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Tunnels in enzymes with buried active sites are key structural features allowing the entry of substrates and the release of products, thus contributing to the catalytic efficiency. Targeting the bottlenecks of protein tunnels is also a powerful protein engineering strategy. However, the identification of functional tunnels in multiple protein structures is a non-trivial task that can only be addressed computationally. We present a pipeline integrating automated structural analysis with an in-house machine-learning predictor for the annotation of protein pockets, followed by the calculation of the energetics of ligand transport via biochemically relevant tunnels. A thorough validation using eight distinct molecular systems revealed that CaverDock analysis of ligand un/binding is on par with time-consuming molecular dynamics simulations, but much faster. The optimized and validated pipeline was applied to annotate more than 17,000 cognate enzyme–ligand complexes. Analysis of ligand un/binding energetics indicates that the top priority tunnel has the most favourable energies in 75% of cases. Moreover, energy profiles of cognate ligands revealed that a simple geometry analysis can correctly identify tunnel bottlenecks only in 50% of cases. Our study provides essential information for the interpretation of results from tunnel calculation and energy profiling in mechanistic enzymology and protein engineering. We formulated several simple rules allowing identification of biochemically relevant tunnels based on the binding pockets, tunnel geometry, and ligand transport energy profiles. Scientific contributions The pipeline introduced in this work allows for the detailed analysis of a large set of protein–ligand complexes, focusing on transport pathways. We are introducing a novel predictor for determining the relevance of binding pockets for tunnel calculation. For the first time in the field, we present a high-throughput energetic analysis of ligand binding and unbinding, showing that approximate methods for these simulations can identify additional mutagenesis hotspots in enzymes compared to purely geometrical methods. The predictor is included in the supplementary material and can also be accessed at https://github.com/Faranehhad/Large-Scale-Pocket-Tunnel-Annotation.git. The tunnel data calculated in this study has been made publicly available as part of the ChannelsDB 2.0 database, accessible at https://channelsdb2.biodata.ceitec.cz/. [ABSTRACT FROM AUTHOR]

Identification of the geographic origin of invasive species can be critical to effective management and amelioration of negative impacts in the introduced range. Liriomyza huidobrensis is a polyphagous leafmining fly that is a devastating pest of many vegetable and floriculture crops around the world. Considered native to South and possibly Central America, L. huidobrensis became invasive in the 1980s and has since spread to at least 30 countries on five continents. We used phylogeographic analysis of over 2 kb of mitochondrial cytochrome oxidase I and II sequence data from 403 field‐collected specimens from both native and introduced populations to investigate the geographic origins of invasive L. huidobrensis worldwide. Within South America, there was substantial genetic variation, as well as the strong phylogeographic structure typical of a native range. In contrast, leafminers from the introduced range and Central America all contained little genetic variation and shared the same small set of haplotypes. These haplotypes trace to Peru as the ultimate geographic origin of invasive populations. Central America is rejected as part of the original geographic range of L. huidobrensis. Within Peru, the primary export region of Lima shared an extremely similar pattern of reduced haplotype variation to the invasive populations. An additional 18 specimens collected at US ports of entry did not share the same haplotype profile as contemporary invasive populations, raising perplexing questions on global pathways and establishment success in this species. [ABSTRACT FROM AUTHOR]

Giam Malut Hopea ferrea Laness (Dipterocarpaceae) is a woody species that has become endangered due to its habitat destruction and overexploitation. In an effort to support and provide conservation and management of this species, we utilized eight microsatellite loci to investigate the genetic diversity and structure of 234 adult trees across eight populations, encompassing its geographic distribution in Vietnam. The genetic diversity of H. ferrea was found to be low in comparison to other dipterocarps, suggesting a reduction in the number of alleles due to anthropogenic activities. Heterozygosity deficits were identified across all studied populations. Interestingly, the coastal populations exhibited higher genetic diversity compared to the Highlands and southeast populations. Bottleneck effects were detected in the majority of populations, with the exception of the two Highlands populations of Chu Mon Ray and York Don. These effects indicated a reduction in the population sizes. The results of genetic differentiation mirrored the genetic structure and revealed three major clusters corresponding to the three distribution areas of the species. A low level of genetic differentiation among populations (FST=0.146) was detected, consistent with the AMOVA analysis. Geographic distance and anthropogenic activities emerged as the major factors limiting gene exchange among populations. Based on these findings, we propose conservation measures for this endangered species. [ABSTRACT FROM AUTHOR]

We provide in this paper a concrete method for training a quantum neural network to maximize the relevant information about a property that is transmitted through the network. This is significant because it gives an operationally well founded quantity to optimize when training autoencoders for problems where the inputs and outputs are fully quantum. We provide a rigorous algorithm for computing the value of the quantum information bottleneck quantity within error ε that requires O (log 2 ⁡ (1 / ϵ) + 1 / δ 2) queries to a purification of the input density operator if its spectrum is supported on { 0 } ⋃ [ δ , 1 − δ ] for δ > 0 and the kernels of the relevant density matrices are disjoint. We further provide algorithms for estimating the derivatives of the QIB function, showing that quantum neural networks can be trained efficiently using the QIB quantity given that the number of gradient steps required is polynomial. [ABSTRACT FROM AUTHOR]

The overabundance of sika deer has become a significant threat to plant communities across Japan. As a result of the deer overgrazing, rare plants are undergoing a demographic bottleneck, leading to a loss of genetic diversity. Genetic diversity is crucial for the reproductive success of self‐incompatible plants, and it also provides evolutionary potential, which increases their long‐term population viability. Therefore, it is essential to appropriately manage the remaining genotypes to conserve local genetic resources. In this study, we exemplify this, via a conservation genetic analysis of Parasenecio peltifolius populations impacted by deer. Genetic data revealed that the small populations confined to isolated refugial sites consisted of effectively single genets. Recent reproductive failures in these populations may be attributed to the loss of genotypic diversity. Despite the bottlenecks, the remaining genets exhibited high individual heterozygosity, which is a good indicator that they have not been affected by severe inbreeding. Hybrid simulations suggested that interpopulation outbreeding between the unique genotypes can be a viable option to promote sexual reproduction and re‐establish genetic diversity within the local populations. Establishing artificial progenies in botanical gardens can serve as a vital genetic resource for the long‐term viability of threatened P. peltifolius populations. [ABSTRACT FROM AUTHOR]

The competitiveness of the companies depends on continuous progress, and the allocation of the continuous improvement is crucial in today’s market competition. The main approaches proposed in the literature are distributed and centralized policies. This research proposes a novel model for resource allocation that surpasses existing methods. It leverages throughput rate evaluation as the core principle. This model considers key improvement parameters and utilizes a mathematical framework to allocate improvement resources to each parameter. The experiments conducted concern failure parameters (Mean Time Between Failures and Mean Time To Repair), setup time, defective rate, bottleneck numbers and the increasing processing time of the bottleneck. The original contribution is twofold: the evaluation considers a wider range of conditions and their impact on flow line’s sustainability. The model emphasizes sustainability by focusing on minimizing the idle time of workstations within the flow line. Numerical analysis of the proposed model reveals a substantial reduction in total idle time improving the related energy consumption. Furthermore, the model achieves a throughput rate that closely aligns with the centralized policy, traditionally considered the most effective approach. [ABSTRACT FROM AUTHOR]

Abstract Following glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears’ mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears.

Abstract Tunnels in enzymes with buried active sites are key structural features allowing the entry of substrates and the release of products, thus contributing to the catalytic efficiency. Targeting the bottlenecks of protein tunnels is also a powerful protein engineering strategy. However, the identification of functional tunnels in multiple protein structures is a non-trivial task that can only be addressed computationally. We present a pipeline integrating automated structural analysis with an in-house machine-learning predictor for the annotation of protein pockets, followed by the calculation of the energetics of ligand transport via biochemically relevant tunnels. A thorough validation using eight distinct molecular systems revealed that CaverDock analysis of ligand un/binding is on par with time-consuming molecular dynamics simulations, but much faster. The optimized and validated pipeline was applied to annotate more than 17,000 cognate enzyme–ligand complexes. Analysis of ligand un/binding energetics indicates that the top priority tunnel has the most favourable energies in 75% of cases. Moreover, energy profiles of cognate ligands revealed that a simple geometry analysis can correctly identify tunnel bottlenecks only in 50% of cases. Our study provides essential information for the interpretation of results from tunnel calculation and energy profiling in mechanistic enzymology and protein engineering. We formulated several simple rules allowing identification of biochemically relevant tunnels based on the binding pockets, tunnel geometry, and ligand transport energy profiles. Scientific contributions The pipeline introduced in this work allows for the detailed analysis of a large set of protein–ligand complexes, focusing on transport pathways. We are introducing a novel predictor for determining the relevance of binding pockets for tunnel calculation. For the first time in the field, we present a high-throughput energetic analysis of ligand binding and unbinding, showing that approximate methods for these simulations can identify additional mutagenesis hotspots in enzymes compared to purely geometrical methods. The predictor is included in the supplementary material and can also be accessed at https://github.com/Faranehhad/Large-Scale-Pocket-Tunnel-Annotation.git . The tunnel data calculated in this study has been made publicly available as part of the ChannelsDB 2.0 database, accessible at https://channelsdb2.biodata.ceitec.cz/ .

The competitiveness of the companies depends on continuous progress, and the allocation of the continuous improvement is crucial in today’s market competition. The main approaches proposed in the literature are distributed and centralized policies. This research proposes a novel model for resource allocation that surpasses existing methods. It leverages throughput rate evaluation as the core principle. This model considers key improvement parameters and utilizes a mathematical framework to allocate improvement resources to each parameter. The experiments conducted concern failure parameters (Mean Time Between Failures and Mean Time To Repair), setup time, defective rate, bottleneck numbers and the increasing processing time of the bottleneck. The original contribution is twofold: the evaluation considers a wider range of conditions and their impact on flow line’s sustainability. The model emphasizes sustainability by focusing on minimizing the idle time of workstations within the flow line. Numerical analysis of the proposed model reveals a substantial reduction in total idle time improving the related energy consumption. Furthermore, the model achieves a throughput rate that closely aligns with the centralized policy, traditionally considered the most effective approach.

Recessive alleles have been shown to directly affect both human Mendelian disease phenotypes and complex traits. Pedigree studies also suggest that consanguinity results in increased childhood mortality and adverse health phenotypes, presumably through penetrance of recessive mutations. Here, we test whether the accumulation of homozygous, recessive alleles decreases reproductive success in a human population. We address this question among the Namibian Himba, an endogamous agro-pastoralist population, who until very recently practiced natural fertility. Using a sample of 681 individuals, we show that Himba exhibit elevated levels of "inbreeding," calculated as the fraction of the genome in runs of homozygosity (FROH). Many individuals contain multiple long segments of ROH in their genomes, indicating that their parents had high kinship coefficients. However, we do not find evidence that this is explained by first-cousin consanguinity, despite a reported social preference for cross-cousin marriages. Rather, we show that elevated haplotype sharing in the Himba is due to a bottleneck, likely in the past 60 generations. We test whether increased recessive mutation load results in observed fitness consequences by assessing the effect of FROH on completed fertility in a cohort of postreproductive women (n = 69). We find that higher FROH is significantly associated with lower fertility. Our data suggest a multilocus genetic effect on fitness driven by the expression of deleterious recessive alleles, especially those in long ROH. However, these effects are not the result of consanguinity but rather elevated background identity by descent.

BackgroundCOVID-19 pandemic mitigation measures, including travel restrictions, limited global circulation of influenza viruses. In Australia, travel bans for non-residents and quarantine requirements for returned travellers were eased in November 2021, providing pathways for influenza viruses to be re-introduced.AimWe aimed to describe the epidemiological and virological characteristics of the re-emergence of influenza in Victoria, Australia to inform public health interventions.MethodsFrom 1 November 2021 to 30 April 2022, we conducted an epidemiological study analysing case notification data from the Victorian Department of Health to describe case demographics, interviewed the first 200 cases to establish probable routes of virus reintroduction and examined phylogenetic and antigenic data to understand virus diversity and susceptibility to current vaccines.ResultsOverall, 1,598 notifications and 1,064 positive specimens were analysed. The majority of cases (61.4%) occurred in the 15-34 years age group. Interviews revealed a higher incidence of international travel exposure during the first month of case detections, and high levels of transmission in university residential colleges were associated with return to campus. Influenza A(H3N2) was the predominant subtype, with a single lineage predominating despite multiple importations.ConclusionEnhanced testing for respiratory viruses during the COVID-19 pandemic provided a more complete picture of influenza virus transmission compared with previous seasons. Returned international travellers were important drivers of influenza reemergence, as were young adults, a group whose role has previously been under-recognised in the establishment of seasonal influenza epidemics. Targeting interventions, including vaccination, to these groups could reduce future influenza transmission.

Martaban camphor [Cinnamomum parthenoxylon (Jack) Meisn] is a woody tree in India, China, Indonesia, Thailand, and Vietnam and has been widely utilized for commercial purposes. It is threatened due to fragmented habitats, over-deforestation, and oil extraction. To conserve this species, the investigation of genetic diversity and population structure of this species is essential. Herein, we analyzed 192 adult trees from eight populations covering its natural distribution range in Vietnam using ten polymorphic EST-SSR markers. Medium levels of genetic diversity (R = 2.7, Ho = 0.399, He = 0.426) and genetic differences between populations (Fst = 0.223) were determined. Two populations, Cuc Phuong and Xuan Nha have undergone recent bottlenecks. These results indicated that anthropogenic activities may be the major factor for the low heterozygosity and influenced the number of alleles in all C. parthenoxylon populations. Clustering analyses revealed three genetic clusters that related to gene flow between different areas. We proposed in situ conservation for some populations with high levels of allelic richness, genetic diversity, or private alleles. The collecting of the seeds of the remaining populations for ex-situ conservation could be performed.

Understanding the dynamics of population recovery in threatened species requires robust longitudinal monitoring datasets. However, evidence‐based decision‐making is often impeded by variable data collection approaches, necessitating critical evaluation of restricted available baselines. The Hainan gibbon, the world's rarest primate, had possibly declined to only seven or eight individuals in 1978 at Bawangling National Nature Reserve but has experienced subsequent population growth. Past population estimates lack detailed reporting of survey effort, and multiple conflicting estimates are available, hindering assessment of gibbon recovery. We investigated all reported estimates of Bawangling gibbon population size from 1978 to 2022, to evaluate the biological signal of population trends and the extent to which noise associated with varying survey effort, reporting and estimation may mask or misrepresent any underlying signal. This longitudinal dataset demonstrates that the Bawangling population experienced a series of bottlenecks and recoveries, with three successive periods of growth interspersed by population crashes (1978–1989, 1989–2000 and 2000–2022). The rate of gibbon population recovery was progressively slower over time in each successive period of growth, and this potential decline in recovery rate following serial bottlenecks suggests that additional management strategies may be required alongside "nature‐based solutions" for this species. However, population viability analysis suggests the 1978 founder population is unlikely to have been as low as seven individuals, raising concerns for interpreting reported historical population counts and understanding the dynamics of the species' recovery. We caution against overinterpreting potential signals within "messy" conservation datasets, and we emphasise the crucial importance of standardised replicable survey methods and transparent reporting of data and effort in all future surveys of Hainan gibbons and other highly threatened species. [ABSTRACT FROM AUTHOR]

Migration plays a central role in many ecological and evolutionary processes. Global patterns of climatic variation are having a profound influence upon animal migration patterns. Even though regular counts of bird migrations at bottleneck sites can certainly offer insights into how natural populations of different species at different scales are responding to changes in weather conditions, they have not yet been widely used. By analysing a time series of regular counts, collected during autumn, of 126 species migrating during the daytime through one of the most important migratory bottlenecks in Western Europe, we found that an increase in temperature at the regional scale, as well as a decrease in precipitation level during the breeding period, may result not only in a decrease in the migration rate during autumn but also in a delay in the timing of fall migration. Furthermore, adverse weather conditions at the local scale interrupted bird migration through the bottleneck until favourable weather conditions returned. Importantly, temporal variation in the number of migratory birds followed a nonlinear pattern, something which might be partially due to the idiosyncratic responses of migratory species with different life‐history characteristics to changes in weather conditions. Our results highlight that migration is a nonlinear, multiscale and multi‐faceted process, suggesting that it will be difficult to predict the responses of idiosyncratic migratory species to the unpredictable effects of climate change. [ABSTRACT FROM AUTHOR]

Species reintroductions have the potential to cause genetic bottleneck events resulting in increased genetic drift, increased inbreeding, and reduced genetic diversity creating negative fitness consequences for populations. Roosevelt elk (Cervus canadensis roosevelti Erxleben, 1777) are "at risk" in British Columbia (BC), Canada. Once widespread along the west coast, Roosevelt elk were likely extirpated from the mainland by 1900 and experienced a substantial population bottleneck on Vancouver Island at that time, and again in the 1950s. Reintroduced to the mainland from Vancouver Island in the 1980s, this re-established population became the source for subsequent mainland translocations. To understand the effects of reintroduction strategy on genetic diversity, we analyzed genetic variation in 355 Roosevelt elk from Vancouver Island and mainland BC. Using mitochondrial DNA and 10 microsatellite loci, molecular analyses showed overall reduced genetic diversity relative to other extant elk populations, genetic isolation of the southern Vancouver Island population, and increased genetic drift among reintroduced herds. Four reintroduced populations were found to have increased levels of inbreeding. Results of this study contribute to our knowledge of reintroduction biology and can be used to guide continued conservation and management of at-risk species. [ABSTRACT FROM AUTHOR]

Automated material transfer between workstations is a key feature of flexible manufacturing systems. The aim of automation is to increase the output rate while reducing the manufacturing throughput. However, machine idle time contributes significantly to the overall throughput time and cannot be completely eliminated; it can only be minimized. Accurately locating the bottleneck and synchronizing it with other assembly line equipment can help reduce throughput. The process or activity with no idle or waiting time is known as the bottleneck in a production system. In this paper, we will analyze the bottleneck in Coca-Cola's production line at Lae and provide suggestions for reducing throughput. [ABSTRACT FROM AUTHOR]

Because a hospital is an interconnected, interdependent network of care units, allocating resources—beds, nurses, and improvement initiatives—to one unit to reduce its congestion may have spillover effects on other units. If such congestion spillover is substantial, ignoring it may lead to unintended consequences and missed opportunities. We use data collected over five years from a hospital with 16 inpatient units to empirically examine whether and how much congestion propagates through the network of inpatient units. Our estimation result suggests that the magnitude of the congestion spillover is indeed substantial in our study hospital. For example, increasing one inpatient unit's utilization by 10 percentage points today can increase its neighboring inpatient unit's utilization by up to 4.33 percentage points tomorrow. Using counterfactual analyses, we estimate the effect of adding a bed to each unit. We find that due to congestion spillover, adding one bed to the bottleneck unit can free up 4.14 beds in the hospital, which translates to 383.53 more hospital visits per year or a 3% increase in hospital throughput. This effect is about three times bigger in magnitude compared with what one can achieve by naively choosing which unit to add a bed to. Hospitals and other manufacturing and service systems with complex interdependence across resources can use our empirical framework to examine the spillover effect of resources on performance metrics and leverage such understanding to effectively improve their operations. This paper was accepted by Vishal Gaur, operations management. Funding: This work was supported by the Creative-Pioneering Researchers Program through Seoul National University. Supplemental Material: The data files and online appendices are available at https://doi.org/10.1287/mnsc.2023.4887. [ABSTRACT FROM AUTHOR]

This article examines the EUMR’s purpose and ex-ante control against the background of ‘killer’ or ‘zombie’ acquisitions that evaded scrutiny by falling below merger control thresholds, while other concentrations were permitted due to debatable market definitions or inadequate theories of harm. Recognizing these shortcomings, the article discusses ex-post control following Towercast and Continental Can. It submits that the conditionality introduced in these judgments constitutes (1) an effort by the CJEU to limit ex-post merger control, (2) an ultra vires restriction on the application of Art 102 TFEU, or (3) a de facto acquisition ban for bottleneck holders and ecosystem orchestrators. [ABSTRACT FROM AUTHOR]

This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii. The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis. Among the 10 fish genomes, there were significant gene family expansions (8–2387) and contractions (16–2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii. [ABSTRACT FROM AUTHOR]

There are two primary measures of the amount of genetic variation in a population at a locus: heterozygosity and the number of alleles. Effective population size (Ne) provides both an expectation of the amount of heterozygosity in a population at drift‐mutation equilibrium and the rate of loss of heterozygosity because of genetic drift. In contrast, the number of alleles in a population at drift‐mutation equilibrium is a function of both Ne and census size (NC). In addition, populations with the same Ne can lose allelic variation at very different rates. Allelic variation is generally much more sensitive to bottlenecks than heterozygosity. Expressions used to adjust for the effects of violations of the ideal population on Ne do not provide good predictions of the loss of allelic variation. These effects are much greater for loci with many alleles, which are often important for adaptation. We show that there is a linear relationship between the reduction of NC and the corresponding reduction of the expected number of alleles at drift‐mutation equilibrium. This makes it possible to predict the expected effect of a bottleneck on allelic variation. Heterozygosity provides good estimates of the rate of adaptive change in the short‐term, but allelic variation provides important information about long‐term adaptive change. The guideline of long‐term Ne being greater than 500 is often used as a primary genetic metric for evaluating conservation status. We recommend that this guideline be expanded to take into account allelic variation as well as heterozygosity. [ABSTRACT FROM AUTHOR]

Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in 4 species, including 2 paedophages, which began during the 1970s to 1980s, and population size rebounded during the 1990s to 2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines" disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the 4 species that likely experienced bottleneck, Haplochromis sp. "matumbi hunter," a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the 5 paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck. [ABSTRACT FROM AUTHOR]

Abstract Identification of the geographic origin of invasive species can be critical to effective management and amelioration of negative impacts in the introduced range. Liriomyza huidobrensis is a polyphagous leafmining fly that is a devastating pest of many vegetable and floriculture crops around the world. Considered native to South and possibly Central America, L. huidobrensis became invasive in the 1980s and has since spread to at least 30 countries on five continents. We used phylogeographic analysis of over 2 kb of mitochondrial cytochrome oxidase I and II sequence data from 403 field‐collected specimens from both native and introduced populations to investigate the geographic origins of invasive L. huidobrensis worldwide. Within South America, there was substantial genetic variation, as well as the strong phylogeographic structure typical of a native range. In contrast, leafminers from the introduced range and Central America all contained little genetic variation and shared the same small set of haplotypes. These haplotypes trace to Peru as the ultimate geographic origin of invasive populations. Central America is rejected as part of the original geographic range of L. huidobrensis. Within Peru, the primary export region of Lima shared an extremely similar pattern of reduced haplotype variation to the invasive populations. An additional 18 specimens collected at US ports of entry did not share the same haplotype profile as contemporary invasive populations, raising perplexing questions on global pathways and establishment success in this species.

A successful reintroduction of Phengaris teleius performed in the Netherlands by translocating 86 individuals from a Polish metapopulation in 1990 represents a unique opportunity to study changes in butterflies from a source and reintroduced metapopulation after such a common conservation practice. Using multilevel comparisons, we tested morphological and genetic changes that occurred after 30 generations since the reintroduction. We also assessed the climatic and connectivity changes that occurred over time in both metapopulation networks. Unexpectedly, we found more significant morphological changes in the current individuals from the source metapopulation, where both sexes had bigger hindwings with different shapes in comparison to the individuals from the original metapopulation in the year of the reintroduction and the ones from the current reintroduced metapopulation. The butterflies from the Dutch metapopulation also had smaller thorax width compared to the ones from the current source metapopulation. The observed morphological changes can be shaped by various factors like changes in climatic conditions and habitat connectivity. Additionally, the genetic analysis revealed a differentiation between the source and reintroduced metapopulation. We found a loss of half of the allelic richness and a bottleneck effect in the reintroduced metapopulation compared to the current Polish one. Our results show that Phengaris butterflies have the potential to adapt to new habitats and respond to climatic changes despite their complex life cycle. A proper long-term habitat management in reintroduced butterfly metapopulations and habitat restoration are key factors influencing the success of reintroduction.

Modern food is evolving in the direction of green, healthy, and convenient products, and developing natural products with health benefits is an important direction for the food industry. Chlorella is rich in nutrients, such as carotene and fatty acids, which provide it with a variety of health benefits, and therefore widely used in the food industry as a health or functional food. This study reviews the research progress and specific applications of Chlorella in health, functional, and other foods, and expounds on the bottlenecks faced in the use of Chlorella in food industry. This review provides a theoretical basis for the research, utilisation, and production of new food materials involving Chlorella.

Understanding how phenotypic divergence arises among natural populations remains one of the major goals in evolutionary biology. As part of competitive exclusion experiment conducted in 1971, 10 individuals of Italian wall lizard (Podarcis siculus (Rafinesque‐Schmaltz, 1810)) were transplanted from Pod Kopište Island to the nearby island of Pod Mrčaru (Adriatic Sea). Merely 35 years after the introduction, the newly established population on Pod Mrčaru Island had shifted their diet from predominantly insectivorous towards omnivorous and changed significantly in a range of morphological, behavioural, physiological and ecological characteristics. Here, we combine genomic and quantitative genetic approaches to determine the relative roles of genetic adaptation and phenotypic plasticity in driving this rapid phenotypic shift. Our results show genome‐wide genetic differentiation between ancestral and transplanted population, with weak genetic erosion on Pod Mrčaru Island. Adaptive processes following the founder event are indicated by highly differentiated genomic loci associating with ecologically relevant phenotypic traits, and/or having a putatively adaptive role across multiple lizard populations. Diverged traits related to head size and shape or bite force showed moderate heritability in a crossing experiment, but between‐population differences in these traits did not persist in a common garden environment. Our results confirm the existence of sufficient additive genetic variance for traits to evolve under selection while also demonstrating that phenotypic plasticity and/or genotype by environment interactions are the main drivers of population differentiation at this early evolutionary stage. [ABSTRACT FROM AUTHOR]

The psychological refractory period (PRP) effect occurs when two stimuli that require separate responses are presented sequentially, particularly with a short and variable time interval between them. Fatigue is a suboptimal psycho-physiological state that leads to changes in strategies. In recent years, numerous studies have investigated the effects of transcranial direct current stimulation (tDCS) on motor control. The present study aimed to investigate the effects of two tDCS methods, anodal and cathodal, on PRP in ten different conditions of stimulus-onset asynchronies (SOAs) under non-fatigue and mental fatigue conditions. The participants involved 39 male university students aged 19 to 25 years. In the pre-test, they were assessed using the PRP measurement tool under both non-fatigue and mental fatigue conditions. The mental fatigue was induced by a 30-min Stroop task. The test consisted of two stimuli with different SOAs (50, 75, 100, 150, 300, 400, 600, 900, 1200, and 1500 ms). The first was a visual stimulus with three choices (letters A, B, and C). After a random SOA, the second stimulus, a visual stimulus with three choices (colors red, yellow, and blue), was presented. Subsequently, participants were randomly assigned to the anodal, cathodal, and sham stimulation groups and underwent four consecutive sessions of tDCS stimulation. In the anodal and cathodal stimulation groups, 20 min of tDCS stimulation were applied to the PLPFC area in each session, while in the sham group, the stimulation was artificially applied. All participants were assessed using the same measurement tools as in the pre-test phase, in a post-test phase one day after the last stimulation session, and in a follow-up phase four days after that. Inferential statistics include mixed ANOVA, one-way ANOVA, independent, and dependent t-tests. The findings indicated that the response time to the second stimulus was longer at lower SOAs. However, there was no significant difference between the groups in this regard. Additionally, there was no significant difference in response time to the second stimulus between the fatigue and non-fatigue conditions, or between the groups. Therefore, tDCS had no significant effect. There was a significant difference between mental fatigue and non-fatigue conditions in the psychological refractory period. Moreover, at lower SOAs, the PRP was longer than at higher SOAs. In conditions of fatigue, the active stimulation groups (anodal and cathodal) performed better than the sham stimulation group at higher SOAs. Considering the difference in response to both stimuli at different SOAs, some central aspects of the response can be simultaneously parallel. Fatigue also affects parallel processing. This study supports the response integration phenomenon in PRP, which predicts that there will be an increase in response time to the first stimulus as the interval between the presentation of the two stimuli increases. This finding contradicts the bottleneck model. In this study, the effectiveness of cathodal and anodal tDCS on response time to the second stimulus and PRP was found to be very small. [ABSTRACT FROM AUTHOR]

Introduction: Quaternary glaciations, in particular the last glacial maximum (LGM), have shaped the contemporary distribution of many species. In Europe, survival of temperate species during range contractions was mainly associated with refugia in Mediterranean peninsulas, allowing south to north recolonization. Additionally, the Ponto-Caspian refugium provided an east to west migration route. Methods: Here, we investigated genetic diversity and structure of the dispersal-restricted Primula vulgaris Huds., a temperate herb of supposed Caucasian origin, using 12 highly polymorphic nuclear microsatellite loci to trace the colonization of this species in three European regions. We studied 38 populations, namely an eastern mountainous region (Caucasus), a central region (Carpathian Mountains and Dinaric Alps) and a western lowland region (North European Plain). The role of an eastern refugium of the species was tested by performing Approximate Bayesian computation analyses to elucidate its demographic and phylogeographic history, detecting bottleneck and expansion events, and estimating effective (ancestral and current) population sizes and time of divergence. Results and discussion: We found the eastern and central regions featuring the highest allelic richness and genetic differentiation being strong between and within regions. Stepwise-like mutation processes (RST > FST), together with isolation-by-distance patterns, contributed to genetic differentiation. Demographic event models showed that P. vulgaris experienced bottlenecks as well as expansions across its range during the Quaternary glacial cycles, with the last expansion about 6,000, 4,000, and 2,000 generations ago for eastern, central, and western populations, respectively. The best supported origin model pointed to the Caucasus population being closest to an ancestral situation, and from where central and western populations diverged subsequently. Divergence time of the Caucasus populations from an ancestral lineage referred to the Upper Pleistocene (Middle Weichselian). Divergence of Carpathian populations, including a Lower Danube valley corridor, was estimated during and across the LGM (Late Weichselian), confirming central populations as potential secondary cryptic refugium. Western populations recently diverged during the Holocene, most probably in the Atlanticum phase (7,000-3,900 years ago). Within regions, genetic structure was also shaped by latitude, longitude, or altitudinal migration, and for western lowlands, by recent bottleneck and genetic drift processes. [ABSTRACT FROM AUTHOR]

Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long‐term viability. The effective population size (Ne) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate Ne of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The Ne/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14 years period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2% in 2005–2018 and 44.8% in 2021). Increased harvest rates decreased Ne in the simulations, but less sex biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased Ne. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long‐term genetic viability of wildlife populations subject to a disease will also depend on population impacts of the disease and how these interact with management actions. [ABSTRACT FROM AUTHOR]

Yellow catfish Tachysurus fulvidraco is an important commercial fish species in South Korea. However, due to their current declines in its distribution area and population size, it is being released from hatchery populations into wild populations. Hatchery populations also produced from wild broodstocks are used for its captive breeding. We reported 15 new microsatellite DNA markers of T. fulvidraco to identify the genetic diversity and structure of its hatchery and wild populations, providing baseline data for useful resource development strategies. The observed heterozygosity of the hatchery populations ranged from 0.816 to 0.873, and that of the wild populations ranged from 0.771 to 0.840. Their inbreeding coefficient ranged from −0.078 to 0.024. All populations experienced a bottleneck (p < 0.05), with effective population sizes ranging from 21 to infinity. Their gene structure was divided into two groups with STRUCTURE results of K = 2. It was confirmed that each hatchery population originated from a different wild population. This study provides genetic information necessary for the future development and conservation of fishery resources for T. fulvidraco. [ABSTRACT FROM AUTHOR]

Many Cycad species may not survive the current extinction crisis, despite belonging to the oldest living seed plant lineage. Conservation of endangered and threatened species will require a combination of in situ and ex situ programs, both of which will benefit from better knowledge of species' population genetic structure, as will assessments of threatened status. Here we develop a cost-effective method of obtaining population-level genomic data from across the range of the Mexican cycad, Dioon holmgreni, and use these data to characterize the genetic structure and diversity of the species. We also reconstruct aspects of the demographic history of the species and evaluate the taxonomic cohesion of populations across the range using genomic and morphological data. We find that D. holmgrenii harbors moderate genetic diversity across genetically and geographically isolated populations that each possess a substantial percentage of private alleles. We further find that the history of this species likely includes a widespread range expansion followed by fragmentation due to population contraction. These results argue for conservation of all populations and their unique alleles but also suggest an unexpected ability of this species to maintain genetic diversity despite dramatic reductions in population size. [ABSTRACT FROM AUTHOR]

This article examines the EUMR’s purpose and ex-ante control against the background of ‘killer’ or ‘zombie’ acquisitions that evaded scrutiny by falling below merger control thresholds, while other concentrations were permitted due to debatable market definitions or inadequate theories of harm. Recognizing these shortcomings, the article discusses ex-post control following Towercast and Continental Can. It submits that the conditionality introduced in these judgments constitutes (1) an effort by the CJEU to limit ex-post merger control, (2) an ultra vires restriction on the application of Art 102 TFEU, or (3) a de facto acquisition ban for bottleneck holders and ecosystem orchestrators. [ABSTRACT FROM AUTHOR]

Understanding pedestrian dynamics at bottlenecks and how pedestrians interact with their environment—particularly how they use and move in the space available to them—is of safety importance, since bottlenecks are a key point for pedestrian flow. We performed a series of experiments in which participants walked through a bottleneck individually for varying combinations of approaching angle, bottleneck width and walking speed, to investigate the dependence of the movement on safety-relevant influencing factors. Trajectories as well as 3D motion data were recorded for every participant. This paper shows that (1) the maximum amplitude of shoulder rotation is mainly determined by the ratio of the bottleneck width to the shoulder width of the participant, while the direction is determined by the starting angle and the foot position; (2) the 'critical point' is not invariant to the starting angle and walking speed; (3) differences between the maximum and minimum speed values arise mainly from the distribution of deceleration patterns; and (4) the position of crossing shifts by 1.75 cm/10 cm, increasing the bottleneck width in the direction of origin. [ABSTRACT FROM AUTHOR]

Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high‐arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest‐induced demographic bottleneck that occurred during the 17–20th centuries. Here, we investigate changes in genetic diversity, population structure, and gene‐specific differentiation during and after this overharvesting event. Using whole‐genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90) to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near‐extirpation followed by pronounced genetic drift has altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 26%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre‐harvest diversity and a complex post‐harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high‐arctic case study therefore emphasize the need to understand the long‐term interplay of past, current, and future stressors in wildlife conservation. [ABSTRACT FROM AUTHOR]

Although it is well known that humans substantially altered the Malagasy ecosystems, the timing of the human arrival as well as the extension of their environmental impact is yet not well understood. This research aims to study the influence of early human impact and climate change on rainforests and wildlife in northern Madagascar during the past millennia. Results obtained from the lake sediment in a montane environment showed significant changes in vegetation within the lake catchment associated with a major drought that started approximately 1100 years ago. Human impact, revealed by fires, began at roughly the same time and occurred outside the lake catchment. Although this does not dismiss the impacts that humans had at a regional scale, this result demonstrates that the late Holocene natural drought also significantly impacted the ecosystems independently of anthropogenic activities. At a regional scale, a review of species demographic history revealed a substantial number of population bottlenecks during the last millennia, probably resulting from this combination of human-related impact and natural climate changes. This research highlights the importance of a multi-site and multi-proxy comparison for deciphering the nature and succession of environmental changes.

Abstract Understanding the dynamics of population recovery in threatened species requires robust longitudinal monitoring datasets. However, evidence‐based decision‐making is often impeded by variable data collection approaches, necessitating critical evaluation of restricted available baselines. The Hainan gibbon, the world's rarest primate, had possibly declined to only seven or eight individuals in 1978 at Bawangling National Nature Reserve but has experienced subsequent population growth. Past population estimates lack detailed reporting of survey effort, and multiple conflicting estimates are available, hindering assessment of gibbon recovery. We investigated all reported estimates of Bawangling gibbon population size from 1978 to 2022, to evaluate the biological signal of population trends and the extent to which noise associated with varying survey effort, reporting and estimation may mask or misrepresent any underlying signal. This longitudinal dataset demonstrates that the Bawangling population experienced a series of bottlenecks and recoveries, with three successive periods of growth interspersed by population crashes (1978–1989, 1989–2000 and 2000–2022). The rate of gibbon population recovery was progressively slower over time in each successive period of growth, and this potential decline in recovery rate following serial bottlenecks suggests that additional management strategies may be required alongside “nature‐based solutions” for this species. However, population viability analysis suggests the 1978 founder population is unlikely to have been as low as seven individuals, raising concerns for interpreting reported historical population counts and understanding the dynamics of the species' recovery. We caution against overinterpreting potential signals within “messy” conservation datasets, and we emphasise the crucial importance of standardised replicable survey methods and transparent reporting of data and effort in all future surveys of Hainan gibbons and other highly threatened species.

Abstract There are two primary measures of the amount of genetic variation in a population at a locus: heterozygosity and the number of alleles. Effective population size (Ne) provides both an expectation of the amount of heterozygosity in a population at drift‐mutation equilibrium and the rate of loss of heterozygosity because of genetic drift. In contrast, the number of alleles in a population at drift‐mutation equilibrium is a function of both Ne and census size (NC). In addition, populations with the same Ne can lose allelic variation at very different rates. Allelic variation is generally much more sensitive to bottlenecks than heterozygosity. Expressions used to adjust for the effects of violations of the ideal population on Ne do not provide good predictions of the loss of allelic variation. These effects are much greater for loci with many alleles, which are often important for adaptation. We show that there is a linear relationship between the reduction of NC and the corresponding reduction of the expected number of alleles at drift‐mutation equilibrium. This makes it possible to predict the expected effect of a bottleneck on allelic variation. Heterozygosity provides good estimates of the rate of adaptive change in the short‐term, but allelic variation provides important information about long‐term adaptive change. The guideline of long‐term Ne being greater than 500 is often used as a primary genetic metric for evaluating conservation status. We recommend that this guideline be expanded to take into account allelic variation as well as heterozygosity.

The rise in cyberattacks targeting critical network infrastructure has spurred an increased emphasis on the development of robust cybersecurity measures. In this context, there is a growing exploration of effective Intrusion Detection Systems (IDS) that leverage Machine Learning (ML) and Deep Learning (DL), with a particular emphasis on autoencoders. Recognizing the pressing need to mitigate cyber threats, our study underscores the crucial importance of advancing these methodologies. Our study aims to identify the optimal architecture for an Intrusion Detection System (IDS) based on autoencoders, with a specific focus on configuring the number of hidden layers. To achieve this objective, we designed four distinct sub-models, each featuring a different number of hidden layers: Test 1 (one hidden layer), Test 2 (two hidden layers), Test 3 (three hidden layers), and Test 4 (four hidden layers).We subjected our models to rigorous training and testing, maintaining consistent neuron counts of 30 and 60. The outcomes of our experimental study reveal that the model with a single hidden layer consistently outperformed its counterparts, achieving an accuracy of 95.11% for NSL-KDD and an impressive 98.6% for CIC-IDS2017. The findings of our study indicate that our proposed system is viable for implementation on critical network infrastructure as a proactive measure against cyber-attacks.

The present paper shows how to develop an I3oT (Industrializable Industrial Internet of Things) tool for continuous improvement in production line efficiency by means of the sub-bottleneck detection method. There is a large amount of scientific literature related to the detection of bottlenecks in production lines. However, there is no scientific literature that develops tools to improve production lines based on the bottlenecks that go beyond rebalancing tasks. This article explores the concept of a sub-bottleneck. In order to detect sub-bottlenecks in a massive way, the use of one of the I3oT (Industrializable Industrial Internet of Things) tools developed in our previous work, the mini-terms, is proposed. These mini-terms use the existing sensors for the normal operation of the production lines to measure the sub-cycle times and use them to predict the deterioration of the machine components found in the production lines. The sub-bottleneck algorithms proposed are used in two real twin lines at the Ford manufacturing plant in Almussafes (Valencia), the (3LH) and (3RH), to show how the lines can be continuously improved by means of sub-bottleneck detection.

Congestion and queues are crucial factors in high-passenger flow areas, affecting both traffic efficiency and pedestrian comfort. Ensuring pedestrian safety in bottleneck areas is of utmost importance, and understanding flow characteristics is essential to improving resilience levels. In this study, a comparative experiment was conducted to investigate crowd dynamics in different transition bottleneck types, including straight, right-angle, and curve transitions. Pedestrian flow data were analyzed to examine the impact of transition shape on pedestrian characteristics, such as passing time, speeds, trajectories, and densities within the bottleneck. The results indicate that the curve bottleneck outperforms the other two types, significantly improving traffic capacity, particularly when the pedestrian rate ranges from 0.5 to 1.25 person/s. The curve bottleneck demonstrates the minimum passing time, lowest density, and fastest passing speed. Moreover, under various flow rates, the cumulative maximum pedestrian density of curve bottlenecks is consistently smaller than the other types. These findings offer valuable insights for designing and managing pedestrian flow in bottleneck areas to ensure safety and resilience levels. [ABSTRACT FROM AUTHOR]

Implementation of long‐lasting insecticide‐treated net (LLIN) programs to control human malaria transmission leads to substantial reductions in the abundance of Anopheles mosquitoes, but the impact on the population genetic structure of the malaria vectors is poorly known, nor has it been investigated in Papua New Guinea, where malaria is highly endemic and where several species of Anopheles have vector roles. Here, we applied Wright's F‐statistic, analysis of molecular variance, Bayesian structure analysis, and discriminant analysis of principle components to microsatellite genotype data to analyze the population genetic structure of Anopheles farauti between and within the northern and southern lowland plains and of Anopheles punctulatus within the northern plain of Papua New Guinea after such a program. Bottleneck effects in the two malaria vectors were analyzed using Luikart and Cornuet's tests of heterozygosity. A large, panmictic population of An. punctulatus pre‐LLIN program diverged into two subregional populations corresponding to Madang and East Sepik provinces post‐LLIN distribution and experienced a genetic bottleneck during this process. By contrast, the An. farauti population existed as two regional populations isolated by mountain ranges pre‐LLIN, a genetic structure that persisted after the distribution of LLINs with no further geographic differentiation nor evidence of a genetic bottleneck. These findings show the differential response of populations of different vector species to interventions, which has implications for program sustainability and gene flow. [ABSTRACT FROM AUTHOR]