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Abstract Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.

Knowledge of forest recovery processes after severe disturbances, such as tropical cyclones, is essential for understanding the mechanisms maintaining forest diversity and ecosystem functioning. However, studies examining the impact of tropical cyclones on forest dynamics are still rare, especially in Northeast Asia. Here, we explore the complex responses of vegetation and soil chemistry to severe tropical cyclone disturbances in Hallasan National Park in South Korea. Vegetation and soil were examined five years before and five years after passages of tropical cyclones in 2012 in natural broadleaf and coniferous forests along an elevation gradient from 950 to 1770 m a.s.l., including the largest population of endemic Abies koreana. Tropical cyclones caused abundant tree mortality, resulting in a 46% decrease in stem basal area. Tropical cyclone disturbances triggered the spread of pioneer trees and shrubs and intense clonal propagation of graminoids, including dwarf bamboo, resulting in less diverse understory vegetation, especially in coniferous forests. In contrast, broadleaf forests at lower elevations experienced only minor disturbance. Opening of canopies after tropical cyclone disturbance led to the decrease in soil cations and doubling of available soil phosphorus stock, which likely contributed to the increased coverage of clonal graminoids, especially in coniferous forests (from 36 to 66%). Hence, increased competition of graminoids and reduction in seed fall and seedling recruitment prevented A. koreana regeneration. The subalpine forest dominated by A. koreana is forecasted to gradual loss due to the fact of temperature increases, intensified tropical cyclones and, particularly, due to the altered competition between dwarf bamboo and fir seedlings.

Salmonella enterica subspecies enterica serotype Choleraesuis is a swine adapted serovar. S. Choleraesuis variant Kunzendorf is responsible for the majority of outbreaks among pigs. S. Choleraesuis is rare in Europe, although there have been serious outbreaks in pigs including two outbreaks in Denmark in 1999–2000 and 2012–2013. Here, we elucidate the epidemiology, possible transmission routes and sources, and clonality of European S. Choleraesuis isolates including the Danish outbreak isolates. A total of 102 S. Choleraesuis isolates from different European countries and the United States, covering available isolates from the last two decades were selected for whole genome sequencing. We applied a temporally structured sequence analysis within a Bayesian framework to reconstruct a temporal and spatial phylogenetic tree. MLST type, resistance genes, plasmid replicons, and accessory genes were identified using bioinformatics tools. Fifty-eight isolates including 11 out of 12 strains from wild boars were pan-susceptible. The remaining isolates carried multiple resistance genes. Eleven different plasmid replicons in eight plasmids were determined among the isolates. Accessory genes were associated to the identified resistance genes and plasmids. The European S. Choleraesuis was estimated to have emerged in ∼1837 (95% credible interval, 1733–1983) with the mutation rate of 1.02 SNPs/genome/year. The isolates were clustered according to countries and neighbor countries. There were transmission events between strains from the United States and European countries. Wild boar and pig isolates were genetically linked suggesting cross-border transmission and transmission due to a wildlife reservoir. The phylogenetic tree shows that multiple introductions were responsible for the outbreak of 2012–2013 in Denmark, and suggests that poorly disinfected vehicles crossing the border into Denmark were potentially the source of the outbreak. Low levels of single nucleotide polymorphisms (SNPs) differences (0–4 SNPs) can be observed between clonal strains isolated from different organs of the same animal. Proper disinfection of livestock vehicles and improved quality control of livestock feed could help to prevent future spread of S. Choleraesuis or other more serious infectious diseases such as African swine fever (ASF) in the European pig production system.

The aim of this study was to evaluate the seasonal behavior and milk yield of dairy cows of Czech Fleckvieh cattle. The subject of the monitoring was one section (housed in one quarter of barn) with 103 free cubicle beds with an average of 95 lactating dairy cows of Czech Fleckvieh cattle. In the seasons (spring, summer, autumn, winter) temperature (°C), relative humidity (%) and temperature-humidity index (THI) were monitored. Furthermore, behavioral signs were also observed (a total of 4,940 observations): dairy cows were either lying down (3,432 observations) or standing up (1,508 observations). In the conditions that dairy cows were standing up in the cubicle, up to 585 observations were proved. If dairy cows were standing up outside of the cubicle (923 observations), they were either lying on the left side (1,924 observations) or right side (1,508). Significant seasonal influence was found out (p < 0.05) on the number of dairy cows standing up (a maximum of 410 observations in the spring, a minimum of 342 observations in the summer) and then the number of cows lying both on the left (a maximum of 519 observations in the autumn and a minimum of 444 observations in the spring) and on the right side (a maximum of 415 observations in the winter, a minimum of 320 observations in the autumn). The seasonal influence was no significant (p > 0.05) in the remaining behavioral signs. With regard to milk yield, a significant seasonal influence was proved. The highest milk yield was reached with dairy cows in spring (29.27 kg of milk) and the lowest in the autumn (24.58 kg of milk). No significant differences of milk yield were detected between behavioral signs (p > 0.05). The maximum difference of milk yield was found out up to 1.39 kg between dairy cows lying down on the left side (28.35 kg) and the dairy cows standing up in a cubicle (26.96 kg) in the winter but even this difference was not statistically significant (p > 0.05).

V příspěvku se autoři zabývají modulovým řešením návrhu nového terminálu kombinované přepravy se všemi dopady na používanou technologii překládky. Autoři pak dle navržených modulů terminálu provedli zhodnocení vlastních návrhů řešení, zejména po stránce technologické.

The objective of the study was to evaluate and compare sires based on results of their offspring in the Criteria of Young Horses. The Criteria of Young Horses are intended for stallions and mares of 4 to 6 years of age. The competitions are announced by the Czech Equestrian Federation in co-operation with breeders’ associations of the Bohemian warm-blood, Slovakian warm-blood, Kinský horse and Moravian warm-blood breeds. The horses were evaluated in the arena by the assessor and given three marks: for show jumping, agility and readiness of the horse. Data were obtained in co-operation with the Czech Equestrian Federation. Evaluated were the results of the Criteria of Young Horses in show jumping competitions held in 1998–2007. Only sires with 7 and more offspring were assessed. Ana­ly­sis of variance was carried out followed by tests according to Scheffe. The Excel 2003 and Statistica version 8 were used for processing the database and for statistical processing. Comparisons based on marks given by the assessor in the arena showed that the highest-placed stallion was Acord II and was followed by Catango Z, Calido I and Landos. The offspring of the Hanoverian stallion Walzerkönig were the lowest-placed; the second worst-placed were the offspring of Diktant slatiňanský, a stallion of Czech origin. The differences among these stallions were statistically significant. In comparisons based on marks as the second indicator, the offspring of stallions Acord II, Catango Z and Ascot were the highest-placed and offspring of stallion Diktant slatiňanský were the lowest-placed. The dif­fe­rence between these stallions was statistically significant. Based on the third indicator the offspring of stallions Acord II and Catango Z were the highest-placed. By contrast, the worst were offspring of stallions Duramus II and Duman. The differences between Acord II and Duramus II were statistically significant. According to the resulting total evaluation the highest rating went to offspring of stallion Acord II, followed by Catango Z, Autonom s.v. and Landos. The worst rating went to offspring of stallions Duman, Walzerkönig, Cattaro and Diktant slatiňanský. Comparisons showed that the dif­fe­rences were statistically significant only between Acord II and Diktant slatiňanský.

Message queues are a way for different software components or applications to communicate with each other asynchronously by passing messages through a shared buffer. This allows a sender to send a message without needing to wait for an immediate response from the receiver, which can help to improve the system’s performance, reduce latency, and allow components to operate independently. In this paper, we compared and evaluated the performance of four popular message queues: Redis, ActiveMQ Artemis, RabbitMQ, and Apache Kafka. The aim of this study was to provide insights into the strengths and weaknesses of each technology and to help practitioners choose the most appropriate solution for their use case. We primarily evaluated each technology in terms of latency and throughput. Our experiments were conducted using a diverse array of workloads to test the message queues under various scenarios. This enables practitioners to evaluate the performance of the systems and choose the one that best meets their needs. The results show that each technology has its own pros and cons. Specifically, Redis performed the best in terms of latency, whereas Kafka significantly outperformed the other three technologies in terms of throughput. The optimal choice depends on the specific requirements of the use case. This paper presents valuable insights for practitioners and researchers working with message queues. Furthermore, the results of our experiments are provided in JSON format as a supplement to this paper.

In the world of microservices, companies must be able to create systems that operate in the most efficient way. To achieve this, anti-patterns must be avoided because of their detriment to the quality of the system. Some of the most troubling anti-patterns are hard to detect because of their appearance at runtime. Effectively removing anti-patterns from a system requires dynamic analysis because of the large size of microservice-based systems. While the detection of anti-patterns is helpful, being able to visualize them offers a great benefit to companies working with microservices. Seeing how the overall system is flowing and recognizing the existence of anti-patterns can help improve microservice-based systems. In this paper, a systematic mapping study was performed to find the current state of research on visualizing anti-patterns in microservices from the dynamic perspective. Several hundred papers were examined and a total of 31 were found to be relevant to the research topic. The papers, when analyzed, revealed that there are mechanisms to detect anti-patterns at runtime in microservices, and there are also mechanisms for visualizing the architecture of a microservice-based system. This study’s findings could help to identify and remove anti-patterns that occur during runtime in microservices, as well as a means of visualizing these anti-patterns.

As microservices become more popular, more drawbacks become apparent to developers. One issue that many teams face today is the failure to visualize the entire system architecture holistically. Without a full view of the system, the architecture can become convoluted as teams add and subtract from their system without reconciling their changes. One established practice to determine a view on the entire system involves dynamic analysis of microservice interaction and dependencies. In this mapping study, we investigate dynamic analysis as a way to visualize system architecture. Capturing the architectural view with dynamic analysis has the ability to build the system and then show its behavior at run-time. We identify dynamic analysis techniques, the corresponding tools, and the models that these practices can generate. The findings of this study are relevant to developers of decentralized systems looking for a way to visualize their system architecture in a dynamic perspective.

Software code is present on multiple levels within current Internet of Things (IoT) systems. The quality of this code impacts system reliability, safety, maintainability, and other quality aspects. In this paper, we provide a comprehensive overview of code quality-related metrics, specifically revised for the context of IoT systems. These metrics are divided into main code quality categories: Size, redundancy, complexity, coupling, unit test coverage and effectiveness, cohesion, code readability, security, and code heterogeneity. The metrics are then linked to selected general quality characteristics from the ISO/IEC 25010:2011 standard by their possible impact on the quality and reliability of an IoT system, the principal layer of the system, the code levels and the main phases of the project to which they are relevant. This analysis is followed by a discussion of code smells and their relation to the presented metrics. The overview presented in the paper is the result of a thorough analysis and discussion of the author’s team with the involvement of external subject-matter experts in which a defined decision algorithm was followed. The primary result of the paper is an overview of the metrics accompanied by applicability notes related to the quality characteristics, the system layer, the level of the code, and the phase of the IoT project.

Static code analysis of software systems has proven beneficial for a broad range of domains, including security assessments, coding practice, error detection, and others. However, as modern systems have grown in complexity and heterogeneity over the past few decades, advances in development frameworks have dominated. Rather than involving low-level language constructs, these frameworks typically focus on software components, including data entities, controllers, and endpoints. As a result, current code analysis approaches have become unsuitable for analyzing these modern systems due to their focus on low-level constructs in a single language. Thus, code analysis has become a far more complicated endeavor thanks to the plethora of languages, frameworks, and design approaches in modern software development. This paper presents a novel approach to solving the problem of being tied to a single language and its low-level constructs. The system’s source code is transformed into an intermediate representation called a language-agnostic abstract-syntax tree. This system representation is then assessed by generalized component parsers that extract relevant high-level information, such as components, from low-level structures. The design of the approach is presented here in detail, along with its evaluation in a case study involving two large, heterogeneous, cloud-native system benchmarks (Java and C++ microservices). The study demonstrates a unified identification approach to determine system data entities and endpoints. Utilizing higher-level constructs, such as components, can advance the current practice of system analysis to better face broader problems introduced by modern system development practices.

Protecting the resources of a cloud-native application is essential to meet an organization’s security goals. Cloud-native applications manage thousands of user requests, and an organization must employ a proper access control mechanism. However, unfortunately, developers sometimes grumble when designing and enforcing access decisions for a gigantic scalable application. It is sometimes complicated to choose the potential access control model for the system. Cloud-native software architecture has become an integral part of the industry to manage and maintain customer needs. A microservice is a combination of small independent services that might have hundreds of parts, where the developers must protect the individual services. An efficient access control model can defend the respective services and consistency. This study intends to comprehensively analyze the current access control mechanism and techniques utilized in cloud-native architecture. For this, we present a systematic mapping study that extracts current approaches, categorizes access control patterns, and provides developers guidance to meet security principles. In addition, we have gathered 234 essential articles, of which 29 have been chosen as primary studies. Our comprehensive analysis will guide practitioners to identify proper access control mechanisms applicable to ensuring security goals in cloud-native architectures.

Security is a significant priority for cloud-native systems, regardless of the system size and complexity. Therefore, one must utilize a set of defensive mechanisms or controls to protect the system from exploitation by potential adversaries. There is an expanding amount of research on security issues, including attacks against individual microservices or overall systems and their corresponding defense mechanism options. This study intends to provide a comprehensive overview of currently used defense mechanisms involving static analysis that can detect and react against associated attacks and vulnerabilities. We present a systematic literature review that extracts current approaches for the security analysis of microservices and the violation of security principles. We gathered 1049 relevant publications, of which 50 were selected as primary studies. We are providing practitioners and developers with a structured survey of the existing literature of defensive solutions for microservice architectures and cloud-native systems to aid them in identifying applicable solutions for their systems.

Understanding software systems written by others is often challenging. When we want to assess systems to reason about them, i.e., to understand dependencies, analyze evolution trade-offs, or to verify conformance to the original blueprint, we must invest broad efforts. This becomes difficult when considering decentralized systems. Microservice-based systems are mainstream these days; however, to observe, understand, and manage these systems and their properties, we are missing fundamental tools that would derive various simplified system abstract perspectives. Microservices architecture characteristics yield many advantages to system operation; however, they bring challenges to their development and deployment lifecycles. Microservices urge a system-centric perspective to better reason about the system evolution and its quality attributes. This process review paper considers the current system analysis approaches and their possible alignment with automated system assessment or with human-centered approaches. We outline the necessary steps to accomplish holistic reasoning in decentralized microservice systems. As a contribution, we provide a roadmap for analysis and reasoning in microservice-based systems and suggest that various process phases can be decoupled through the introduction of system intermediate representation as the trajectory to provide various system-centered perspectives to analyze various system aspects. Furthermore, we cover different technical-based reasoning strategies and metrics in addition to the human-centered reasoning addressed through alternative visualization approaches. Finally, a system evolution is discussed from the perspective of such a reasoning process to illustrate the impact analysis evaluation over system changes.

Code analysis brings excellent benefits to software development, maintenance, and quality assurance. Various tools can uncover code defects or even software bugs in a range of seconds. For many projects and developers, the code analysis tools became essential in their daily routines. However, how can code analysis help in an enterprise environment? Enterprise software solutions grow in scale and complexity. These solutions no longer involve only plain objects and basic language constructs but operate with various components and mechanisms simplifying the development of such systems. Enterprise software vendors have adopted various development and design standards; however, there is a gap between what constructs the enterprise frameworks use and what current code analysis tools recognize. This manuscript aims to challenge the mainstream research directions of code analysis and motivate for a transition towards code analysis of enterprise systems with interesting problems and opportunities. In particular, this manuscript addresses selected enterprise problems apparent for monolithic and distributed enterprise solutions. It also considers challenges related to the recent architectural push towards a microservice architecture. Along with open-source proof-of-concept prototypes to some of the challenges, this manuscript elaborates on code analysis directions and their categorization. Furthermore, it suggests one possible perspective of the problem area using aspect-oriented programming.

Internet of Things (IoT) is an emerging technology that has the promising power to change our future. Due to the market pressure, IoT systems may be released without sufficient testing. However, it is no longer acceptable to release IoT systems to the market without assuring the quality. As in the case of new technologies, the quality assurance process is a challenging task. This paper shows the results of the first comprehensive and systematic mapping study to structure and categories the research evidence in the literature starting in 2009 when the early publication of IoT papers for IoT quality assurance appeared. The conducted research is based on the most recent guidelines on how to perform systematic mapping studies. A set of research questions is defined carefully regarding the quality aspects of the IoT. Based on these questions, a large number of evidence and research papers is considered in the study (478 papers). We have extracted and analyzed different levels of information from those considered papers. Also, we have classified the topics addressed in those papers into categories based on the quality aspects. The study results carry out different areas that require more work and investigation in the context of IoT quality assurance. The results of the study can help in a further understanding of the research gaps. Moreover, the results show a roadmap for future research directions.

It is important in software development to enforce proper restrictions on protected services and resources. Typically software services can be accessed through REST API endpoints where restrictions can be applied using the Role-Based Access Control (RBAC) model. However, RBAC policies can be inconsistent across services, and they require proper assessment. Currently, developers use penetration testing, which is a costly and cumbersome process for a large number of APIs. In addition, modern applications are split into individual microservices and lack a unified view in order to carry out automated RBAC assessment. Often, the process of constructing a centralized perspective of an application is done using Systematic Architecture Reconstruction (SAR). This article presents a novel approach to automated SAR to construct a centralized perspective for a microservice mesh based on their REST communication pattern. We utilize the generated views from SAR to propose an automated way to find RBAC inconsistencies.

Technologies for the Internet of Things (IoT) are maturing, yet no common standards dictate their direction, leaving space for a plethora of research directions and opportunities. Among the most important IoT topics is security. When we design a robust system, it is important to know the available options for facing common tasks related to access control, authentication, and authorization. In this review, we systematically analyze 1622 peer-reviewed publications from October 2017 to December 2020 to find the taxonomy of security solutions. In addition, we assess and categorize current practices related to IoT security solutions, commonly involved technologies, and standards applied in recent research. This manuscript provides a practical road map to recent research, guiding the reader and providing an overview of recent research efforts.

Microservice architecture has become the leading design for cloud-native systems. The highly decentralized approach to software development consists of relatively independent services, which provides benefits such as faster deployment cycles, better scalability, and good separation of concerns among services. With this new architecture, one can naturally expect a broad range of advancements and simplifications over legacy systems. However, microservice system design remains challenging, as it is still difficult for engineers to understand the system module boundaries. Thus, understanding and explaining the microservice systems might not be as easy as initially thought. This study aims to classify recently published approaches and techniques to analyze microservice systems. It also looks at the evolutionary perspective of such systems and their analysis. Furthermore, the identified approaches target various challenges and goals, which this study analyzed. Thus, it provides the reader with a roadmap to the discipline, tools, techniques, and open challenges for future work. It provides a guide towards choices when aiming for analyzing cloud-native systems. The results indicate five analytical approaches commonly used in the literature, possibly in combination, towards problems classified into seven categories.

Microservice Architecture (MSA) is becoming the predominant direction of new cloud-based applications. There are many advantages to using microservices, but also downsides to using a more complex architecture than a typical monolithic enterprise application. Beyond the normal poor coding practices and code smells of a typical application, microservice-specific code smells are difficult to discover within a distributed application setup. There are many static code analysis tools for monolithic applications, but tools to offer code-smell detection for microservice-based applications are lacking. This paper proposes a new approach to detect code smells in distributed applications based on microservices. We develop an MSANose tool to detect up to eleven different microservice specific code smells and share it as open-source. We demonstrate our tool through a case study on two robust benchmark microservice applications and verify its accuracy. Our results show that it is possible to detect code smells within microservice applications using bytecode and/or source code analysis throughout the development process or even before its deployment to production.

An effective means of engaging spectators at live events involves providing real-time information from a variety of sources. Consumers demand personalized experience; thus, a single channel perspective fails. Modern entertainment must extend to spectator mobile devices and adapt content to individual interests. Moreover, such systems should take advantage of venue screens to engage in sharing live information, aggregated social media, etc. We propose a second screen application, providing each audience member a personalized perspective, involving mobile devices equipped with Wi-Fi, and spanning to venue screens in hotels, halls, arenas, elevators, etc. Such a system engages both local audience and remote spectators. Our work provides a case study involving experience from the deployment of such an application at the ACM-ICPC World Finals with audiences at the event and around the world. We analyze and categorize its features, consider its impact on the audience, and measure its demands.

Understanding how past climate changes affected biodiversity is a key issue in contemporary ecology and conservation biology. These diversity changes are, however, difficult to reconstruct from paleoecological sources alone, because macrofossil and pollen records do not provide complete information about species assemblages. Ecologists therefore use information from modern analogues of past communities in order to get a better understanding of past diversity changes. Here we compare plant diversity, species traits and environment between late-glacial Abies, early-Holocene Quercus, and mid-Holocene warm-temperate Carpinus forest refugia on Jeju Island, Korea in order to provide insights into postglacial changes associated with their replacement. Based on detailed study of relict communities, we propose that the late-glacial open-canopy conifer forests in southern part of Korean Peninsula were rich in vascular plants, in particular of heliophilous herbs, whose dramatic decline was caused by the early Holocene invasion of dwarf bamboo into the understory of Quercus forests, followed by mid-Holocene expansion of strongly shading trees such as maple and hornbeam. This diversity loss was partly compensated in the Carpinus forests by an increase in shade-tolerant evergreen trees, shrubs and lianas. However, the pool of these species is much smaller than that of light-demanding herbs, and hence the total species richness is lower, both locally and in the whole area of the Carpinus and Quercus forests. The strongly shading tree species dominating in the hornbeam forests have higher leaf tissue N and P concentrations and smaller leaf dry matter content, which enhances litter decomposition and nutrient cycling and in turn favored the selection of highly competitive species in the shrub layer. This further reduced available light and caused almost complete disappearance of understory herbs, including dwarf bamboo.