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Identifying the factors that influence the citation of articles helps authors improve the impact and reach of their research. Analysis of publications in the Journal of Fish Biology between 2008 and 2021 revealed that variables such as the number of keywords, abstract length, number of authors, and page length were associated with higher impact papers. These trends applied to both review and regular papers. These findings suggest that papers that are more informative, have higher numbers of authors, and have more keywords are more likely to be cited. Adoption of some simple "best‐practice" behaviors can improve the likelihood that a paper is cited. [ABSTRACT FROM AUTHOR]

The Society for the Study of Species Biology has announced the recipient of the 17th Plant Species Biology Best Paper Award. The winning paper, titled "Environmental and genetic effects on phenotypic differences between Elaeocarpus photiniifolia ecotypes in dry and mesic habitats on a Japanese oceanic island," explores how different environmental conditions have led to reproductive isolation and genetic differentiation in a specific plant species. Another paper, titled "The epiphytic orchid Vanda falcata is predominantly associated with a single Tulasnellaceae fungus in adulthood, and Ceratobasidiaceae fungi strongly induce its seed germination in vitro," investigates the symbiotic relationships between orchids and mycorrhizal fungi at different stages of growth. Both papers are featured in recent issues of Plant Species Biology. [Extracted from the article]

This paper celebrates the life and legacy of psychiatrist and Jungian author Anthony Stevens, who passed away at age 90 on July 13, 2023. It outlines Stevens's origins as a research fellow in Greece, where his work on infant attachment led to a lifelong dedication to establishing the biological and evolutionary foundation of psychiatry. It details his instrumental role in the debate about the theory of archetypes and describes the current state of the literature including the responses and reactions to Stevens's biological innatist position. The paper concludes with a career retrospective in which Stevens's major works are introduced and briefly described. [ABSTRACT FROM AUTHOR]

A complete workflow was presented for estimating the concentration of microorganisms in biological samples by automatically counting spots that represent viral plaque forming units (PFU) bacterial colony forming units (CFU), or spot forming units (SFU) in images, and modeling the counts. The workflow was designed for processing images from dilution series but can also be applied to stand-alone images. The accuracy of the methods was greatly improved by adding a newly developed bias correction method. When the spots in images are densely populated, the probability of spot overlapping increases, leading to systematic undercounting. In this paper, this undercount issue was addressed in an empirical way. The proposed empirical bias correction method utilized synthetic images with known spot sizes and counts as a training set, enabling the development of an effective bias correction function using a thin-plate spline model. Its application focused on the bias correction for the automated spot counting algorithm LoST proposed by Lin et al. Simulation results demonstrated that the empirical bias correction significantly improved spot counts, reducing bias for both fixed and random spot sizes and counts. [ABSTRACT FROM AUTHOR]

Biomimetics is an emerging field that allows mimicry of living organisms in nature to develop different techniques so as to solve hard and complex problems related to optimization. The different techniques developed in this field takes inspiration from biology or nature. Biology acts as a powerful tool for imitating, copying, learning, understanding and inspiring the development of new systems and models. The different techniques discussed in this paper include techniques based on evolutionary algorithms, neural network and swarm intelligence. All these techniques are biologically inspired and provide good accuracy. The accuracy of all these algorithms can be increased by using them in hybrid form with other techniques and using different datasets. The comparative analysis of these techniques is done using advantages, disadvantages and applications of these techniques. [ABSTRACT FROM AUTHOR]

In May 2023, herpetologists from six countries converged at the 8th Conference on the Biology of Plethodontid Salamanders in Hammond, Louisiana to share their latest cutting-edge research. The conference was hosted by the Department of Biological Sciences at Southeastern Louisiana University. Dr. Richard Bruce was the honoree. The presentations covered a diverse array of topics from gene expression to behavior to speciation, illustrating the value of plethodontid salamander biology to a range of disciplines. This special issue of Herpetologica includes 16 papers highlighting a range of research on plethodontids and encouraging new approaches to tackle old and new questions. [ABSTRACT FROM AUTHOR]

Space and time, which should properly be taken conjointly, are both communicatively produced and created with certain contextual perspectives—they are not independent physical entities. The standpoint of production makes the relationship between space and time comprehensible. They can either be mental-subjective, physical-objective, or social-intersubjective. Social and intersubjective (or E-series) spacetime might shed new light on biological thinking. For general readers, this paper provides a clue regarding an alternative conceptualization of spacetime based on biology. [ABSTRACT FROM AUTHOR]

Background: While the effectiveness of tutoring‐style videos has been reported in previous studies conducted in laboratories, how these types of videos facilitate students' learning experiences and achievement has not been much explored in prior studies, which prevents discussion on how to design such tutoring‐style videos. Objectives: In this study, we addressed the limitations reported in studies conducted in authentic classes and attempted to explore students' learning patterns and experiences with tutoring‐style videos involving interactions between the instructor and agents. In addition, we attempted to reveal what instructional strategies can be used in tutoring‐style videos to enhance students' engagement and achievement. Methods: The study took place in an undergraduate introductory biology class offered at a university located in the Midwest of the United States. The same instructor taught two sections of this course which lasted for 15 weeks during a Spring semester. The two sections were randomly assigned to an experimental group in which participants watched tutoring‐style videos and a control group with participants watching traditional videos. The experiment was administered in a module lasting two and a half weeks focused on microbiology. Surveys and tests were conducted to determine whether the tutoring‐style videos had a positive impact on student engagement and achievement. In addition, a video content analysis was carried out to elicit insights on how to design effective tutoring‐style videos. Results: For students' emotional engagement and perceived usefulness, no significant difference was found between the two groups, even though the descriptive statistics indicated slightly higher scores from the experimental group than the control group on both subscales. In terms of achievement, the participants reported significantly more learned concepts from watching rich‐interactions in the tutoring‐style videos than the participants in the control group; and they also reported a significantly smaller number of learned concepts from watching one‐interactions in the videos than the control group participants. We also found that instruction in the tutoring‐style videos used effective strategies for facilitating students' participation and cognitive processing. Conclusions: Our findings indicate that tutoring‐style videos can be effective learning materials by allowing students to engage in interactions between instructors and agents in the videos. The more instructional strategies used to facilitate the interactions between the instructor and the agents, the higher engagement can be expected from viewers. Our study would inform the design and development of effective tutoring‐style videos. Lay Description: What is already known about this topic: One‐on‐one tutoring is the gold standard in teaching.Tutoring‐style videos are found to be effective in teaching as well. What this paper adds: Tutoring‐style videos that film rich interactions lead to better learning.Tutoring‐style videos that film limited interactions are ineffective.Students who see agents in tutoring‐style videos as helpful perform better. Implications for practice and/or policy: Tutoring‐style videos should film rich interactions of tutoring sessions.Strategies should be used in videos to facilitate perceived agents' usefulness.Tutoring sessions filmed in videos should encourage a participatory atmosphere. [ABSTRACT FROM AUTHOR]

Pope Leo XIII's publication of Aeterni Patris (1879) was a major factor in the great revival of Thomistic thought in the late 19th and the first half of the 20th centuries. Among the authors that took up the challenge implicit in the Pope's document of bringing Aquinas and his thought into the intellectual debates of the times we find two interesting proposals. The first is that of Juan González Arintero, a Spanish Dominican, and the second one is that of Josef Donat, a Jesuit born and raised in the Austrian Empire. Arintero is mostly known in Catholic circles for his influential works on mysticism, but in fact he devoted much of his early work to the subject of evolution, and how it could interact with the Catholic faith in general, and with Thomism in particular. Donat is the author of a Summa Philosophiae Christianae, a collection that was widely read in Catholic seminaries well into the 20th century. In this paper we will focus on the differing ways in which these authors tackled the problems and questions presented by Darwinian evolutionism to the post-Aeterni Patris Thomism. [ABSTRACT FROM AUTHOR]

The emerging field of genomic medicine offers an opportunity for biology and anatomy teachers to bring the topics of DNA, genetics, molecular processes, and evolution together into one experience. Through the genomic medicine paradigm, students see the unbroken connection between small biological topics such as mutations and their potential connection to disease phenotypes. In this paper, we present as a main example cystic fibrosis, which is an often-studied genetic disease in general biology class, for examination through the genomic medicine lens. Concepts such as genes, the plasma membrane, variation, mutations, the nucleus, and chromosomes can be used in a narrative and visual approach to genetics through the genomic medicine standpoint to engage and connect students with next-generation genomics and with the fundamental unit of life—the cell. It is through the genomic medicine lens that the cell's context and relationship to the evolving world takes place. [ABSTRACT FROM AUTHOR]

Mitochondria are commonly perceived as "cellular power plants". Intriguingly, power conversion is not their only function. In the first part of this paper, we review the role of mitochondria in the evolution of eukaryotic organisms and in the regulation of the human body, specifically focusing on cancer and autism in relation to mitochondrial dysfunction. In the second part, we overview our previous works, revealing the physical principles of operation for proton-pumping complexes in the inner mitochondrial membrane. Our proposed simple models reveal the physical mechanisms of energy exchange. They can be further expanded to answer open questions about mitochondrial functions and the medical treatment of diseases associated with mitochondrial disorders. [ABSTRACT FROM AUTHOR]

Simple Summary: The reduviid genus Sycanus Amyot & Serville, 1843, possesses higher aesthetic value and plays a crucial role as a natural enemy in the control of agricultural and forestry pests. However, Sycanus from China has not undergone a comprehensive review for over four decades. Based on both molecular data and morphological evidence, we conducted a systematic review of the 14 Chinese Sycanus species, including a description of three new species. Due to the variability of body coloration and morphological similarity among closely related species, unresolved issues and debates still persist in the taxonomic study of the genus Sycanus from China. In this study, we conducted phylogenetic analyses and species delimitation for Sycanus in China based on a COI DNA barcoding dataset comprising 81 samples. The results revealed that all the samples could be classified into 12 species by integrating molecular analyses with morphological comparison. This paper provides a comprehensive systematic review of the Sycanus species found in China, including descriptions of three new species: S. taiwanensis Zhao & Cai sp. nov., S. flavicorius Li & Cai sp. nov., and S. hainanensis Wang & Cai sp. nov. Furthermore, it is proposed that S. croceovittatus Dohrn, 1859, S. leucomesus Walker, 1873, and S. villicus Stål, 1863, are three synonyms of S. bifidus (Fabricius, 1787); S. bicolor Hsiao, 1979, is a synonym of S. versicolor Dohrn, 1859; and S. hsiaoi Maldonado-Capriles, 1990, is a synonym of S. marginellus Putshkov, 1987. Additionally, brief biological information is provided for two species, S. falleni Stål, 1863, and S. croceus Hsiao, 1979. [ABSTRACT FROM AUTHOR]

This opinion piece, written by ethnobiologists from different parts of the world, emphasizes the importance of ethnobiology research in advancing contemporary biology, natural resource management, biodiversity conservation, sustainable development, and, especially, contributing to the ecological transition and more just and inclusive world. To achieve these goals, it is essential to develop research and collaborate with social groups that live in close relationship with nature in research activities, such as Indigenous Peoples and Local Communities (IPLC), as well as Afro-descendants and other Marginalized, Minority or Minoritized Communities (AMMC). Ethnobiology can identify and provide locally appropriate solutions to local problems, enabling sustainable resource management at the landscape level. The text explores important aspects that need to be considered to guide the future of ethnobiology in the next 20 years, aiming to integrate and amplify previous discussions held in the discipline and identify points that demand ongoing attention. This paper highlights reflections from diverse researchers, emphasizing how ethnobiology can embrace different perspectives and employ rigorous analysis of complex phenomena toward effective policies and practices. This approach holds the potential to address the challenges the planet is currently facing in the coming decades. [ABSTRACT FROM AUTHOR]

This journal article provides information about the upcoming 96th National Congress of the Italian Society for Experimental Biology, which will take place in L'Aquila, Italy from April 25-28, 2024. The article includes a table of contents for the journal issue, featuring various topics such as anthropology, aging, environment and health, aquatic environments, biology of reproduction and infertility, regenerative medicine, micro- and nanovesicles, neuroscience, nutrition, oncology, cell stress, and miscellaneous subjects. Additionally, the article includes summaries of three research papers: one on the relationship between comparative anthropology and urban biodiversity in forensic practice, another on the use of infrared spectroscopy in analyzing the preservation state of archaeological remains, and a third on dental morphology and its impact on periodontal disease in primates. The article also discusses two studies on the potential benefits of using probiotic Streptococcus thermophilus and Artemisia absinthium extract as skincare and mouthwash ingredients, respectively. These studies provide insights into the potential applications of probiotics and herbal extracts in improving skin health and oral hygiene. [Extracted from the article]

Thomas Cavalier‐Smith, born in London, U.K., on October 21, 1942, was a Professor of Evolutionary Biology in the Department of Zoology at the University of Oxford at the time of his death on March 19, 2021. Credited with at least 235 research works and over 20,000 citations, Cavalier‐Smith was a well‐known and widely respected scientist who took a bold and detailed approach to understanding major transitions in evolution, including the role of endosymbiosis. He was noted for his willingness to question theories and constantly accumulate and evaluate data, motivated by science for the sake of science. This paper reviews Thomas Cavalier‐Smith's major accomplishments, examines his theoretical approaches, and provides highlights from the "Tree of Life Symposium" sponsored by the International Society of Protistologists (ISOP) and the International Society of Evolutionary Protistology (ISEP) on June 21, 2021, to celebrate Tom's life and work. [ABSTRACT FROM AUTHOR]

High-grade serous tubo-ovarian cancer (HGSTOC) is the most lethal tumor of the female genital tract. The foregoing therapy consists of cytoreduction followed by standard platinum/taxane chemotherapy; alternatively, for primary unresectable tumors, neo-adjuvant platinum/taxane chemotherapy followed by delayed interval cytoreduction. In patients with suboptimal surgery or advanced disease, different forms of targeted therapy have been accepted or tested in clinical trials. Studies on HGSTOC discovered its genetic and proteomic heterogeneity, epigenetic regulation, and the role of the tumor microenvironment. These findings turned attention to the fact that there are several distinct primary tumor subtypes of HGSTOC and the unique biology of primary, metastatic, and recurrent tumors may result in a differential drug response. This results in both chemo-refractoriness of some primary tumors and, what is significantly more frequent and destructive, secondary chemo-resistance of metastatic and recurrent HGSTOC tumors. Treatment possibilities for platinum-resistant disease include several chemotherapeutics with moderate activity and different targeted drugs with difficult tolerable effects. Therefore, the question appears as to why different subtypes of ovarian cancer are predominantly treated based on the same therapeutic schemes and not in an individualized way, adjusted to the biology of a specific tumor subtype and temporal moment of the disease. The paper reviews the genomic, mutational, and epigenetic signatures of HGSTOC subtypes and the tumor microenvironment. The clinical trials on personalized therapy and the overall results of a new, comprehensive approach to personalized therapy for ovarian cancer have been presented and discussed. [ABSTRACT FROM AUTHOR]

Bacterial genomes often harbor integrated viruses (prophages), which provide novel functions but also lyse cells under stressful conditions. A new paper combines mathematical models with experimental evolution to determine how prophages are maintained in bacterial populations despite their fitness costs. [ABSTRACT FROM AUTHOR]

"Scientific Papers Made Easy" by Stuart West and Lindsay Turnbull is a comprehensive guide to writing academic papers in biology. The book covers all aspects of constructing a paper, including abstracts, introductions, methods, results, and discussions. The authors emphasize the importance of clear and concise writing, and provide practical tips and examples to help researchers improve their writing skills. While the book is primarily aimed at biologists, scientists from other disciplines can also benefit from reading it. However, the book does not cover collaborative writing or other forms of scientific writing, such as blogging or op-eds. Overall, "Scientific Papers Made Easy" is a valuable resource for researchers looking to improve their scientific writing abilities. [Extracted from the article]

The article discusses the trends in submissions and publications for the Annals of Applied Biology journal. While there was a steady increase in submissions until 2021, there was a reduction in submissions in 2022 and 2023. However, the number of published papers remained consistent. The journal encourages researchers to consider submitting their work to Annals of Applied Biology and highlights the various types of publications they accept. The article also acknowledges the support of the Association of Applied Biologists and Wiley in promoting and publishing the journal. Special issues linked to AAB-organized events are also announced, and new editors are welcomed to the board. The article concludes by inviting readers to follow the journal on social media and providing links to the journal's website and the AAB website. [Extracted from the article]

The Earth and life sciences are replete with portmanteau (blended) words and neologisms. Researchers at the interfaces between the traditional disciplines within the Earth and life sciences have coined dual titles for ‘new’ disciplines, such as geobiology/biogeology and ecohydrology/hydroecology. An upsurge in such coinage over the last few decades reflects a healthy willingness of many researchers to cross traditional disciplinary boundaries and to include the human sphere within their domains. However, some of the titles cause confusion because their meanings are not self-evident; rather, they sometimes demand extra research to reveal their meanings, thus rendering science less ‘open’ at a time when Open Science is being vigorously encouraged. After discussing the question of disciplinary neologisms, the paper probes the interchangeability of 15 dual ‘new’ discipline titles and concludes that six are more-or-less synonymous, three are nonsynonymous, and six are indeterminate for varying reasons. We question the usefulness of some, but by no means all, disciplinary neologisms, given that their meanings are not immediately apparent. Looking beyond portmanteau titles and other neologisms, the paper discusses the rise of interdisciplinary and transdisciplinary research, as seen in the concepts of the Critical Zone, multifunctional landscapes, and Earth System Science, the last of which supports a conceptual model of the planet as an interdependent set of spheres from global to local scales that has the advantages of combining the biotic, abiotic, and human spheres. [ABSTRACT FROM AUTHOR]

[Display omitted] • Based on the constructed confocal micro-Raman spectroscopy detection system, the visual detection of microplastics in fish was realized, which achieved the integration of spectra and improved the detection efficiency. • The microplastic fluorescence labeling technology was used to eliminate the interference of impurities and achieve rapid pre-screening of microplastics. • Differential Raman spectroscopy was used to solve the problem of fluorescence signal interference in Raman spectroscopy. • Based on the ELM identification model, an easy-to-operate microplastic identification software was written to assist in the rapid characterization of microplastics. • A set of rapid detection methods for microplastics in organisms, including confocal Raman spectroscopy, fluorescence imaging, differential Raman spectroscopy, and rapid identification of microplastics based on ELM modeling assistance, was established. Aiming at the problems of low extraction efficiency, high false detection rate, weak Raman signal and serious interference by fluorescence signal in the detection of microplastics in marine organisms, this paper establishes a set of rapid detection methods for microplastics in organisms, including confocal Raman spectroscopy, fluorescence imaging, differential Raman spectroscopy, and rapid identification of microplastics based on the ELM modeling assistance. Firstly, to address the problem of low extraction efficiency of microplastics, we explored and optimized the digestion method of tissues, which effectively improved the digestion effect of fish tissues and excluded the influence of tissues on microplastics detection. Aiming at the problems of high misdetection rate and low pre-screening efficiency of microplastics, fluorescence imaging technology is adopted to realize the visualization and detection of microplastics, which effectively improves the detection efficiency and precision of microplastics. Based on the confocal microscopy Raman spectroscopy detection system built independently in the laboratory, using 784/785 nm as the excitation light, the differential Raman spectroscopy technique effectively excludes the interference of fluorescence signals in the Raman spectra, and improves the signal-to-noise ratio of the Raman spectra, and the recovery rate of the Raman characteristic peaks in the differential Raman spectroscopy reaches 100 % compared to the traditional baseline correction method, which is 33.3 % higher than that of the baseline correction method. Finally, a microplastic identification model is constructed based on ELM to assist in realizing the rapid and accurate identification of microplastics. The more complete detection method of microplastics in marine organisms proposed in this paper can realize the rapid and nondestructive, efficient and accurate detection of microplastics in fish, which can help to further promote the development of marine microplastics monitoring technology. [ABSTRACT FROM AUTHOR]

Despite overwhelming evidence to the contrary, the concept of 'race' as a biological unit continues to persist in various scientific disciplines, notably in the field of medicine. This paper explores the persistence of 'race as biology' in medical research via examining select citational practices that have perpetuated this problematic concept. Citations serve as a cornerstone in scientific literature, signifying reliability and expert affirmation. By analyzing citation threads and historical patterns, we aim to shed light on the creation and perpetuation of false scientific truths and their impact on medical research, training, and practice. We focus on two prominent examples, eGFR and Spirometry, and trace key articles' citational histories, highlighting the flawed evidence in support of racial corrections in medical assessments. The eGFR equation incorporates 'race' as a factor based on the erroneous belief that Black individuals have higher muscle mass than white individuals. Our analysis reveals that key cited sources for this belief lack robust and well-developed datasets. Similarly, Spirometry measurements incorporate racial correction factors, relying on questionable evidence dating back to the Civil War era. Citations serve as a cornerstone in scientific literature, signifying reliability and expert affirmation. They play a crucial role in shaping theoretical positions and validating data and assumed knowledge. Evaluating citation threads and key articles consistently referenced over time can reveal how falsehoods and erroneous assertions are constructed and maintained in scientific fields. This study underscores the need for critical examination of citational practices in medical research and urges a shift toward a more cautious approach when citing sources that support 'race as biology.' The paper calls for a reevaluation of pedagogical approaches and assigned readings in medical education to prioritize an anti-racist perspective in future research endeavors. • Algorithms in contemporary medicine often involve "race" as a biological variable. • We offer a review of the citation threads in eGFR and Spirometry algorithms. • Support for race as variable relies on faulty, weak, and unsupportive citations. • Medical training must attend to and use caution around "truths" about racialized bodies. [ABSTRACT FROM AUTHOR]

Ervin Bauer (1890–1938) outlined the paradigm of theoretical biology from the perspective of biophysics and bioenergetics. His molecular-based biological theory is centered on the principle of sustainable non-equilibrium, which is continuously produced and maintained by all biological systems throughout their life. Ervin Bauer became the victim of Stalin's Great Terror. Here we present two of the fundamental works of Ervin Bauer in English translation: the paper "The definition of living beings on the basis of their thermodynamic properties, and the fundamental biological principles that follow from it" published in Naturwissenschaften (1920) and the excerpts from his magnum opus "Theoretical Biology" (1935). These works became a bibliographical rarity. A complete English translation of "Theoretical Biology" is an important task for the future. [ABSTRACT FROM AUTHOR]

. Edited by Victor S. Kennedy and Brian F. Beal. Bethesda (Maryland): American Fisheries Society. $79.00 (paper). xiv + 595 p.; ill.; index. ISBN: 978-1-934874-74-5. 2023. [Extracted from the article]

The article discusses a book titled "Evolutionary Biology: Contemporary and Historical Reflections Upon Core Theory. Evolutionary Biology—New Perspectives on Its Development, Volume 6," edited by Thomas E. Dickins and Benjamin J. A. Dickins. The book explores the debate surrounding the need for an "Extended Evolutionary Synthesis" (EES) and includes 12 original papers from 19 biologists and philosophers. While some chapters reiterate arguments for or against the EES, others evaluate specific claims made by proponents of the EES. The book also features a unique structure with each chapter followed by a response from another contributor, allowing for further discussion and analysis. [Extracted from the article]

• I briefly summarize Michael Savageau's "Biochemical Systems Analysis" papers, published in volumes 25 and 26 of the journal. • These papers kickstarted Biochemical Systems Theory, which originated many of the core concepts and tools of Systems Biology. • I identify the most relevant developments in Biochemical Systems Theory since 1969. Michael Savageau's Biochemical Systems Analysis I, II, III papers, published in volumes 25 and 26 of the journal, kickstarted a research programme that originated many of the core concepts and tools of Systems Biology. This article briefly summarizes these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication. [ABSTRACT FROM AUTHOR]

Ervin Bauer (1890–1938) was the first to build a general molecular-based biological theory. He defined the basic principles of theoretical biology from a thermodynamic perspective, focusing on the capacity of biological systems to produce and support the state of sustainable non-equilibrium. His central work "Theoretical Biology" (1935) was written long before modern advances in molecular biology, genetics, and information theory. Ervin Bauer and his wife Stefánia were executed in Stalin's Great Terror. This paper presents a brief introduction to Ervin Bauer's life and includes his short biography. [ABSTRACT FROM AUTHOR]

Ervin Bauer was the only biologist who recognized that the best way to develop theoretical biology on an equal footing with theoretical physics was to follow the method that has ensured the great successes of modern theoretical physics: the general method of science. Following this method, he succeeded to find the universal principle of biology. From this principle he managed to derive all the basic equations of biology, that of metabolism, reproduction, growth, responsiveness and successfully explained all the fundamental phenomena of life. In this paper, I introduce Bauer's theoretical biology and discuss whether he understood it within the framework of the modern physical worldview, or in a broader framework. I point out that the theoretical biology of Ervin Bauer is the first to go beyond the physical worldview, to establish a deeper, biological worldview, and thus to represent a major advance in our understanding of the nature of life, with a significance even greater than that of the Copernican turn. Clarifying the difference between the living and the non-living, it is important to consider the difference between machines and living organisms. It is well known that machines are the manifestations of a dual control; globally, their behavior is controlled by their given structure, while locally, their behavior is governed by the physical laws. Based on Bauer's theoretical biology, it is pointed out that living organisms manifest a three-level causality; the 'additional', biological level corresponds to the autonomous, time-dependent control of their structures. [ABSTRACT FROM AUTHOR]

• I briefly describe the Boolean modeling approach to investigate gene regulatory networks (GRNs). • I discuss the foundational contributions by the three seminal manuscripts more than 15 years ago. • Finally, the applications of the Boolean modeling approach to the large-scale omics data is discussed. Boolean modeling is a mathematical modeling framework used for defining and studying gene-regulatory networks (GRNs). It serves as a means to develop mechanistic models, offering insights into the trajectories and dynamic properties of GRNs. In this review, I delve into seminal papers published in the Journal of Theoretical Biology that have spearheaded this field. Additionally, I explore the application of these modeling methods in the current era of data-intensive science. [ABSTRACT FROM AUTHOR]

In this work, a novel lysosome-targeted Cys fluorescent probe, LN-NCS , was synthesized by introducing an isothiocyanate (ITC) moiety as a recognition site for Cys in the naphthalimide fluorophore and combining it with a morpholine moiety for targeting the lysosome. The probe LN-NCS has a large Stokes shift (140 nm), low cytotoxicity, low detection limit (16.3 nM), and high selectivity, and probe LN-NCS reacts with Cys to produce the compound LN-NH 2 with good fluorescence quantum yield (Ф = 0.81). Probe LN-NCS can be used to detect Cys in cells, zebrafish, plant roots, food samples, and environmental water samples. In addition, by mimicking cellular inflammation, the probe LN-NCS was shown to detect changes in Cys concentration induced by cellular inflammation, providing a potential tool to better study the cellular inflammatory environment. [Display omitted] • LN-NCS is a novel Cys probe with the function of targeting lysosomes. • LN-NCS is capable of detecting Cys in food samples and water samples. • LN-NCS allows detection of Cys in cells, zebrafish and Arabidopsis. • LN-NCS was able to detect inflammation-induced changes in Cys concentration. Cysteine (Cys) is a sulfur-containing amino acid that plays an important role in living systems. The most common way to supplement the body with exogenous Cys is through the consumption of Cys-rich foods. Therefore, it is important to detect and analyze Cys in living systems and food samples. However, most of the Cys fluorescent probes developed so far are limited to the detection of the cellular environment only, and very few probes can take into account the detection of Cys in plant roots and food samples. In this paper, a novel fluorescent probe LN-NCS targeting the detection of Cys in lysosomes was designed and synthesized by modifying the naphthalimide fluorophore. The probe LN-NCS has a large Stokes shift (140 nm), low cytotoxicity, low detection limit (16.3 nM), and high selectivity, and probe LN-NCS reacts with Cys to produce the compound LN-NH 2 with good fluorescence quantum yield (Ф = 0.81). Probe LN-NCS can be used to detect Cys in cells, zebrafish, plant roots, food samples, and environmental water samples. In addition, by modeling cellular inflammation, we have demonstrated that probe LN-NCS can detect changes in Cys concentration induced by cellular inflammation, providing a potential tool to better study the cellular inflammatory environment. [ABSTRACT FROM AUTHOR]

A range of studies published in the last few decades promotes the cognitive aspects of life: all organisms, from bacteria to mammals, are capable of sensing/perception, decision-making, problem-solving, learning, and other cognitive functions, including sentience and consciousness. In this paper I present a scientific and philosophical synthesis of these studies, leading to an integrated view of cognitive biology. This view is expressed through the four principles applicable to all living systems: (1) sentience and consciousness, (2) autopoiesis, (3) free energy principle and relational biology, and (4) cognitive repertoire. The principles are circular, and they reinforce themselves. The circularity is not rigid, meaning that hierarchical and heterarchical shifts are widespread in the biosphere. The above principles emerged at the dawn of life, with the first cells, bacteria and archaea. All biogenic forms and functions that emerged since then can be traced to the first cells – indivisible units of biological agency. Following these principles, I developed the concept of biocivilisations to explain various forms of social intelligence in different kingdoms of life. The term biociviloisations draws on the human interpretation of the concept of civilisation, which searches for non-human equivalents of communication, engineering, science, medicine, art, and agriculture, in all kingdoms of life by applying the principles of cognitive biology. Potential avenues for testing the concept of biocivilisations are highlighted. [ABSTRACT FROM AUTHOR]

The Bay of Biscay is a structurally complex region, exhibiting high biodiversity and productivity and hosting a wide variety of benthic habitats. Unfortunately, current scientific knowledge of deep-sea ecosystems is limited. Our investigation provides an updated vision of the existing knowledge on key aspects of the deep-sea ecosystem and identifies research priorities for the definition of a research roadmap in support of sustainable management, including the protection and conservation of deep-sea ecosystem of the Bay of Biscay. To achieve this, firstly a revision of projects, surveys and studies conducted in the region, was carried out resulting in the identification of 62 publicly available scientific documents. Secondly, an online survey was carried out, receiving 51 responses from 24 research institutions in 9 countries. Finally, a workshop was attended by 39 scientists to identify and discuss ways forward on deep-sea research in the Bay of Biscay. Results indicate that knowledge of benthic habitats, and vulnerable and sensitive habitats/species is good or very good for 45% of the respondents, while limited knowledge was reported for deep pelagic habitats. Almost 75% of the scientists agreed that deep-sea processes affect shallower areas. Funding (71%) and research vessel availability (57%) were considered the most constraining aspects limiting deep-sea research. More than 50% of the scientists perceived a short- or medium-term threat from human activities and pressures, while over than 40% of the respondents considered that there are no, or limited, data available to assess the environmental status. Regarding climate change, 55% of scientists partially or fully agreed with the existence of evidence of climate change effects, but 47% of them totally or partially considered that climate change monitoring is insufficient to assess eventual changes and effects. Most respondents (63%) considered that deep-sea ecosystems are not properly represented in the current Marine Protected Areas network. In terms of future needs, the development of monitoring strategies to reduce costs and guarantee an optimal design, data sharing and an increase in transnational collaboration are most cited. Finally, a proposal for a roadmap to fill in knowledge gaps for a better understating of the ecosystem processes of the deep sea of the Bay of Biscay is delivered. • Scientific knowledge of the deep-sea ecosystem in the Bay of Biscay is limited. • An updated vision of current knowledge on key aspects of the deep-sea ecosystem is provided. • Research priorities for the definition of a research roadmap are identified. • Intended to support sustainable management, protection and conservation. [ABSTRACT FROM AUTHOR]

We studied the structure of digestive system of deep-sea torquaratorid Quatuoralisia malakhovi including the food-obtaining apparatus, microanatomy of all regions of digestive tract, and fine structure of various regions of the gut. The mouth of Q. malakhovi is surrounded by two symmetrical triangular lateral collar lips and one midventral collar lip, which may retract into the mouth. The ventral ciliary grooves run along the anterior-ventral edges of lateral lips and lead into the internal canals of the lips. The pharyngeal cavity is divided by left and right parabranchial ridges into the median pharyngeal zone with gill bars and two symmetrical peripheral canals, which fuse behind the site of genesis of new gill bars. The gill pharynx is followed by the hepatic region with metameric hepatic sacculations comprising cells with numerous large phagosomes indicating active intracellular digestion. The intestine is filled with undigested food residues including detritus flakes and remnants of various organisms. The intestine content was examined using SEM and histological studies. We analyzed the ratio of organic and mineral components of the bottom sediment from the habitat of Q. malakhovi , and the stable isotope composition of carbon and nitrogen in the intestine content, in the tissues, and in the sediment from the habitat of the studied acorn worm. Using the obtained data and the photographs and videotapes in situ , we have proposed a hypothesis explaining the feeding mechanism of Q. malakhovi. The width of the ventral ciliary groove of the lateral collar lips (100–200 μm) regulates the maximum size of particles that enter the pharynx of the animal. The minimum size of the sediment particles selected by Q. malakhovi is determined by the width of the gill pores and is 1–3 μm. The selected sediment particles move through the peripheral pharyngeal canals to the hepatic region, where the digestion of the food is carried out. In the posthepatic intestine, weight of the gut contents might serve as an anchor that holds the heavily watered jelly-like torquaratorid body at the bottom during the feeding. • Food-obtaining apparatus and digestive system of deep-sea acorn worm Quatuoralisia malakhovi from the Bering Sea. • Stable isotope composition of carbon and nitrogen in gut content, tissues, and sediment from habitat of studied acorn worm. • Hypothesis explaining the feeding mechanism of Quatuoralisia malakhovi. [ABSTRACT FROM AUTHOR]