92 putative PKs clustering within the AGC, CAMK, CK1, CMGC, STE, TKL, aPK and OPK groups. Although containing the universally conserved PKA (AGC group), S. neurona kinome was devoid of PKB and PKC, but contained the six apicomplexan conserved CDPKs (CAMK group). The OPK group was represented by ROPKs 19A, 27, 30, 33, 35 and 37, but was devoid of the virulence-associated ROPKs 5, 6, 18 and 38. Two out of the three S. neurona CK1 enzymes had high sequence similarities to T. gondii TgCK1-α and TgCK1-β and the Plasmodium PfCK1. Docking of four inhibitors onto homology models of putative ROP27 and PKA indicated that inhibition of S. neurona PKs is feasible, but needs to be experimentally tested. The essentiality of apicomplexan PKs makes the elucidation of S. neurona kinome a key milestone for development of novel therapeutics for EPM.

Performing optimisation and scale-up studies of crystallisation systems requires accurate and computationally efficient mathematical models. The assumption of the ideal mixing conditions in batch reactors typically produce inaccurate results while the computational expense of CFD models is still prohibitively high. Therefore, in this work, a new intermediary approach is proposed that takes into account the non-ideal mixing conditions in the reactor and requires less computational resources than full CFD simulations. Starting with the Danckwerts concept of the intensity of segregation, an analogy between its application to chemical reactions and the kinetics of the crystallisation phenomena (such as nucleation and growth) has been made. As a result, the modified kinetics expressions have been derived which incorporate the effect of non-idealities present in stirred reactors. This way, based on the experimental measurements of the mixing time using the Laser Induced Fluorescence (LIF) technique, computationally more efficient mathematical models can be developed in two ways: (1) the accurate semi-empirical correlations are available for standard mixing configurations with the most often used types of impellers, (2) CFD simulations can be utilised for estimation of the mixing time; in this case it is necessary to simulate only the mixing process. The benefits offered by the LIF experimental technique have been demonstrated and some frequent problems in its application analysed. The mixing time results for configurations with and without baffles for three types of impellers and four different rotational speeds have been presented. The false shorter mixing times in the non-baffled configurations have been observed and this phenomena explained by the existence of two segregated zones in the reactor and confirmed by additional experiments. The precise measurements in these cases have been shown as difficult using the LIF technique, particularly for higher rpms. The experimental data has been compared to the preliminary simulation results obtained from the Smoothed Particle Hydrodynamics method and the standard k-ε turbulence model with the modest success. The shortcomings of the SPH model have been recognized and the directions for the future work discussed.

It is desirable to upgrade previous evolutionary theories, which have remained incomplete and controversial for decades. Here we employ the concept of carbon-based entities (CBEs), which include methane, amino acids, proteins, organisms, and other entities containing relatively many carbon atoms. We deduce the driving force, mechanisms, steps, modes, tempos of CBE evolution, through integration of biology, physics, and chemistry using logics for complex issues. We hence establish the Carbon-Based Evolutionary Theory (CBET). The CBET suggests that evolution is the increase in hierarchy, diversity, fitness of CBEs under natural selection and driven by thermodynamics due to the chemical effect of the thermodynamic features of the Earth on CBEs. It provides better explanations for life origin, macroevolution events, natural selection, sympatric speciation, and evolution tempos than previous evolutionary theories. It reveals the evolutionary basis of multiple important social notions, including diversity, collaboration, altruism, obeying rules, and proper increase in freedom. It refutes some wrong notions in thermodynamics, including negative entropy (negentropy) and that biological order is equal to thermodynamic order, which have misled many people. The CBET is supported by its deduction and application. It could be a rare bridge linking laws of thermodynamics, evolution of life, and development of human society, and could have great significance in various sciences.

We have shown that three astrometric solar-system anomalies can be explained satisfactorily by using evolutionary gravitational constant G and speed of light c in the Einstein’s field equation. These are: a) the Pioneer acceleration anomaly; b) the anomalous secular increase of Moon-orbit eccentricity; and c) the anomalous secular change in the astronomical unit AU. The gravitational constant G and the speed of light c both increase as dG/dt = 5.4GH₀ and dc/dt = 1.8cH₀ with H₀ as the Hubble constant. We also show that the Planck’s constant ħ increases as dħ/dt = 1.8ħH₀. Additionally, the new approach fits the supernovae Ia redshift vs distance modulus data as well as the standard ΛCDM model with just one adjustable parameter H₀.

Tiny by physical size, the State of Israel retains some of the world’s most important cultural treasures, along with many other great cultural institutions. Archeological treasures have yielded much information as far as biblical history and have been well adapted to a Zionist narrative by both the Jewish press and international news organizations, such as the New York Times whose archives are replete with reports of Jewish history being dug up by the Jewish people. Once the State of Israel gained independence in 1948, the course was set for the development of historical museums whose discourse would reflect the most significant events in Jewish history, most especially the Holocaust and the state of constant warfare that continues to imbue the cultural consciousness of its citizens. In this paper we outline, through categorization, the various historical museums, which are currently operating. Furthermore, this article hopes to shed some light upon the cultural sensibilities conveyed through these institutions.

Drag reduction by laminarization, an innovative technology in aerodynamics design, provides the possibility to improve significantly the aerodynamic performance of aircraft and remains to be one of the most promising and effective technologies. In this paper, the design method for transonic natural laminar flow (NLF) wing at high Reynolds number is investigated in details and a new optimization model is established to solve conflicts between the increase of a laminar flow region and the shock wave strength at the trailing edge. In order to numerically handle this competitive situation efficiently, a two-objective hierarchical variable fidelity Pareto evolutionary optimization model based on search space contraction is proposed and implemented. Numerical experiments show that it can capture simultaneously a Pareto front of the two-objectives: a wave drag minimization and a laminar flow region maximization. The results also show that both wave drag and skin friction drag performances of non-dominated Pareto members can be significantly improved via the optimal laminar wing shape and shock wave control device. Nearly 40% of the laminar flow area on the wing surface is achieved at the Reynolds number of 107. It is concluded that the present hierarchical variable-fidelity multi-objective evolutionary optimization method is computationally efficient, and illustrate its potential for solving complex engineering design problems.

To achieve real-time identification of soybean seedlings and weeds in soybean seedling fields on agricultural intelligent terminal devices, this article constructs a real-time evolutionary identification system ESWIM driven by computational complexity under few-shot training. Firstly, based on the identification task, high-quality image samples are collected and annotated. By analyzing the terrain, the weather during the growth period, image acquisition methods, and the status of equipment fieldwork, we obtained a suitable enhancement algorithm. This algorithm not only effectively simulates the diversity of actual images, but also solves the problem of significant imbalance in the number of targets. Then, using the computational complexity driven approach and YOLOv5n as the foundation model, a soybean seedling and weed recognition model SWIM is constructed. The model's computational space and time complexity are reduced by 45.19% and 42.86%, respectively, while mAP (0.5) increased by 0.1%. Finally, by utilizing human-computer interaction to enable real-time and effective evolution of the dataset, an evolutionary strategy is designed to rapidly iterate and update model parameters, resulting in the development of the evolutionary system ESWIM. Laboratory experiments have shown that the ESWIM system can quickly adjust the recognition system during device operation to achieve target identification tasks in different environments.

The rapid development of advanced AI technologies poses serious existential threats and necessitates research on safe and responsible Human-AI alignment. We hypothesize that the evolution of AI may be viewed not as something accidental or artificial, but as a natural part of the evolution of intelligence in living species. This perspective suggests a different view of the Human-AI relationship, where AI is not seen as a threat or a mere enhancement of humans, but as a mean of revealing and establishing true human nature — achieving greater freedom and self-determination. While in previous evolutionary stages, more freedom was attained through inculturation, AI can serve as a tool in the next stage by providing a direct connection between individuals and culture, overcoming the limitations of traditional cultural acquisition processes and giving rise to post-human free beings. A specific step-by-step framework rooted in cognitive evolution theories is proposed, along with potential directions for empirical research.

Attention-Deficit/Hyperactivity Disorder (ADHD) exhibits a notable prevalence across diverse populations, with estimates ranging from 4% to 6%. This wide range prompts an investigation into the evolutionary and genetic underpinnings of ADHD, especially considering the markedly different environments faced by ancestral human populations compared to today's structured societies. This study examines the potential adaptive advantages of ADHD-associated traits in hunter-gatherer contexts, where hyperactivity, impulsivity, and novelty-seeking behaviors may have conferred survival benefits. We employ the principles of population genetics, including Hardy-Weinberg equilibrium, selection coefficients, and genetic drift, to model the dynamics of ADHD allele frequencies over time. Additionally, we discuss balancing selection as a mechanism for maintaining genetic diversity and how gene-environment interactions (GxE) contribute to the expression of ADHD in contemporary settings. Our analysis suggests that traits associated with ADHD, while potentially maladaptive in modern structured environments, could have been preserved through evolutionary processes due to their adaptive value in ancestral contexts. Understanding these dynamics provides a comprehensive view of ADHD's prevalence and highlights the significance of genetic and environmental interplay in shaping human behavior.

We propose a novel interpretation of consciousness and an enlarged definition of locality, which provide a solution to the problem of the consistency of measurements in quantum mechanics: consciousness is a characteristics of the Universe as a whole. Besides its physical conse- quences, this interpretation has also moral implications: individuality comes out naturally to be just an accident functional to evolution which shaped past and present history through competition, and re- alizing this fact should enforce cooperation.

Transposable elements (TEs) ubiquitously exist in the human genome, and some have the ability to copy and paste themselves to other locations, resulting in new insertions. Organisms have evolved with mechanisms and machineries to repress such activity. TEs are also co-opted for beneficial functions by the host and are thus maintained in the genome. During the lifetime of humans, aberrant TE activity might cause or contribute towards diseases including neurological conditions such as Alzheimers Disease (AD) and cancer. While inflammatory pathways linked to TEs may be a part of the disease pathology, on the other hand altered TE activity involving inflammatory pathways could be recognised by disease suppression mechanisms. For this reason, TEs could be targeted for therapeutic applications aiming to prevent TE activity or reduce initial inflammatory pathways as well as to activate disease suppression mechanisms. In this review, we describe the contributory and potential preventative roles of TEs in neurological conditions and cancer from a molecular and evolutionary perspective. Evolutionary paradigms both at the unicellular and organismal level aid understanding the role of TEs in disease. These observations could pave the way for the development of novel therapeutic approaches targeting TEs.

Ruminants perhaps appeared about 50 million years ago (Ma). Five ruminant families had been extinct and about 200 species in 6 ruminant families are living today. The first ruminant family probably was small omnivore without functional ruminal microbiota to digest fiber. Subsequently, other ruminant families evolved around 18-23 Ma along with woodlands and grasslands. Probably, ruminants started to consume selective and highly nutritious plant leaves and grasses similar to concentrates. By 5-11 Ma, grasslands expanded and some ruminants used more grass in their diets with comparatively low nutritive values and high fibers. Historically, humans have domesticated 9 ruminant species that are mostly utilizer of low quality forages for human benefits. Thus, the non-functional rumen microbiota to predominantly concentrate fermenting microbiota, followed by predominantly fiber digesting microbiota had evolved for mutual complementary benefits of holobiont over the million years. The core microbiome of ruminant species seems the resultant of hologenome interaction in an evolutionary unit. The inertia and resilience properties of ruminal ecosystem seem to be due to this core microbiota, which makes the ecosystem most stable in response to perturbations because this core microbiota has evolutionary advantages with logically more generalists (i.e., wide metabolic versatile and redundancy). Also, a part of the ruminal microbiome shows highly plasticity, which is likely useful for evolutionary adaptability of holobiont. This review discusses ecological characteristics of ruminal microbial community in evolutionary perspectives. The updated understanding of ecological traits of ruminal microbiome would be helpful to better modulate the ruminal fermentation favorably for human benefits.

We propose the traditional goal of cancer therapists to develop a single drug or drug combination that can, by itself, eliminate all cancer cells within a host has neglected potential treatments that may achieve curative outcomes by strategically combining agents that are individually effective but non-curative. We derive basic principles for such an approach from the eco-evolutionary dynamics of background extinctions in which a “first strike” reduces the size and heterogeneity of the initial population and is followed immediately by demographic and ecological “second strikes” that push the population below an extinction threshold. This proposed strategy appears identical to the empirically-derived curative therapy in childhood Acute Lymphocytic Leukemia.

System-of-systems (SoS) evolution is a complex and unpredictable process. Although various principles to facilitate collaborative SoS evolution have been proposed, there is a lack of experimental data validating their effectiveness. To address these issues, we present an Agent-Based Model (ABM) for SoS evolution in the Internet of Vehicles (IoV) , serving as a quantitative analysis tool for SoS research. By integrating multiple complex and rational behaviors of individuals, we aim to simulate real-world scenarios as accurately as possible. To simulate the SoS evolution process, our model employs multiple agents with autonomous interactions and incorporates external environmental variables. Furthermore, we propose three evaluation metrics: evolutionary time, degree of variation, and evolutionary cost, to assess the performance of SoS evolution. Our study demonstrates that enhanced information transparency significantly improves the evolutionary performance of distributed SoS. Conversely, the adoption of uniform standards only brings limited performance enhancement to distributed SoSs. Although our proposed model has limitations, it stands out from other approaches that utilize Agent-Based Modeling to analyze SoS theories. Our model focuses on realistic problem contexts and simulates realistic interaction behaviors. This study enhances the comprehension of SoS evolution processes and provides valuable insights for the formulation of effective evolutionary strategies.

The relationship between living things and their respective environments highly dependent on body temperature regulation. The human capacity to effectively thermoregulate evolved at a time when the environmental temperature was likely around 25°C during the Eocene epoch, some ~ 50-60 million years ago. This effectively meant that homeothermy settled on a core temperature balance point of ~ 37°C. When Homo split from chimpanzee around 5 million years ago the Earth was entering a cooling period where the balance point temperature was always well above that of the environment and body heat balance could be maintained. Following this cooling period, the Earth’s rewarming by 7 °C took over approximately 5,000 years, whereas the current estimates indicate 0.7 °C over the past 100 years; ten times the rate of ice-age-recovery warming, or 20 times faster compared with the last 2 million years. As such, if the predicted continued rise in global temperature continues, and surface temperature reaches values where heat load cannot be dumped as the body temperature balance point is at or near the environmental temperature, areas of the Earth would become inhospitable. This effectively means that we will need to deal with both physiological and behavioral limitations since our ability to adapt will be limited by a thermoregulatory strategy that evolved over millions of years for a different kind of environment, not one that is predicted to change rapidly over the next century. This paper outlines the basis on which Homo settled on a thermoregulatory balance point and what limitations this presents for us in the future.

Today, we are all threatened by an unprecedented pandemic: COVID-19. How different is it from other coronaviruses? Will it be attenuated or become more virulent? Which animals may be its original host? In this study, we analyzed 377 publicly available complete genome sequences for the COVID-19 virus, the previously known flu-causing coronaviruses (HCov-229E, HCov-OC43, HCov-NL63 and HCov-HKU1) and the lethal, pathogenic P3/P4 viruses, SARS, MERS, Victoria, Lassa, Yamagata, Ebola, and Dengue. We found strong similarities between the current circulating COVID-19 and SARS and MERS, as well as COVID-19 in rhinolophines and pangolins. On the contrary, COVID-19 shares little similarity with the flu-causing coronaviruses and the other P3/P4 viruses. Strikingly, we observed divergence of COVID-19 strains isolated from human hosts has steadily increased from December 2019 to March 2020, suggesting COVID-19 is actively evolving in human hosts. From all existing human COVID-19 genome sequences, we calculated the first common model that represents the shared sequences of the human COVID-19 strains, which provides important information for vaccine and antibody development. Geographic and time-course analysis of the evolutionary trees of the human COVID-19 reveals possibly heterogeneous evolutional paths among strains from 21 countries. This finding has important implications to the management of COVID-19 and the development of vaccines.

The second article in the series presents the application of the Smoothed Particle Hydrodynamics (SPH) method to modelling of batch crystallisation in stirred tanks. A methodology to integrate the population balance equations (PBE) in parallel and independently from the Navier-Stokes equations is demonstrated. The benefits of the proposed methodology in terms of computational requirements, accuracy and availability of the crystal size distribution are discussed. The specific formulation of the SPH equations where the resulting system of ordinary differential equations is solved using the weighted contributions rather than numerically by solving a linear system of equations allows for massive parallelisation and a very loose coupling of the population balance and the fluid dynamics. It has been demonstrated, that the population balance equations can be solved on a Shared Memory Architecture (SMA) system using the OpenMP interface while the fluid dynamics equations being computed independently on a General Purpose Graphics Processing Unit (GPGPU) using the NVidia CUDA technology. This way, a significant portion of the computational overhead due to the large number of additional transport equations resulting from the discretisation of the population balance was removed: the SPH simulation coupled with 200 population balance equations was only 40% slower compared to SPH-only simulation. Two methods for the solution of population balance equations that preserve full crystal size distribution were implemented: discretised population balance (DPB) and method of characteristics (MOCH). The DPB equations are solved using the high-resolution finite-volume method with flux limiter and the effect of a large number of different flux limiters have been investigated. Both methods were validated using the case studies from the literature where an analytical solution can be derived. The developed models were applied to a numerical solution of coupled computational fluid dynamics and population balance equations to model a batch crystallization process. The effect of the hydrodynamics on the local temperature/supersaturation and the resulting crystal size distribution was captured and compared to the ideal mixing case. The simulation results from the DPB and MOCH methods were compared in terms of computational requirements and accuracy and MOCH selected as computationally more efficient and accurate.

Rett syndrome (RTT) is mainly caused by mutations in methyl CpG-binding protein 2, cyclin-dependent kinase-like 5, or forkhead box protein G1. These RTT-causing proteins harbor an intrinsically disordered region (IDR) whose conformation exhibits spatiotemporal heterogeneity, which not only confer versatility to the protein, but also implicates them in diseases. The IDR generally evolves more rapidly than an ordered structure. In this study, we examined the relationship between pathogenic RTT-associated point mutations in RTT-causing proteins and the evolutionary dynamics of sequence features including structural order–disorder, phosphorylation sites, and evolutionary rates. We also analyzed the molecular properties and evolution of proteins that interact with RTT-causing proteins in terms of phylogenetic profiles, tissue specificity, subcellular localization, expression level, and functions. The results indicate that constrained IDRs may function by forming contacts with other regions in the protein sequence causing pathogenic missense mutations likely to arise in the rapidly evolving IDR and affect molecular networks, leading to disease. The results also provide novel insights into the genetic basis for RTT and the evolution of the neocortex in higher vertebrates.

Late-life diseases result from the poorly understood process of senescence (aging), that is largely genetically determined. According to a recently proposed evolutionary physiology-based account, the multifactorial model, senescence is largely caused by evolved but non-adaptive programmatic mechanisms specified by the wild-type (i.e. normal) genome. These act together with disruptions to wild-type function (due e.g. to infectious pathogens, mechanical injury and malnutrition) in a variety of combinations to generate diverse late-life diseases. Here the utility of this model is explored by testing its capacity to provide an account of one complex, late-life disease, osteoarthritis (OA), and a framework for understanding OA etiology suggested. In this framework, the core OA disease mechanism is a futile endochondral ossification quasi-program (non-adaptive developmental program), in which hypertrophic articular chondrocytes alter joint architecture. Programmatic changes prime chondrocytes for quasi-program activation, which can be triggered by secondary causes of OA (e.g. joint mechanical injury). A suggested evolutionary cause of this priming, involving antagonistic pleiotropy, is selection to maximize early life tissue repair benefits at the expense of late-life programmatic costs.

In this essay, I revisit Neural Networks (NNs) through the lens of evolutionary dynamics. From the two most important features of NNs, I recover the two most general equations of evolutionary dynamics. These two equations may thus serve as a connection between NNs and a body of knowledge that has been built over multiple centuries and has found application across a vast range of disciplines. This connection may therefore also help explain why NNs with the two features in question are applicable across a much broader range of domains than initially envisioned.

Animals are distinguished by their complex developmental programs, in which transcription factors play essential roles in coordinating the regulation of the genome. Thus, it has been hypothesized that animal origins involved the evolution of increasingly complex transcriptional regulatory mechanisms that permit greater spatiotemporal control over gene expression. Here, we revisit this hypothesis in light of new genomic and functional data from diverse phylogenetically-relevant taxa, including early branching animals (sponges, ctenophores) and close relatives of animals (choanoflagellates, filastereans, ichthyosporeans). We argue that many of the mechanisms posited to explain animal transcriptional complexity, such as large increases in transcription factor numbers, new transcription factor families, and distal enhancers, did not factor significantly into animal origins. Instead, we propose that the re-purposing of pre-existing transcriptional regulatory modules through cis-regulatory evolution and gene duplication events, combined with new protein-protein interactions among TFs, may have been fundamental to the transcriptional regulatory architecture of the first animals.

Evolutionary Machine Learning (EML) has demonstrated its effectiveness in modeling various real-world application domains, including the dynamics of diseases and the creation of predictive models across diverse fields. However, the challenge of data imbalance adversely impacts the performance of EML models. While strategies involving misclassification costs or cost-sensitive learning exist to address this issue, their integration into EML has yet to be thoroughly explored. This paper aims to fill this gap by investigating the application of cost-sensitive EML for intelligent health risk prediction. More specifically, this paper delves into the utilization of cost-sensitive genetic programming (CSGP) and cost-sensitive genetic algorithms (CSGA), which are among the most widely used algorithms in the EML category. The study entails training CSGP and CSGA to predict the early onset of three chronic conditions (hypertension, diabetes, and fatty acid-related disorders) through the development of an EML model. Subsequently, the model's performance is evaluated through standard fitness functions such as sensitivity, specificity, and F1-score. From the experimental results, EML models demonstrate promising results in identifying the occurrence of chronic diseases. Further optimization of the cost-sensitive EML model holds the potential for enhanced outcomes in modeling medical problems.

Recent successes in the field of evolutionary cancer cell biology (ECCB) have brought to a head two of the most important controversies regarding cancer origin. The first concerns the question of whether carcinogenesis is initiated only by genetic alterations, mutations, and driver genes, as the mutational theory teaches. The ECCB, claims that a large number of polyploidy-related cancers (PGCC cancers) are not due to mutations, but rather to inadequate ancient repair mechanisms used by DNA-damaged stem cells for their repair. Somatic mutations are merely secondary. The second controversy, described in the previous article, concerns the non-mutational theory itself: Are non-mutational polyploid cancers an atavism - as previously thought - or rather the effect of an ancient gene regulatory network aGRN that controls genome reprogramming in precancerous DNA-damaged cells as well in the transformed cells. Finally, the unicellular gene module of cancer, of which the aGRN is a part, has evolved along with the multicellular genome during the last 1000 My of evolution. and non-mutated cancer cell systems are under the control of the aGRN. The atavistic theory relies on phylostratigraphic evidence to determine the age of cancer genes. It states that most cancer-like genes arose during the transition period from unicellularity to multicellularity, but also during the early metazoan era. In our opinion, the atavistic theory is flawed and suffers from many misunderstandings. It provides little insight into the origin and coevolution of the cancer cell system and its control by the ancient gene regulatory network aGRN.

Multicellular life forms have evolved many times in our planet, suggesting that this is a common evolutionary innovation. Multiple advantages have been proposed for multicellularity (MC) to emerge. In this paper we address the problem of how the first precondition for multicellularity, namely "stay together" might have occurred under spatially limited resources exploited by a population of unicellular agents. Using a minimal model of evolved cell-cell adhesion among growing and dividing cells that exploit a localised resource with a given size, we show that a transition occurs at a critical resource size separating a phase of evolved multicellular aggregates from a phase where unicellularity (UC) is favoured. The two phases are separated by an intermediate domain where where both UC and MC can be selected by evolution. This model provides a minimal approach to the early stages that were required to transition from Darwinian individuality to cohesive groups of cells associated with a physical cooperative effect: when resources are present only in a localised portion of the habitat, MC is a desirable property as it helps cells to keep close to the available local nutrients.

Though the cancer research community has used mouse xenografts for decades more than zebrafish xenografts, zebrafish have much to offer: they are cheap, easy to work with, and the embryonic model is relatively easy to use in high-throughput assays. Zebrafish can be imaged live, allowing us to observe cellular and molecular processes in vivo in real time. Opponents dismiss the zebrafish model due to the evolutionary distance between zebrafish and humans, as compared to mice, but proponents argue for the zebrafish xenograft’s superiority to cell culture systems and its advantages in imaging. This review places the zebrafish xenograft in the context of current views on cancer and gives an overview of how several aspects of this evolutionary disease can be addressed in the zebrafish model. Zebrafish are missing homologs of some human proteins and (of particular interest) several members of the matrix metalloproteinase (MMP) family of proteases, which are known for their importance in tumour biology. This review draws attention to the implicit evolutionary experiment taking place when the molecular ecology of the xenograft host is significantly different than that of the donor.

Today, Colebrook’s equation is mostly accepted as an informal standard for modeling of turbulent flow in hydraulically smooth and rough pipes including transient zone in between. The empirical Colebrook’s equation relates the unknown flow friction factor (λ) with the known Reynolds number (R) and the known relative roughness of inner pipe surface (ε/D). It is implicit in unknown friction factor (λ). Implicit Colebrook’s equation cannot be rearranged to derive friction factor (λ) directly and therefore it can be solved only iteratively [λ=f(λ, R, ε/D)] or using its explicit approximations [λ≈f(R, ε/D)]. Of course, approximations carry in certain error compared with the iterative solution where the highest level of accuracy can be reached after enough number of iterations. The explicit approximations give a relatively good prediction of the friction factor (λ) and can reproduce accurately Colebrook’s equation and its Moody’s plot. Usually, more complex models of approximations are more accurate and vice versa. In this paper, numerical values of parameters in various existing approximations are changed (optimized) using genetic algorithms to reduce maximal relative error. After this improvement computational burden stays unchanged while accuracy of approximations increases in some of the cases very significantly.

Capulus danieli, a distinct member of Capulidae, exhibits a unique ecological behaviour by attaching and drilling onto the pecten, distinguishing itself from other gastropods. Herein, we present the first characterisation of the mitochondrial genome of Capulus danieli. The results showed that the genome spans 15600 base pairs, with an A + T content of 71.12% and a G + C content of 28.88%. Within this genetic makeup, we identified 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. Phylogenetic analysis revealed a close evolutionary relationship between Capulus danieli and members of the Ficoidea superfamily. The divergence time estimation suggested that Capulus danieli diverged approximately 52.29 million years ago. These findings significantly contribute to our understanding of the evolutionary history and genetic architecture of Capulus danieli, shedding light on its unique ecological adaptations to the marine environment.

The optimal structural design is imperative to minimize material consumption and reduce the environmental impact of construction. Given the complexity in the formulation of structural design problems, the process of optimization is commonly performed using artificial intelligence (AI) global optimization, such as Genetic Algorithm (GA). However, the integration of AI-based optimization together with visual programming (VP) in building information modeling (BIM) projects warrants further investigation. This study proposes a workflow by combining structure analysis, VP, BIM, and GA to optimize trusses. The methodology encompasses several steps including: (i) generation of parametric trusses in Dynamo VP; (ii) performing the finite element modeling (FEM) using Robot Structural Analysis (RSA); (iii) retrieving and evaluating the FEM results interchangeably between Dynamo and RSA; (iv) finding the best solution using GA; and (v) importing the optimized model into Revit, enabling the user to perform simulations and engineering analysis, such as life cycle assessment (LCA) and quantity surveying. The feasibility of the proposed workflow was tested on benchmark problems and compared with open literature. The outcomes of this study offer insight into the opportunities and limitations of combining VP, GA, FEA, and BIM for structural optimization applications, particularly to enhance structural efficiency and sustainability in construction.

The first half of the 20th century was noteworthy for the introduction of a unique group of drugs – antibiotics. It drastically changed concepts of infectious diseases treatment, which for centuries remained a scourge of the human population. With improvement of the antibiotic treatment efficacy, humanity has faced the problem of a dramatic increase in antibiotic resistance in bacteria. The COVID-19 pandemic has only exacerbated the problem and posed a new challenge to the medical community in finding solutions, both clinical and organizational and methodological, to fight antibiotic resistance widespread all over the globe. This publication covers some aspects of evolutionary processes in either pathogens or diseases, including ethical perspective.

Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have collectively transformed our understanding of the evolutionary history of animals. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and traditional phylogenies. Here, I argue that tackling this multifaceted problem lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent developments in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence and theory. I then argue that integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond.

We have shown that the use of evolutionary gravitational constants G, the speed of light c, and cosmological constant Λ in the Einstein’s field equations leads to a very simple model that fits the supernovae Ia data with a single parameter as well as the standard ΛCDM model with two parameters, and has the predictive capability superior to the latter. We have shown that at the current time G and c both increase as dG/dt = 5.4GH₀ and dc/dt = 1.8cH₀ with H₀ as the Hubble constant, and Λ decreases as dΛ/dt = −1.2ΛH₀. Negative finding on the variation of G with time derived from the analysis of lunar laser ranging data in several studies has been attributed to the fact that these studies did not consider the variation of c simultaneously with G.

The evolution of human societal dynamics over the course of decades and centuries has led to an ever-increasingly complex digital modern life, one of the hallmark of which is the need for multi-tasking, inclusive of that with media. Is there an empirical mapping between this macroscopic (digital) evolution of the human societal dynamics (in terms of multi-tasking) and the microscopic evolution of the functional molecular units within cells (i.e., proteins) and their manifold cross-talks? Multi-tasking requires a certain degree of intrinsic or adapted flexibility which is as true at the bio-molecular level. Evolutionary diversification of structure-function relationship in proteins emphasizes the functional importance of intrinsically disordered entities (IDPs/IDRs) which are highly dynamic biological soft matters. Multi-functionality is favorably supported by their fluid-like shapes and other new malleable members of the protein family. The new wealth of knowledge coming from recent research on protein intrinsic disorder, fold-switching, moonlighting, hub proteins etc. has given us new insights into protein structure – functional relationship. This has led to a paradigm shift in protein science, clearly diverging from the traditional 'one structure – one function' model applicable to enzyme classes to a more complex understanding of protein functionality. This paradigm shift has caused scientists to delve deeper into the subject, exploring various evolutionary toys and tools to fit the cumulative multi-functional demands in higher organisms. This commentary covers the different evolutionary arsenals to achieve the growing multi-functionality and argues in favor of protein intrinsic disorder as probably the sharpest weapon of all.

Bats are natural hosts for a wide variety of viruses and could therefore be the reservoir, source and spillover for several mammalian viruses, including adenoviruses. We examined faecal samples from 12 bats (five species of the family Vespertilionidae) from central Russia (Moscow Region) and found that two of them (16%) were positive for mastadenoviruses. One of the identified viruses was isolated from faeces of Nyctalis noctule and named BatAdV/MOW15-Nn19. The genome of the BatAdV/MOW15-Nn19 was 37,915 bp in length. Comparative studies have shown significant divergence of the nucleotide sequence of the BatAdV/MOW15-Nn19 genome from European mastadenoviruses, the highest genome sequence similarity was to isolate WA3301 from an Australian bat. Phylogenetic analysis, as well as a comparative analysis of the protein coding genes to homologous available from public database, showed evidence of novel species within Mastadenovirus genus (preliminary named «K»). Analysis of the short part of the DNA polymerase gene of BatAdV/MOW15-Nn19 reveals few NCBI records from Europe with high identity to the new virus, i.e. mastadenoviruses related to the new species are circulating in European bats. The partial genome of another mastadenovirus from Pipistrellus nathusii was identified, it represented bat adenovirus species B, which is widely distributed in European Vespertilionidae bats. New data on the genetic diversity of bat adenoviruses may help to better understand how they evolved in mammals and spread across Europe.

Cell-culture meat is a novel concept to replace traditional meat produced from animals, and to satisfy rising food demands due to the world population growth. It is still a young field and requires to solve technical issues including cell sources and types, efficient culture for large scale production, taste and texture for customer satisfaction. The current review summarized traditional beef meat production and evaluation methods for customer satisfaction. In particular, serum biomarkers for beef meat evaluation are discussed, which can be applicated for cell-culture meat production.

This paper addresses the parameter identification of a one-link flexible manipulator based on the experimental measurement of the inputs/outputs, the finite element model, and the application of evolutionary algorithms. A novel approach is proposed to find the values of inertia, stiffness, and damping parameters by minimizing the difference between the numerical model’s outputs and the testbed’s outputs, considering the joint position and acceleration of the link’s tip. The dynamic model is initially obtained using the finite element method and the Lagrange principle. A prototype of a single one-link flexible manipulator is used in the experimental application wherein the servomotor applies the input torque, and the outputs are the joint angle and the link’s tip acceleration. Then, an optimization problem minimizes the difference between numerical and experimental outputs to determine the set of parameters using evolutionary algorithms. A comparative analysis to obtain the identified parameters is established using genetic algorithms, particle swarm optimization, and differential evolution. The proposed identification approach permitted the determination of the dynamic parameters based on the complete dynamic model of the flexible-link manipulator, which is different from the approaches reported in the literature that identify a simplified model. This information is essential for the design of the motion and vibration control laws.

Purpose: This study's objective was to examine international research trends in behavior management that had been written about in journals that were indexed by Scopus and authored by scientists from all around the world.Patients and methods: We examined publications in the Scopus database using bibliometric and content analysis. We only retrieved English-language articles. The VOSviewer program was used for content analysisResults: We found 808 papers on behavior management during the previous 50 years by following the study strategy. The study concentrated more on authors, nations, institutions, journals, documents, and keywords, as well as the annual scientific production (classification by subject area and document type)Conclusion: The finding prompts a discussion regarding behavior management for next research.

The evolutionary systems (ES) include software applications that solve problems using heuristic methods instead of the deterministic ones. The classical computing used for ES development involves random methods to improve different kinds of genomes. The mappings of these genomes lead to individuals that correspond to the searched solutions. The individual evaluations by simulations serve for the improvement of their genotypes. Quantum computations, unlike the classical computations, can describe and simulate a large set of individuals simultaneously. This feature is used to diminish the time for finding the solutions. Quantum Petri Nets (QPNs) can model dynamical systems with probabilistic features that make them appropriate for the development of ES. Some examples of ES applications using the QPNs are given to show the benefits of the current approach.

Cooperative localization under complex urban environments has become a solution to replace the Global Navigation Satellite System (GNSS) positioning. Due to utilizing distance measured and information exchanged between vehicles, cooperative localization results in high computational complexity and heavy communication overhead. This paper proposes a cooperative localization method based on evolutionary coalitional game theory, which implements vehicles' location estimation with less communication cost. We select the neighboring vehicles to form a coalition based on the node's square position error bound and communication cost. The location is obtained via exchanging information between vehicles. It is evident from the simulations and results that the proposed method holds low communication overhead while maintaining localization accuracy.

Transporter proteins, P-glycoprotein (P-gp) and P4ATPase-CDC50, are responsible for the transport of Miltefosine drug across cell membrane of a protozoan parasite Leishmania major. Mutations or change in activity of these proteins may lead to emergence of resistance in the parasite. Owing to the structural and functional importance of these transporter proteins, in this ppaper, we have tried to decipher the evolutionary divergence of these Miltefosine transporter proteins across different forms of life including Protists, Fungi, Plants and Animals. We retrieved 96, 207, and 189 sequences of P-gp, P4ATPase and CDC50 proteins respectively, across diverse variety of organisms for the conserved analysis. Phylogenetic trees were constructed for these three transporter proteins based on Bayesian posterior probability inference. The evolutionary analysis concluded that these proteins remain highly conserved throughout the species diversity but still substantial differences in the proteins for host (Homo sapiens) and parasite (L. major) were observed which have led in targeting these Miltefosine transporter proteins in a parasite specific manner.

Machine learning research has been able to solve problems in multiple aspects. An open area of research is machine learning for solving optimisation problems. An optimisation problem can be solved using a metaheuristic algorithm, which is able to find a solution in a reasonable amount of time. However, there is a problem, the time required to find an appropriate metaheuristic algorithm, that would have the convenient configurations to solve a set of optimisation problems properly. A solution approach is shown here, using a proposal that automatically creates metaheuristic algorithms aided by a reinforced learning approach. Based on the experiments performed, the approach succeeded in creating a metaheuristic algorithm that managed to solve a large number of different continuous domain optimisation problems. This work's implications are immediate because they describe a basis for the generation of metaheuristic algorithms in real-time.

We applied evolutionary game theory to extend a resource constrained security game model for confidentiality attacks in an Advanced Metering Infrastructure (AMI), which is a component of IoT-enabled Smart Grids. The AMI is modelled as a tree structure where each node aggregates the information of its children before encrypting it and passing it on to its parent. As a part of the model, we developed a discretization scheme for solving the replicator equations. The aim of this work is to explore the space of possible behaviours of attackers and to develop a framework where the AMI nodes adaptively select the most profitable strategies. Using this model, we simulated the evolution of a population of attackers and defenders on various cases resembling the real life implementation of AMI. We discuss in depth how to enhance security in AMI using evolutionary game theory either by a priori analysis or as a tool to run dynamic and adaptive infrastructure defence.

The constraint equations in Maxwell theory are investigated. In analogy with some recent results on the constraints of general relativity it is shown, regardless of the signature and dimension of the ambient space, that the "divergence of a vector field" type constraints can always be put into linear first order hyperbolic form for which global existence and uniqueness of solutions to an initial-boundary value problem is guaranteed.

This study investigates the spatial and temporal dynamics of Paomo restaurants in Xi'an's central urban area from 2012 to 2023, leveraging Point of Interest (POI) data through a series of sophisticated analytical techniques. Methods including nearest neighbor distance, kernel density estimation, and band set statistical analysis were employed to thoroughly examine the evolutionary patterns and key drivers influencing the spatial distribution of these eateries. Our results highlight a notable trend of expansion from the central city to the periphery, characterized by significant spatial agglomeration. Initially concentrated in the city center, the distribution of Paomo restaurants has progressively shifted towards multiple distinct cores, reflecting the dual influence of urban policy initiatives and the dynamics of market competition. Furthermore, the research identifies several pivotal factors shaping this spatial distribution, particularly transportation access, residential quality of life, and the availability of commercial services. These findings demonstrate the profound effects of urban spatial reconfiguration and socioeconomic development on the specialized catering industry. The insights gleaned from this analysis offer valuable guidance for urban planners and policymakers, providing strategic recommendations for the spatial planning of specialty catering services to optimize urban layouts and foster sustainable economic progress.

Cancer is a complex and devastating disease that has engaged scientists and researchers for decades. Despite tremendous efforts, previous hypotheses about cancer development have not achieved significant breakthroughs. Evolutionary Cancer Cell Biology (ECCB) is a novel and emerging branch of oncological science that provides an evolutionary perspective on the origin of cancer. It reveals that the cancer genome evolved hundreds of millions of years ago, long before multicellular organisms such as metazoans and humans emerged. ECCB aims to unify all evolutionary insights, hypotheses, and theories into a cohesive framework. It investigates the intricate relationship between cancer genomics and ancient pre-metazoan genes that emerge when normal cells transform into cancer cells. It challenges the conventional wisdom of cancer research by suggesting that cancer could arise through intrinsic cellular mechanisms without genetic alterations and mutations. Furthermore, it postulates that somatic mutations are only secondary, downstream events in the process of oncogenesis.

Polycystic ovary syndrome (PCOS) is increasingly recognized as a complex metabolic disorder that manifests in genetically susceptible women following a range of negative exposures to nutritional and environmental factors related to contemporary lifestyle. The hypothesis that PCOS phenotypes are derived from a mismatch between ancient genetic survival mechanisms and modern lifestyle practices is supported by a diversity of research findings. The proposed evolutionary model of the pathogenesis of PCOS incorporates evidence related to evolutionary theory, genetic studies, in-utero developmental epigenetic programming, transgenerational inheritance, metabolic features including insulin resistance, obesity and the apparent paradox of lean phenotypes, reproductive effects and subfertility, the impact of the microbiome and dysbiosis, endocrine disrupting chemical exposure, and the influence of lifestyle factors such as poor quality diet and physical inactivity. Based on these premises, the diverse lines of research are synthesized into a composite evolutionary model of the pathogenesis of PCOS. It is hoped that this model will assist clinicians and patients to understand the importance of lifestyle interventions in the prevention and management of PCOS and provide a conceptual framework for future research. It is appreciated that this theory represents a synthesis of the current evidence and that it is expected to evolve and change over time.

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH introgressed with archaic hominins once they left the African continent. Current out of African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

Decision sciences (DSC) involve studying complex dynamic systems and processes to aid informed choices subject to constraints in uncertain conditions. It integrates multidisciplinary methods, techniques, and strategies to evaluate decision engineering processes, identifying alternatives and providing insights towards enhancing prudent decision-making. This study analyzes the evolutionary trends and innovation in DSC education and research to uncover the transformations over the years. We employ the science mapping method, text analytics, and metadata from bibliographic databases to evaluate thematic and social structures. The results highlight data science methods, including data mining and business/learning analytics as essential components. The evolutionary trends in DSC education and research mirror the development in practice, including technological transformation, computer science advances, and engineering processes. Sustainable education through virtual/online learning also constitutes a significant component of scientific production. The evolutionary trends in DSC education and research highlight innovative pedagogical approaches and strategies, including computer simulation and games ('play and learn'). The current era witnessed generative artificial intelligence (GenAI) adoption (e.g., ChatGPT) in teaching, learning, and scholarly activities amidst challenges (academic integrity, plagiarism, intellectual property violations, and other ethical and legal issues). Future research will implement and integrate AI automatic detection systems to address some GenAI adoption challenges.

Based on a literature review, a framework for digital organizational culture with a focus on innovation is proposed. This digital organizational culture becomes relevant today since digital transformation requires an appetite for risk and a willingness to undertake, aspects that are strengthened by an environment and atmosphere that motivate individuals to generate new ideas. The proposal begins with a diagnosis of the existing organizational culture, which allows identifying the differences between the components of the current organizational culture and the innovation-oriented digital organizational culture. Through this diagnosis, the gaps that need to be addressed to achieve a digital organizational culture with innovative characteristics are identified. In addition, specific recommendations are proposed to carry out this transformation. In the process, the assumptions underlying the current typology of the company's organizational culture are highlighted. The importance of integrating creativity, risk readiness, and entrepreneurial willingness into the digital organizational culture aimed at innovation is emphasized. These elements are essential to create an environment

The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and secondary meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understanding of SAM morphology and regulation is based on studies conducted mainly on some angiosperms, including economically important crops such as maize (Zea mays) and rice (Oryza sativa), and the model species Arabidopsis (Arabidopsis thaliana). However, studies in other plant species from the gymnosperm class are scant, making difficult comparative analyses that help us understand SAM regulation in diverse plant species. This limitation prevents deciphering the mechanisms by which evolution gave rise to the multiple plant structures within the plant kingdom, and determined the conserved mechanisms involved in SAM maintenance and operation. This review aims to integrate and analyze the current knowledge of SAM evolution by combining the morphological and molecular information recently reported from the plant kingdom.

Polycystic ovary syndrome (PCOS) is a common endocrinopathy of reproductive-aged women characterized by hyperandrogenism, oligo-anovulation and insulin resistance closely linked with preferential abdominal fat accumulation. As an ancestral primate trait, PCOS was likely further selected in humans when scarcity of food in hunter-gatherers of the late Pleistocene additionally programmed for enhanced fat storage to meet the metabolic demands of reproduction in later life. As an evolutional model for PCOS, healthy normal-weight women with hyperandrogenic PCOS have subcutaneous (SC) abdominal adipose stem cells that favor fat storage through exaggerated lipid accumulation during development to adipocytes in vitro. In turn, fat storage is counterbalanced by reduced insulin sensitivity and preferential accumulation of highly-lipolytic intra-abdominal fat in vivo. This metabolic adaptation in PCOS balances energy storage with glucose availability and fatty acid oxidation for optimal energy use during reproduction; its accompanying oligo-anovulation allowed PCOS women from antiquity sufficient time and strength for childrearing of fewer offspring with a greater likelihood of childhood survival. Heritable PCOS characteristics are now affected by today’s contemporary environment through epigenetic events that predispose to lipotoxicity with excess weight gain and pregnancy complications, calling for an emphasis on preventive healthcare to optimize the long-term, endocrine-metabolic health of PCOS women in today’s obesogenic environment.

Supervised machine learning (SML) is a powerful method for predicting a small number of well-defined output groups (e.g., potential buyers of a certain product) by taking as input a large number of known well-defined measurements (e.g., past purchases, income, ethnicity, gender, credit record, age, favorite color, favorite chewing gum). SML is predicated upon the existence of a training dataset in which the correspondence between the input and output is known to be true. SML has had enormous success in the world of commerce, and this success has prompted a few scientists to employ it in the study of molecular and genome evolution. Here, we list the properties of SML that make it an unsuitable tool in evolutionary studies. In particular, we argue that SML cannot be used in an evolutionary exploratory context for the simple reason that training datasets that are known to be a priori true do not exist. As a case study, we use an SML study in which it was concluded that most human genomes evolve by positive selection through soft selective sweeps (Schrider and Kern 2017). We show that in the absence of legitimate training datasets, Schrider and Kern (2017) used (1) simulations that employ many manipulatable variables and (2) a system of cherry-picking data that would put to shame most modern evangelical exegeses of the Bible. These two factors, in addition to the lack of methodological detail and the lack of either negative controls or corrections for multiple comparisons, lead us to conclude that all evolutionary inferences derived from so-called SML algorithms (e.g., discoal) should be taken with a huge shovel of salt.

Contemporary climate change is exposing plant populations to novel combinations of temperatures, drought stress, [CO₂] and other abiotic and biotic conditions. These changes are rapidly disrupting the evolutionary dynamics of plants. Despite the multifactorial nature of climate change, most studies typically manipulate only one climatic factor. In this opinion piece, we seek to explore how climate change factors interact with each other and with biotic pressures to alter evolutionary processes. We first explore the ramifications of climate change for key life history stages (germination, growth and reproduction). We then examine how mating system variation influences population persistence under rapid environmental change and propose that mixed mating could be advantageous in future climates. Furthermore, we discuss how spatial and temporal mismatches between plants and their mutualists and antagonists could promote or constrain adaptive responses to climate change. For example, plant-virus interactions vary from highly pathogenic to mildly facilitative, and are partly mediated by temperature, moisture availability and [CO₂]. Will host plants exposed to novel, stressful abiotic conditions be more susceptible to viral pathogens? Finally, we propose novel experimental approaches that could illuminate how plants will cope with unprecedented global change, such as resurrection studies combined with experimental evolution, genomics or epigenetics.

The ongoing mutations in the structural proteins of SARS-CoV-2 is the major impediment for prevention and control of the COVID-19 disease. The envelope (E) protein of SARS-CoV-2 is a structural protein existing in both monomeric and homopentameric forms, associated with a multitude of functions including virus assembly, replication, dissemination, release of virions, infection, pathogenesis, and immune response stimulation. In the present study, 81,818 high quality E protein sequences retrieving from the GISAID were subjected to mutational analyses. Our analysis revealed that only 0.012 % (982/81818) stains possessed amino acid (aa) substitutions in 63 sites of the genome while 58.77% mutations in the primary structure of nucleotides in 134 sites. We found the V25A mutation in the transmembrane domain which is a key factor for the homopentameric conformation of E protein. We also observed a triple cysteine motif harboring mutations (L39M, A41S, A41V, C43F, C43R, C43S, C44Y, N45R) which may hinder the binding of E protein with spike glycoprotein. These results therefore suggest the continuous monitoring of each structural protein of SARS-CoV-2 since the number of genome sequences from across the world are continuously increasing.

Human language and social cognition are two key disciplines that have traditionally been studied as separate domains. However, emerging research from detailed studies of comparative animal behavior, human social behavior, language acquisition in children, social cognitive neuroscience, and the cognitive neuroscience of language suggest that language and social cognition are two deeply interrelated capacities of the human species. For instance, recent developmental studies on the acquisition of language in infants and young children, draw attention to the important crucial benefits associated with several different aspects of social stimulation for youngsters, including the quantity and quality of linguistic input, dyadic infant/child-to-parent verbal and non-verbal social interactions, and other important social cues integral for facilitating language learning and social bonding. Studies of the adult human brain further suggest a high degree of specialization for sociolinguistic information processing, memory retrieval, and comprehension, suggesting the function of these regions may link language with social cognition and social bonding. In effect, the social brain and social complexity hypotheses may jointly help to explain how neurotypical children and adults learn language, why autistic adults and children exhibit simultaneous deficits in language and social cognition, and why nonhuman primates and other animals with significant computational abilities do not acquire the capacity for language. But perhaps most critically, the following article argues that this and related research will allow scientists to generate a holistic profile and deeper understanding of the healthy adult social brain, while developing more innovative and effective diagnoses, prognoses, and treatments for maladies and deficits also associated with the social brain.

Promoting close and sustainable cooperation between schools, enterprises, and government has become an important concern in many countries. Based on evolutionary game theory, this paper constructs a tripartite evolutionary game model of schools, enterprises, and government in order to analyze the stability of strategies of the different players. The results show that the main factor that influences the stability of the strategies of schools and enterprises is the reward of positive cooperation from sources other than the government, and the main factor that influences the stability of the strategy of the government is the benefit of positive cooperation strategy under the scenario where schools cooperate with enterprises. Therefore, the government should focus on implementing more effective policies, such as increasing the incentives and penalties, improving the mechanism for managing conflicts, ensuring the fairness of benefits distribution, and clarifying the responsibilities of different departments; schools should focus on providing more practical curricula and programs for students, training high-quality teachers, and perfecting talent cultivation to meet the needs of enterprises; and enterprises should focus on providing job experiences for students and transforming the results of schools’ teaching and theoretical research into practical productivity.

The genetic systems of Paspalum species have not been extensively studied. We analysed the ploidy, reproductive mode, mating system, and fertility of four Paspalum species - P. durifolium, P. ionan-thum, P. regnellii, and P. urvillei. An analysis of 378 individuals from 20 populations of north-eastern Argentina was conducted. All populations of the four Paspalum species were pure tetraploid and had a sexual and stable reproductive mode. However, some populations of P. durifolium and P. ionanthum showed low levels of apospory. Populations of P. durifolium and P. ionanthum had low seed sets under self-pollination but were fertile under open pollination, showing that self-incompatibility likely caused self-sterility. In contrast, populations of P. regnellii or P. urvillei showed no evidence of apospory and seed set in both self- and open pollination conditions were high, suggesting that they are self-compatible, due to the absence of pollen-pistil molecular in-compatibility mechanisms. The evolutionary origin of the four Paspalum species could explain these differences. This study supplies valuable insights into the genetic systems of Paspalum species, which could have implications for their conservation and management.

Since its advent in the mid-twentieth century, the field of artificial intelligence (AI) has been heavily influenced by biology. From the structure of the brain to evolution by natural selection, core biological concepts underpin many of the fundamental breakthroughs in modern AI. Here, focusing specifically on artificial neural networks (ANNs) that have become commonplace in machine learning, we show the numerous connections between theories based on coevolution, multi-level selection, modularity and competition and related developments in ANNs. Our aim is to illuminate the valuable but often overlooked inspiration biologists have provided AI research and to spark future contributions at this intersection of biology and computer science. Although recent advances in AI have been swift, many significant challenges remain requiring innovative solutions. Thankfully, biology in all its forms still has a lot to teach us, especially when trying to create truly intelligent machines.

In order to reconstruct the origin and pathways of variola virus (VARV) dispersion, we analyzed 47 VARV isolates available in public databases and their SNPs. The mean substitution rate of the whole genomes was 9.41x10-6 (95%HPD:8.5-11.3x10-6) substitutions/site/year. The time of the tree root was estimated to be a mean 68 years (95%HPD:60.5–75.9). The phylogeographical analysis showed that the Far East and India were the most probable locations of the tree root and of the inner nodes, respectively, whereas for the outer nodes it corresponded to the sampling locations. The Bayesian Skyline plot showed that the effective number of infections started to grow exponentially in 1915-1920, peaked in the 1940s, and then decreased to zero. Our results suggests that the VARV major strains circulating between 1940s-1970s probably shared a common ancestor originated in the Far East; subsequently moved to India, which became the center of its dispersion to eastern and southern Africa, and then to central Africa and the Middle East, probably following the movements of people between south-eastern Asia and the other places with a common colonial history. These findings may help to explain the controversial reconstructions of the history of VARV obtained using long- and short- term calibrations.

This study aimed to compare the levels of physical activity and quality of life reported by Chileans with and without osteoarthritis (OA). Educational level and monthly income data were collected from eighty-two participants (62 women and 20 men), of whom 41 had OA. Concerning the medical information of the persons suffering from OA, diseases, and date of diagnosis were indicated. The International Physical Activity Questionnaire-Short Form (IPAQ-SF) and its Elderly version (IPAQ-E) estimated physical activity levels. The Short Form 36 Questionnaire (SF-36) assessed health-related quality of life. The findings indicate that non-OA subjects scored higher on all dimensions of the SF-36, including physical function, physical role, bodily pain, general health, vitality, social function, emotional role, and mental health. Individuals with OA reported better physical function and role, general health, vitality, social function, and mental health when they walked more. However, no associations were found between any physical activity levels and the degree of pain in people with OA. Our findings underscore the critical role of investigating physical activity in OA patients to enhance their quality of life, particularly in light of the increased sedentary behavior observed post-pandemic.

Cleomella serrulata is a native flowering plant found in North America. Even though this plant is of ecological and native medicinal importance, very little is known about the genomic makeup of Cleomella and the Cleomaceae family at large. Here we report the complete chloroplast genome of Cleomella serrulata and provide an evolutionary comparison to other chloroplast genomes from Cleomaceae and closely related families. This study confirms the taxonomic placement of Cleomella as a distinct genus, but also provides phylogenetic insights that imply potential adaptive strategies and evolutionary mechanisms driving genomic diversity of the Cleomella genus. Whole genome-based and ANI comparisons indicate that the Cleomella species form a distinct clade that is about equidistant from the other Cleomaceae genera as it is from the genera from the nearby Capparaceae and Brassicaceae. This is the first complete chloroplast-based phylogenetic comparison of Cleomella species to other related genera and helps refine the complex taxonomic distinctions of the Cleomaceae.

Thyroid hormones are essential for regulating the metabolic rate, growth, development, and maintenance of many physiological processes in vertebrates. They are synthesized by the thyroid gland, which is an ancient organ that evolved early in vertebrate evolution. This study aims to characterize the evolutionary path of polymorphic variants associated with the hypothalamus-pituitary-thyroid (HPT) axis by comparing ancient DNA (aDNA) sequences of Late Pleistocene-Holocene hominin populations with those of modern humans. We evaluated the genetic sequences of several populations, including Neanderthals, Denisovans, Palaeolithic hunter-gatherers from European Russia and Sunghir, and Neolithic hunter-gatherers/farmers from Anatolia focusing on genes involved in the development of the thyroid gland and thyroid hormone (TH) biosynthesis, secretion, and transport. Results showed interesting variants in the DIO2 (rs225014), TPO (rs4927611), and TG (rs2069556 and rs1133076) genes. All SNPs seemed to confirm that Neanderthals, and in part Denisovas, were physiologically hypothyroidic. Probably they had lower T3 levels due to defective production or peripheral conversion. From the moment that the most favourable alleles in terms of T3 production appear during the Paleolithic, we are inclined to assume that their selection was linked to environmental pressure.Our study supports insight into the evolutionary history of the endocrine system and can help in providing understanding into the evolution of physiological systems and their adaptation to changing environments. Understanding the evolution of thyroid hormones can also shed light on the mechanisms underlying thyroid disorders in humans.

The escalating reliance of modern society on information and communication technology has rendered it vulnerable to an array of cyber-attacks, with distributed denial-of-service (DDoS) at-tacks emerging as one of the most prevalent threats. This paper delves into the intricacies of DDoS attacks, which exploit compromised machines numbering in the thousands or more to disrupt data services and online commercial platforms, resulting in significant downtime and financial losses. Recognizing the gravity of this issue, various detection techniques have been explored, yet the quantitative and prior detection of DDoS attacks has seen a decline in recent methods. This research introduces an innovative approach by integrating evolutionary optimization algorithms and machine learning techniques. Specifically, the study proposes XGB-GA Optimization, RF-GA Optimization, and SVM-GA Optimization methods, employing Evolutionary Algorithms Opti-mization with TOPOT-Genetic Programming. Datasets pertaining to DDoS attacks were utilized to train machine learning models based on XGB, RF, and SVM algorithms, and 10-fold cross-validation was employed. The models were further optimized using evolutionary algo-rithms, achieving remarkable accuracy scores: 99.99% with the XGB-GA method, 99.50% with RF-GA, and 99.99% with SVM-GA. Furthermore, the study employed TPOT to identify the optimal algorithm for constructing a machine learning model, with the genetic algorithm pinpointing XGB-GA as the most effective choice. This research significantly advances the field of DDoS attack detection by presenting a robust and accurate methodology, thereby enhancing the cybersecurity landscape and fortifying digital infrastructures against these pervasive threats.

Eyes are quintessential complex traits and our understanding of their evolution guides models of trait evolution in general. A long-standing account of eye evolution argues natural selection favors morphological variations that allow increased functionality for sensing light (Darwin 1859; v. Salvini-Plawen and Mayr 1977; Nilsson and Pelger 1994; Nilsson 2013). While certainly true in part, this focus on visual performance does not entirely explain why diffuse photosensitivity persists even after eyes evolve, or why eyes evolved many times, each time using similar building blocks. Here we briefly review a vast literature indicating most genetic components of eyes historically responded to stress caused directly by light, including UV damage of DNA, oxidative stress, and production of aldehydes. We propose light-induced stress had a direct and prominent role in the evolution of eyes by bringing together genes to repair and prevent damage from light-stress, both before and during the evolution of eyes themselves. Stress-repair and stress-prevention genes were perhaps originally deployed as plastic responses to light and/or as beneficial mutations genetically driving expression where light was prominent. These stress-response genes sense, shield, and refract light but only as reactions to ongoing light stress. Once under regulatory-genetic control, they could be expressed before light stress appeared, evolve as a module, and be influenced by natural selection to increase functionality for sensing light, ultimately leading to complex eyes and behaviors. Recognizing the potentially prominent role of stress in eye evolution invites discussions of plasticity and assimilation and provides a hypothesis for why similar genes are repeatedly used in convergent eyes. Broadening the drivers of eye evolution encourages consideration of multi-faceted mechanisms of plasticity/assimilation and mutation/selection for complex novelties and innovations in general.

This project aims to simulate and analyze population dynamics in evolutionary systems, using stochastic differential equations and probabilistic rules for crossbreeding and benefits. The study employs advanced computational techniques to model the evolution of populations over an extended period. Specifically, we explore a scenario with ten distinct groups, each starting with an equal population and evolving under defined genetic and cooperative behaviors. The simulation spans 1000 years, incorporating individual lifespans, stochastic updates, and probabilistic interactions. To ensure robustness and reliability, the study includes detailed statistical analysis, encompassing descriptive statistics, confidence intervals, and ANOVA tests. We further visualize the temporal behavior of populations and subpopulations, providing insights into the evolutionary dynamics and stability of the system. The results demonstrate the effectiveness of balanced cooperation and genetic diversity in maintaining stable population distributions. The project showcases the integration of mathematical modeling, statistical analysis, and computational simulations, contributing valuable insights into evolutionary biology and complex systems. It highlights the importance of interdisciplinary approaches in understanding and predicting population behaviors, with implications for both theoretical research and practical applications in fields such as ecology, genetics, probability and social sciences.

We introduced a novel biotin-binding peptide for sensing biotin, biotinylated proteins, and nu-cleotides. From a 15-mer library displayed on the RNA coliphage Qβ, a 15-amino acid long peptide (HGHGWQIPVWPWGQG) hereby referred to as nanotag was identified to selectively bind biotin. The targets selection was achieved through panning with elution by infection. The selected peptide was tested as a transducer for an immunogenic epitope of the foot-and-mouth disease virus (FMDV) on Qβ phage platform separated by a linker. The biotin-tag showed no significant in-fluence on the affinity of the epitope to its cognate antibody (SD6). The nanotag bound biotin selectively when fused either to the C- or N-terminus of the epitope. The epitope would not bind or recognize SD6 while positioned at the N-terminus of the nanotag. Additionally, the biotin com-peted linearly with the SD6 antibody in a competitive ELISA. Competition assays using the se-lected recombinant phage itself as a probe, or transducer, enable the operationalization of this technology as a biosensor toolkit to sense and quantify SD6 analyte. Herein, the published Strep II nanotag (DVEWLDERVPLVET) was used as a control and has similar functionalities to our pro-posed novel biotin-tag thereby providing a new platform for developing devices for diagnostic purposes.

: Polymer single screw extrusion is a major industrial processing technique used to obtain plastics products. To assure high outputs, tight dimensional tolerances, and excellent product performance, extruder screws may show different design characteristics. Barrier screws, which contain a second flight in the compression zone, have become quite popular as they promote and stabilize polymer melting. Therefore, it is important to design efficiently extruder screws and decide whether a conventional screw will do the job efficiently, or a barrier-screw should be considered instead. This work uses multi-objective evolutionary algorithms to design conventional and barrier screws (Maillefer screws will be studied) with optimized geometry. Processing of two polymers, Low Density Polyethylene and Polypropylene, is analyzed. A methodology based on the use of Artificial Intelligence (AI) techniques, namely data mining, decision making and evolutionary algorithms, is presented and utilized to obtain results with practical significance, based on relevant performance measures (objectives) used in the optimization. For the various case studies selected, Maillefer screws were generally advantageous for processing LDPE, while for PP the use of both types of screws would be feasible.

The role of lactic acid (lactate) in cell metabolism has been significantly revised in recent dec-ades. Initially, lactic acid was attributed to the role of a toxic end product of metabolism, which accumulation in the cell and extracellular space leads to acidosis, muscle pain and other adverse effects. However, it has now become obvious that lactate is not only a universal fuel molecule and the main substrate for gluconeogenesis, but also one of the most ancient metabolites with signaling function, which has a wide range of regulatory activity. The Warburg effect described 100 years ago (that means intensification of glycolysis associated with high lactate production), which is characteristic of many malignant tumors, confirms the key role of lactate not only in physiological conditions, but also in pathologies. The study of lactate’s role in the malignant transformation becomes more relevant in the light of the “atavistic theory of carcinogenesis,” which suggests that tumor cells return to a more primitive hereditary phenotype during micro-evolution. In this review, we attempted to summarize the accumulated knowledges about the functions of lactate in cell metabolism and its role in the process of carcinogenesis, and to con-sider the possible evolutionary significance of the Warburg effect.

A new form of beta coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) causing a recent pandemic outbreak possesses a linear positive ss-RNA genome with a length of 29,903 nt. Here, the genomes of SARS-CoV-2 from 821 samples were characterised for its better understanding of the genomic and evolutionary patterns. The phylogeny of SARS-CoV-2 was reconstructed using concatenated dataset consisting of all peptide encoding sequences under Bayesian Inference (BI) and Maximum Likelihood (ML) approaches. Comparison of all peptide encoding sequences reveals high divergence of amino acid sequences proportional to divergence of nucleotides, indicating that the viral genomic evolution has not been strictly neutral. The most part of the genome was under neutral evolution, however, the specific sites for peptide encoding sequences were evolved under positive selection. As well as providing reliable evidence on transmission routes of the SARS-CoV-2 outbreak, the phylogenetics and network analyses suggest the sample reported from Guangdong province is likely ancestor of the pandemic virus form. The overall substitution rate of SARS-CoV-2 genome was estimated to be 1.65 x 10^-3 per site per year, falling within the range for previously reported RNA viruses. Median estimation of tMRCA from Bayesian coalescent analyses corresponds to 10 September 2019. The exponential growth rate (r), doubling time (Td) and R₀ were estimated to be 47.43 per year, 5.39 days and 2.72, respectively. These findings convincingly emphasise that the use of more comprehensive genome data improves robustness and also enhances understanding of the demographic history of the outbreak.

Non-linear loads in circuits cause the appearance of harmonic disturbances both in voltage and current. In order to minimize the effects of these disturbances and, therefore, to control over the flow of electricity between the source and the load, they are often used passive or active filters. Nevertheless, determining the type of filter and the characteristics of their elements is not a trivial task. In fact, the development of algorithms for calculating the parameters of filters is still an open question. This paper analyzes the use of genetic algorithms to maximize the power factor compensation in non-sinusoidal circuits using passive filters, while concepts of geometric algebra theory are used to represent the flow of power in the circuits. According to the results obtained in different case studies, it can be concluded that the genetic algorithm obtain high quality solutions that could be generalized to similar problems of any dimension.

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of the apomictic species Boechera divaricarpa. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. 27048 protein-coding genes were predicted using a hybrid approach that combines homology-based and de novo methods. Also repeats, tRNA and rRNA genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. Also, a detailed analysis of evolution of the APOLLO apomixis-associated locus was performed. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species such as B. divaricarpa.