Transport System Research Articles

From Gene to Structure: Unraveling Genomic Dark Matter in Ca. Accumulibacter.

"Candidatus Accumulibacter" is a unique and pivotal genus of polyphosphate-accumulating organisms prevalent in wastewater treatment plants and plays mainstay roles in the global phosphorus cycle. However, the efforts to fully understand their genetic and metabolic characteristics are largely hindered by major limitations in existing sequence-based annotation methods. Here, we reported an integrated approach combining pangenome analysis, protein structure prediction and clustering, and meta-omic characterization, to uncover genetic and metabolic traits previously unexplored for Ca. Accumulibacter. The identification of a previously overlooked pyrophosphate-fructose 6-phosphate 1-phosphotransferase gene (pfp) suggested that all Ca. Accumulibacter encoded a complete Embden-Meyerhof-Parnas pathway. A homologue of the phosphate-specific transport system accessory protein (PhoU) was suggested to be an inorganic phosphate transport (Pit) accessory protein (Pap) conferring effective and efficient phosphate transport. Additional lineage members were found to encode complete denitrification pathways. A pipeline was built, generating a pan-Ca. Accumulibacter annotation reference database, covering >200,000 proteins and their encoding genes. Benchmarking on 27 Ca. Accumulibacter genomes showed major improvement in the average annotation coverage from 51% to 82%. This pipeline is readily applicable to diverse cultured and uncultured bacteria to establish high-coverage annotation reference databases, facilitating the exploration of genomic dark matter in the bacterial domain.

Reduced plastid genomes of colorless facultative pathogens Prototheca (Chlorophyta) are retained for membrane transport genes

BackgroundPlastids are usually involved in photosynthesis, but the secondary loss of this function is a widespread phenomenon in various lineages of algae and plants. In addition to the loss of genes associated with photosynthesis, the plastid genomes of colorless algae are frequently reduced further. To understand the pathways of reductive evolution associated with the loss of photosynthesis, it is necessary to study a number of closely related strains. Prototheca, a chlorophyte genus of facultative pathogens, provides an excellent opportunity to study this process with its well-sampled array of diverse colorless strains.ResultsWe have sequenced the plastid genomes of 13 Prototheca strains and reconstructed a comprehensive phylogeny that reveals evolutionary patterns within the genus and among its closest relatives. Our phylogenomic analysis revealed three independent losses of photosynthesis among the Prototheca strains and varied protein-coding gene content in their ptDNA. Despite this diversity, all Prototheca strains retain the same key plastid functions. These include processes related to gene expression, as well as crucial roles in fatty acid and cysteine biosynthesis, and membrane transport.ConclusionsThe retention of vestigial genomes in colorless plastids is typically associated with the biosynthesis of secondary metabolites. In contrast, the remarkable conservation of plastid membrane transport system components in the nonphotosynthetic genera Prototheca and Helicosporidium provides an additional constraint against the loss of ptDNA in this lineage. Furthermore, these genes can potentially serve as targets for therapeutic intervention, indicating their importance beyond the evolutionary context.

Design and dosimetric characterization of a transportable proton minibeam collimation system

BackgroundProton Minibeam Radiation Therapy has shown to widen the therapeutic window compared to conventional radiation treatment in pre-clinical studies. The underlying biological mechanisms, however, require more research.PurposeThe purpose of this study was to develop and characterize a mechanical collimation setup capable of producing 250µm wide proton minibeams with a center-to-center distance of 1000µm.MethodsTo find the optimal arrangement Monte Carlo simulations were employed using the Geant4 toolkit TOPAS to maximize key parameters such as the peak-to-valley dose ratio (PVDR) and the valley dose rate. The experimental characterization of the optimized setup was carried out with film dosimetry at the University Proton Therapy beamline in Dresden and the proton beamline of the University of Washington Medical Center in Seattle with 150MeV and 50.5MeV, respectively. A microDiamond detector (PTW, Freiburg, Germany) was utilized at both beamlines for online proton minibeam dosimetry.ResultsA PVDR of 10 was achieved in Dresden and a PVDR of 14 in Seattle. Dosimetry measurements were carried out with EBT3 films at a depth of 5mm in a polymethylmethacrylate (PMMA) phantom. When comparing film dosimetry with the microDiamond, excellent agreement was observed in the valleys. However, the peak dose showed a discrepancy of approximately 10% in the 150MeV beam and 20% in the 50.5MeV beam between film and microDiamond.DiscussionThe characteristics of the minibeams generated with our system compares well with those of other collimated minibeams despite being smaller. The deviations of microDiamond measurements from film readings might be subject to the diamond detector responding differently in the peak and valley regions. Applying previously reported correction factors aligns the dose profile measured by the microDiamond with the profile acquired with EBT3 films in Dresden.ConclusionThe novel proton minibeam system can be operated independently of specific beamlines. It can be transported easily and hence used for inter-institutional comparative studies. The quality of the minibeams allows us to perform in vitro and in vivo experiments in the future. The microDiamond was demonstrated to have great potential for online dosimetry for proton minibeams, yet requires more research to explain the observed discrepancies.

Effects of alpha-cypermethrin and difenoconazole on survival, growth and biomarkers in European green toad tadpoles (<em>Bufotes viridis</em>, Laurenti 1768)

In recent decades, the decline of amphibian populations has become more pronounced and accelerated, with one of the contributing factors being the excessive use of pesticides. Alpha-cypermethrin, an insecticide, and difenoconazole, a fungicide, are widely employed pesticides globally. To gain a comprehensive understanding of the acute impact of these two pesticides on amphibians, we used European green toad (Bufotes viridis) tadpoles as our model organisms. We assessed mortality and mass as apical endpoints, and examined physiological biomarkers including electron transport system (ETS) activity, catalase activity, and carbonyl protein content. Tadpoles were exposed to varying concentrations of the two pesticides for 48 hours (0.2-10 µg/L for alpha-cypermethrin; 10-100 µg/L for difenoconazole). Our results indicate that the exposure of tadpoles to these pesticides significantly affected their physiology. Mortality was observed exclusively in tadpoles treated with difenoconazole (LC50 = 100.832 µg/L), while a decrease in mass occurred in tadpoles exposed to both pesticides. No significant differences across treatments were found for total ETS activity, catalase activity, or the presence of protein carbonyls. In conclusion, our findings suggest that alpha-cypermethrin at environmentally relevant concentrations poses a risk to European green toad tadpoles, while the effects of difenoconazole are become patent at higher concentrations than those recorded in natural aquatic environments.

How Biochar Addition Affects Denitrification and the Microbial Electron Transport System (ETSA): A Meta-Analysis Based on a Global Scale

Biochar has a significant effect on denitrification, especially in agriculture. The effects of biochar and soil properties on denitrification and ETSA have been invested in individual studies but have not yet been summarized on a global scale. We conducted a meta-analysis of the data from 37 studies to examine the effects of biochar properties, soil physicochemical properties, and ecosystem types on denitrification. Biochar can decrease soil NO3− and N2O emissions by 14.16% and 76.69%, respectively, while denitrification function genes nirK, nirS, and nosZ increased by 10.98%, 34.62%, and 13.19%, respectively. Biochar enhanced ETSA by 8.65%. The results indicate that the effects of biochar on nitrogen cycling and greenhouse gas emissions vary significantly with specific properties, such as feedstock source and pyrolysis temperature, as well as soil characteristics like pH, organic matter, and cation exchange capacity (CEC). In summary, soil-specific biochar applications are necessary to realize optimized agricultural and environmental advantages of biochar, but several limitations have been recognized in this study, including variability across different types of biochar and a lack of longer-term experimental data. Future research should focus on long-term studies that can give a comprehensive understanding of how biochar interacts with microbial communities to create an accurate understanding.

Biochemical Properties of the Acid Ectophosphatase Activity of Phytomonas serpens Involved in Cell Proliferation

Phytomonas is the only kinetoplastid that can parasitize plants, causing economically relevant issues. Phytomonas serpens share similarities with pathogenic trypanosomatids, including surface enzymes that are involved in adhesion to the salivary gland of their experimental host, the insect Oncopeltus fasciatus. Ectophosphatases are cell surface enzymes involved in host–parasite interactions that are widely distributed among microorganisms. This work aimed to perform the biochemical characterization of P. serpens ectophosphatase activity, investigating and discussing its possible physiological role. This activity presented an acidic profile, and its kinetic parameters Km and Vmax were calculated as 1.57 ± 0.08 mM p-NPP and 10.11 ± 0.14 nmol p-NP/(h × 108 flagellates), respectively. It was stimulated by cobalt, inhibited by zinc, and insensitive to EDTA, a divalent metal chelator. The inhibitor sodium orthovanadate was able to decrease P. serpens ectophosphatase activity and growth, suggesting its involvement in cell proliferation. Given that P. serpens can uptake inorganic phosphate (Pi) from the extracellular medium, it is likely that its ectophosphatase activity acts together with the transport systems in the Pi acquisition process. The elucidation of the molecular mechanisms involved in this process emerges as a relevant perspective, providing new strategies for controlling Phytomonas infection.

Intensification of Trade Interactions between the Regions of China and Russia

The article identifies the Chinese provinces that are the points of growth of the Russian imports. Their main supply channels to the Chinese market are concentrated in the eastern coastal regions of China, being traditionally more developed. Russian imports are growing faster through the Chinese pilot free trade zones. However, geographical and product diversification is still slow. The supply structure of Russian products is still dominated by raw materials, while imports of high value added products are growing rapidly in some regions of China. The rapid growth of Russian imports is observed in some regions of the Yangtze River Economic Belt, which creates additional opportunities for the intensification of trade interactions with the Russian regions within the project «Volga-Yangtze». The connection of the export sectors of the economy of the Volga Federal District with the import of China is considered in more detail in the article as a potential for further intensification of trade interactions. The regions with a high level of economic diversification (the Nizhny Novgorod and the Samara regions) have the greatest opportunities for developing trade interactions. Current conditions indicate that prospects for the further intensification of Russian exports to China are determined by the expansion of production (in the regions with a high share of exports to China and other friendly countries), development of transport and logistics system, adaptation of Russian products to the needs of the Chinese consumer. One way to increase exports of Rus-sian high-value-added products is to reduce barriers to the supply of such products in China’s free-trade zones. In a limited international market, Russian regions may have to compete more for Chinese consumers as the domestic market becomes saturated.

Problems of Transport Provision in the Regions of Eastern Siberia and the Far East

The article provides a detailed analysis of the existing transport infrastructure in the East of the country, taking into account the development of export directions. A comprehensive study of two main railways, highways and ports that provide communication in the regions of Eastern Siberia and the Far East was carried out. The advantages, disadvantages and prospects for the development of the largest checkpoints have been identified. It is shown that there is an annual development and strengthening of the international integration of the eastern regions of Russia with the countries of the Asia-Pacific region, while taking into account the national interest of the Russian state. The integration of the eastern regions with the unified transport system of Russia is also developing by increasing the carrying capacity of the Eastern range. The number of border road and rail crossings is growing, port capacities are expanding, and the country’s key logistics hub is being formed. But despite this, it is shown that there are transport problems in the Far Eastern regions of the country: lack of supply railways to seaports, low railway capacity, poor development of transport infrastructure for the development of natural resources. It is concluded that there is a need to develop transport infrastructure in the Far East, which will improve socio-economic indicators in the eastern regions. The development of integration of the railway with sea ports will increase the export of raw materials and products with high added value from the mining and metallurgical, fuel and energy, chemical and agro-industrial complexes. Effective implementation of transit potential will not only make it possible to obtain economic benefits from participation in international transport, but will also create new instruments for Russia’s influence on global economic processes.

EU Railways: Contribution to Decarbonisation Solution

The EU transport system is entering the next phase of fundamental transformation. The railways are becoming one of the key tools for implementing the Green Deal and solving ecological problems for the period up to 2050. A range of documents aimed at advancing the realisation of the Trans-European Transport Network (TEN-T) was adopted at the Union level in recent years. Transfer a large proportion of transport from road and aviation to rail, multimodal transportation, advanced construction and modernisation of high-speed railway lines (HSR) are the priorities of the policy. This article has a twofold objective. First, it analyses the condition and market environment of the railways. Second, it investigates the possibilities of implementing the TEN-T program to reduce greenhouse gas (GHG) emissions, increase multimodal transportation and the construction/upgrading new HSR. The results suggest that a set of obstacles impede GHG emissions reduction in the shifting of transport from road and aviation to rail, multimodal transportation and the construction of HSR. The main trend is that rail transport activity in the EU remained almost constant from 2010 to 2022 with a slight increase in passenger transport and some structural changes. Within the next 25 years, the most tangible impact for the EU economy, ecology and society of all modes of transport can be provided by HSR expansion. The author concludes that in order to form the Union Transport and Economic Space, deep institutional reforms on the railways are needed with special focus on the introduction of uniform standards, norms and regulations for all participating countries.

System Dynamics Models for the Control of the Road Transport System of a Metropolis

System Dynamics Models for the Control of the Road Transport System of a Metropolis

Modeling and Stabilization of Conveyor Transport Systems with Intelligent Control

Modeling and Stabilization of Conveyor Transport Systems with Intelligent Control

Orexin in depression: Evidence from basic and clinical research

Orexin – a neuropeptide – is extensively distributed in the central nervous system and is involved in the regulation of diverse physiological functions and behaviors. Orexin is strongly associated with the onset and development of depression. The most important function of orexin is to interact with the transport system, mediating arousal, and energy homeostasis. Hypothalamic-ventral tegmental and hypothalamic-ventral thalamic pathways provide clues for understanding the function of orexin and related disorders, such as sleep disorders, eating disorders, and substance abuse. This article summarizes the basic and clinical studies on the role of the orexin system in regulating and treating depression, including the relationship between the expression level of orexin in specific brain areas and diseases, relationship between adolescent depression and orexin, orexin receptor antagonists as a treatment for depression, and narcolepsy, which is closely associated with depression. Research progress on the role of orexin in depression and recent relevant studies are summarized, providing novel directions for developing depression treatment strategies.

Prediction of Drivers’ Red-Light Running Behaviour in Connected Vehicle Environments Using Deep Recurrent Neural Networks

Red-light running at signalised intersections poses a significant safety risk, necessitating advanced predictive technologies to predict red-light violation behaviour, especially for advanced red-light warning (ARLW) systems. This research leverages Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU) models to forecast the red-light running and stopping behaviours of drivers in connected vehicles. We utilised data from the Ipswich Connected Vehicle Pilot (ICVP) in Queensland, Australia, which gathered naturalistic driving data from 355 connected vehicles at 29 signalised intersections. These vehicles broadcast Cooperative Awareness Messages (CAM) within the Cooperative Intelligent Transport Systems (C-ITS), providing kinematic inputs such as vehicle speed, speed limits, longitudinal and lateral accelerations, and yaw rate. These variables were monitored at 100-millisecond intervals for durations from 1 to 4 s before reaching various distances from the stop line. Our results indicate that the LSTM model outperforms the GRU in predicting both red-light running and stopping behaviours with high accuracy. However, the pre-trained GRU model performs better in predicting red-light running specifically, making it valuable in applications requiring early violation prediction. Implementing these models can enhance red-light violation countermeasures, such as dynamic all-red extension (DARE), decreasing the likelihood of severe collisions and enhancing road users’ safety.

Endothelial Cell Senescence Effect on the Blood-Brain Barrier in Stroke and Cognitive Impairment.

Age is an important risk factor of stroke, cognitive decline, and dementia. Senescent endothelial cells (ECs) accumulate with advancing age through exposure to cellular stress, such as that exerted by hypertension and diabetes. These senescent ECs have altered characteristics, such as altered tight junction proteins, use of a more indiscriminate transcellular transport system, increased inflammation, and increased immune cell interactions. ECs are the main component of the blood-brain barrier (BBB), separating the brain from systemic circulation. As senescent ECs accumulate in the BBB, their altered functioning results in the disruption of the barrier. They have inadequate barrier-forming properties, disrupted extracellular matrix, and increased transcytosis, resulting in an overly permeable barrier. This disruption of the BBB can have important effects in stroke and cognitive impairment, as presented in this review. Besides increasing the permeability of the BBB, senescent ECs can also impair angiogenesis and vascular remodeling, which in ischemic stroke may increase risk of hemorrhagic transformation and worsen outcomes. Senescent ECs may also contribute to microvascular dysfunction, with disruption of cerebral perfusion and autoregulation. These may contribute to vascular cognitive impairment along with increased permeability. With an aging population, there is growing interest in targeting senescence. Several ongoing trials have been evaluating whether senolytics can slow aging, improve vascular health, and reduce the risk of stroke and cognitive decline.

Urbanization and Urban Sprawl in the Post-Colonial Era Douala City, Cameroon

The history of the port city of Douala spans pre-colonial period, colonial period of the Germans and French occupation, the post- colonial era and the contemporary situation with continuous occupancy of the coastal environment. This article looks at the relationship between the history of the city of Douala to the resulting urban situation focusing on governance structure as well as rapid urbanization. The findings show that governance structure allowing for a duality of modern political system and traditional cultural system of kingships and chiefdoms has an effect to the resulting urban sprawl. Moreover, rapid urbanization under this condition has an overall impact to the challenges resulting from urban sprawl including development of settlements that do not have basic services. Developing comprehensive urban planning policies that prioritize sustainable and green building practices and transport systems, promoting the use of locally sourced building materials, use of technology to encourage generation of renewable energy, encouraging a broader participation of local communities in the planning and development of the city are some possible interventions recommended to ensure a more sustainable and resilient city of Douala.

Energy-based approach to the assessment of traffic flow

This article focuses on modeling vehicle acceleration noise in different road conditions, emphasizing urban, highway, and rural roads in Ukraine. Acceleration noise, which refers to the fluctuations in a vehicle's acceleration, is a critical factor in vehicle safety, fuel efficiency, and driving comfort. The research aims to improve current vehicle dynamics models by integrating multi-body dynamics and machine learning algorithms, allowing for more precise predictions of acceleration variability in real-time. The study is based on the existing literature, showing that road surface quality significantly affects acceleration noise. With frequent stop-and-go traffic, urban roads produce moderate but irregular noise patterns. Highways show stable acceleration noise at moderate speeds, but noise increases sharply as vehicles approach higher speeds due to aerodynamic forces. Rural roads, especially those in poor condition, exhibit the highest variability in acceleration noise, even at low speeds. The proposed model has been validated using real-world data. It demonstrates a strong correlation between the predictions and actual vehicle behavior on various road types. One of the key innovations in this research is the use of machine learning to adjust model parameters in real-time dynamically. This adaptive approach enhances the model’s accuracy and applicability, especially in intelligent transport systems. The model can inform traffic management strategies, allowing for real-time adjustments to speed limits, traffic signals, and routing decisions based on road conditions. This contributes to safer, more efficient, and sustainable transport systems, particularly in regions with inconsistent road infrastructure. The research concludes that integrating acceleration noise modeling into intelligent transport systems can significantly improve traffic flow and vehicle safety. Future research will expand the dataset to include a broader range of vehicle types and road conditions, further refining the model's predictive capabilities.

Analysis of the efficiency of suburban passenger transportation on the Lviv railway sections

A developed transport system ensures the population's needs in safe movement and guarantees stable functioning and development of the production sphere. Despite being consistently unprofitable, suburban transportation by railway remains attractive for many population categories. The developed railway network, the low cost of transportation, and the capacity reserve of most sections partially compensate for the existing shortcomings and contribute to further development and open new prospects for attracting additional users of transport services. The main problems of suburban passenger transport, which worsen the quality of the services provided and affect the competitiveness of railway suburban transport compared to other modes of transport, are examined in this article. During the analysis of the schedule of suburban trains departing and arriving at the Lviv station, irrational management decisions were found that left room for improvement. In addition, the load factor of rolling stock on the routes Lviv-Sambir-Sianky and Sianky-Sambir-Lviv was determined, and it dropped to 40% during the follow-up, which indicates inefficient use of rolling stock. The ratio of the time the train stays at the stops to the total duration of the route in suburban traffic is also calculated. The time on the road for the Sambir- Stryi route was 69%, and the technical speed was only 21.7 km/h. The results obtained in the article are also typical for many other monitoring areas, indicating this problem's repeatability. The positive experience of European countries in solving similar problems allows us to react correctly to the situation and take short-term measures to change the dynamics to a positive one without additional time losses. It is also worth noting that a set of measures to improve the services provided to passengers must be carried out according to the requirements of the Technical Specifications for Interoperability, which must be ensured upon joining the European Union. Further investigations should analyze the flow of passengers at all stations and stopping points to identify the main points of creating passenger flow on researching routes.

Computationally aided design of single‐ion‐conducting block copolymer electrolytes to boost lithium‐ion conductivity

AbstractIn this work, we implement a combinatory approach that integrates molecular dynamics (MD) simulation and a Gaussian process regression (GPR) algorithm to explore optimal design strategies for a generic single‐ion‐conducting block copolymer electrolyte (SIC‐BCPE) model system that covers a rich design parameter space inspired by recently established poly(ethylene oxide)‐based block copolymer electrolytes. The GPR algorithm is employed to efficiently reveal the relationships between the desired lithium‐ion conductivity and four design parameters reflecting both chain architectural control and specific tuning of molecular chemistry. Guided by the GPR results, an optimal combination of four parameter values is inferred, and MD simulation confirms that the corresponding SIC‐BCPE system produces relatively higher lithium‐ion conductivity. To further understand the influence of each molecular parameter on the trends of lithium‐ion conductivity, we analyse the proportion variation of different types of lithium‐ion coordination and identify a strong correlation between the ion coordination pattern and ionic conductivity. Due to its generality, we expect that the MD‐GPR combinatory approach reported in this work is applicable to a broad range of other polymer‐based ion transport systems. © 2024 Society of Chemical Industry.

Spatiotemporal changes in the congestion index of streets and roads in the armed conflict conditions

This article examines the impact of war on the formation of urban transport flows. During armed conflicts, the transport infrastructure of cities undergoes significant changes, which greatly affects the mobility and safety of the population. The need to study this issue is particularly relevant in the context of the ongoing Russian-Ukrainian war, which has caused the largest migration in Europe since World War II. The paper explores the dynamics of these changes and ways to adapt urban transportation systems to war conditions. The study aims to determine the parameters of urban transport zones with specific disruptions in network link congestion indices during different phases of the full-scale invasion of Ukraine by the Russian Federation. The research methodology is based on analyzing statistical data on population movements, applying traffic flow models, and conducting a systematic analysis of the interaction between various components of urban transport systems. The goal of this study is to establish the relationships between the areas of cities where disruptions in congestion indices were observed during the initial phase of the invasion. The cities studied are Lviv and Kyiv, whose road networks are also described in the article. Polynomial regression models with two independent variables (the congestion index and the number of days from the beginning of each phase) were developed for three predefined time phases, each with distinct features of the armed conflict. The dependent variable is the area of the city experiencing disruptions in the congestion index relative to normal traffic flow conditions. The study concludes that the relationship between changes in the congestion index and the area of the city experiencing deviations is directly proportional. The absolute values of the indicators studied are lower for Lviv’s network than for Kyiv’s.

Exact analytic technique for designing controller architecture in multi-axis active magnetic bearings with rotor eccentricities

Multi-coil active magnetic bearing systems require an efficient controller design to maintain stability, maximize performance, and improve flexibility in high-speed transport systems, particularly those used in electric cars, military, and aerospace. By employing Fourier-based frameworks rather than conventional Laplace-based methods, the work reported here simplifies the AMBs controllers, offering more flexibility to complex dynamics and adaptability to non-linearity. For computational and mathematical brevity, the entire formulation has been linearized around a specific range of uncertainty in this work. The magnetic field pattern with rotor eccentricities is characterized by using a subdomain technique and a perturbation methodology. Complex magnetic field formulations are obtained by the estimation of zeroth and first-order formulae in polar coordinates. For every coil, predictive model-based interpolation functions are constructed and optimal controller settings for stability are found by eigenvalue evaluation. The study enhances accuracy and effectiveness by validating these analytical methods against numerical results, offering deeper insights into rotor dynamics and controller adjustments.