Serverless computing in omics data analysis and integration.

A comprehensive analysis of omics data can require vast computational resources and access to varied data sources that must be integrated into complex, multi-step analysis pipelines. Execution of many such analyses can be accelerated by applying the cloud computing paradigm, which provides scalable resources for storing data of different types and parallelizing data analysis computations. Moreover, these resources can be reused for different multi-omics analysis scenarios. Traditionally, developers are required to manage a cloud platform's underlying infrastructure, configuration, maintenance and capacity planning. The serverless computing paradigm simplifies these operations by automatically allocating and maintaining both servers and virtual machines, as required for analysis tasks. This paradigm offers highly parallel execution and high scalability without manual management of the underlying infrastructure, freeing developers to focus on operational logic. This paper reviews serverless solutions in bioinformatics and evaluates their usage in omics data analysis and integration. We start by reviewing the application of the cloud computing model to a multi-omics data analysis and exposing some shortcomings of the early approaches. We then introduce the serverless computing paradigm and show its applicability for performing an integrative analysis of multiple omics data sources in the context of the COVID-19 pandemic.

Comparative Study of Sorption Phenomena Between Three Medications and Syringes Made of Cyclic Olefin Copolymer or Polypropylene.

INTRODUCTION: Medical syringes are widely used in hospitals to store and administer drugs, and the contact time between the drugs and these syringes can vary from a few minutes to several weeks like for pharmaceutical preparations. The aim of this comparative study was to evaluate the potential sorption phenomena occurring between three drugs (paracetamol, diazepam and insulin aspart) and polypropylene syringes (PP) or syringes made of Cyclic Olefin Copolymer (COC). MATERIALS AND METHODS: 50 mL 3-part syringes made of either COC with crosslinked silicone on the barrel inner surface (COC-CLS) and a bromobutyl plunger seal, or PP lubricated with silicone oil (PP-SOL) with a polyisoprene plunger seal were used. RESULTS: COC-CLS syringes induced less sorption of diazepam and insulin than PP-SOL syringes and the plunger seal material seemed to be the main cause of these interactions. An alkalinization of the medications in contact with the PP-SOL syringes was observed. It could be caused by leachable compounds and should be investigated further. CONCLUSION: This work shows once again that it is essential to consider content-container interactions to help improve the safe use of parenteral drugs.

Humans can sense large numbers of objects in a box by touch alone.

Everyday experiences suggest that a container, such as a box of cereal, can convey pertinent information about the nature and quantity of its content. This study investigated how well people can judge large quantities of objects in a container through haptic perception. Stimuli consisted of plastic drinking straws cut to "small" (1.5 cm) or "big" (4.5 cm) pieces contained in plastic food containers. Participants performed both a magnitude estimation of the number of objects and a direct estimation of the proportion of the container perceived to be filled with objects. Overall, participants demonstrated considerable accuracy for both tasks and irrespective of the size of the content. Post-experiment interviews revealed three potential strategies. Participants either focused on the container's contents, the excess space in the container, or the perceived weight of the container (content).

On the Analysis of Inter-Relationship between Auto-Scaling Policy and QoS of FaaS Workloads.

A recent development in cloud computing has introduced serverless technology, enabling the convenient and flexible management of cloud-native applications. Typically, the Function-as-a-Service (FaaS) solutions rely on serverless backend solutions, such as Kubernetes (K8s) and Knative, to leverage the advantages of resource management for underlying containerized contexts, including auto-scaling and pod scheduling. To take the advantages, recent cloud service providers also deploy self-hosted serverless services by facilitating their on-premise hosted FaaS platforms rather than relying on commercial public cloud offerings. However, the lack of standardized guidelines on K8s abstraction to fairly schedule and allocate resources on auto-scaling configuration options for such on-premise hosting environment in serverless computing poses challenges in meeting the service level objectives (SLOs) of diverse workloads. This study fills this gap by exploring the relationship between auto-scaling behavior and the performance of FaaS workloads depending on scaling-related configurations in K8s. Based on comprehensive measurement studies, we derived the logic as to which workload should be applied and with what type of scaling configurations, such as base metric, threshold to maximize the difference in latency SLO, and number of responses. Additionally, we propose a methodology to assess the scaling efficiency of the related K8s configurations regarding the quality of service (QoS) of FaaS workloads.

Environmental consequences in lifecycle changes of container shipping vessels.

To estimate the average lifespan of container vessels, this study specified their most suitable lifespan distribution function using a comprehensive dataset comprising 2188 container vessels manufactured and retired between 1941 and 2018. The lifecycle CO2 emissions of vessels were estimated under different scenarios with varied average lifespans and average carbon intensity improvements per annum through stock-flow model analysis. The results indicated that a normal distribution best represented the lifespan distribution of container vessels, with an estimated average lifespan of approximately 24 years. Furthermore, scenario analyses revealed that shortening the lifespans of container vessels can effectively reduce lifecycle CO2 emissions. This study demonstrates the synergistic contribution of accelerating the replacement cycle of container vessels and implementing stronger energy efficiency regulations for emissions reduction, highlighting the importance of policies regulating vessel lifespans.

[Analysis of symptoms and influencing factors of low back work-related musculoskeletal disorders among workers in a container manufacturing factory].

Objective: To investigate the occurrence of low back work-related musculoskeletal disorders (WMSDs) among workers in a container manufacturing factory, and to explore the influencing factors. Methods: In June 2022, 952 workers from a container factory were selected as the research objects by cluster random sampling. Through questionnaire survey, the incidence of low back WMSDs symptoms among workers in the past one year was collected, and the influencing factors of low back WMSDs were analyzed by logistic regression. Results: The incidence rate of low back WMSDs was 46.7% (445/952). The factors with higher exposure at work were frequent slight bending (77.0%, 733/952), frequent overtime (74.1%, 705/952), and the need to turn around while working (62.3%, 593/952). Multivariate logistic regression analysis showed that age over 40 years old, smoking, drinking, often bending over slightly, sitting for a long time, maintaining a large bending posture for a long time, often working overtime, limited operating space, and there was always a need to complete conflicting things in the container manufacturing factory workers were the risks of increasing the low back WMSDs (OR=1.68, 1.96, 2.47, 1.49, 1.84, 2.11, 1.90, 1.82, 2.00, P<0.05). Standing at work, always friendly colleagues, and always supportive and helpful leaders were protective factors for low back WMSDs (OR=0.60, 0.32, 0.40, P<0.05) . Conclusion: The incidence of low back WMSDs symptoms in container manufacturing workers is high, and work-related factors such as frequent slight bending, long time holding large bending posture and limited operating space are the focus of ergonomic intervention in container manufacturing enterprises.

Climate-ecosystem modelling made easy: The Land Sites Platform.

Dynamic Global Vegetation Models (DGVMs) provide a state-of-the-art process-based approach to study the complex interplay between vegetation and its physical environment. For example, they help to predict how terrestrial plants interact with climate, soils, disturbance and competition for resources. We argue that there is untapped potential for the use of DGVMs in ecological and ecophysiological research. One fundamental barrier to realize this potential is that many researchers with relevant expertize (ecology, plant physiology, soil science, etc.) lack access to the technical resources or awareness of the research potential of DGVMs. Here we present the Land Sites Platform (LSP): new software that facilitates single-site simulations with the Functionally Assembled Terrestrial Ecosystem Simulator, an advanced DGVM coupled with the Community Land Model. The LSP includes a Graphical User Interface and an Application Programming Interface, which improve the user experience and lower the technical thresholds for installing these model architectures and setting up model experiments. The software is distributed via version-controlled containers; researchers and students can run simulations directly on their personal computers or servers, with relatively low hardware requirements, and on different operating systems. Version 1.0 of the LSP supports site-level simulations. We provide input data for 20 established geo-ecological observation sites in Norway and workflows to add generic sites from public global datasets. The LSP makes standard model experiments with default data easily achievable (e.g., for educational or introductory purposes) while retaining flexibility for more advanced scientific uses. We further provide tools to visualize the model input and output, including simple examples to relate predictions to local observations. The LSP improves access to land surface and DGVM modelling as a building block of community cyberinfrastructure that may inspire new avenues for mechanistic ecosystem research across disciplines.

Water-Dispersible Carbon Nano-Test Tubes as a Container for Concentrated DNA Molecules.

Water-dispersible carbon nano-test tubes (CNTTs) with an inner and outer diameter of about 25 and 35 nm, respectively, were prepared by the template technique and then their inner carbon surface was selectively oxidized to introduce carboxy groups. The adsorption behavior of DNA molecules on the oxidized CNTTs (Ox-CNTTs) was examined in the presence of Ca2+ cations. Many DNA molecules are attracted to the inner space of Ox-CNTTs based on the Ca2+ -mediated electrostatic interaction between DNA phosphate groups and carboxylate anions on the inner carbon surface. Moreover, the total net charge of the DNA adsorbed was found to be equal to the total charge of the carboxylate anions. This selective adsorption into the interior of Ox-CNTTs can be explained from the fact that the electrostatic interaction onto the inner concave surface is much stronger than that on the outer convex surface. On the other hand, the desorption of DNA easily occurs whenever Ca2+ cations are removed by washing with deionized water. Thus, each of Ox-CNTTs works well as a nano-container for a large amount of DNA molecules, thereby resulting in the occurrence of DNA enrichment in the nanospace.

CellProfiler plugins - An easy image analysis platform integration for containers and Python tools.

CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that allows for the creation of new modules which integrate with other Python tools or tools that are packaged in software containers. The CellProfiler-plugins repository contains a number of these CellProfiler modules, especially modules that are experimental and/or dependency-heavy. Here, we present an upgraded CellProfiler-plugins repository, an example of accessing containerised tools, improved documentation and added citation/reference tools to facilitate the use and contribution of the community.

Impact of Primary Container Closure System on PS80 Oxidation and the Mechanistic Understanding.

PURPOSE: Polysorbate oxidation can potentially lead to protein degradation and loss of potency, which has been a challenge for the pharmaceutical industry for decades. Many factors have been reported to impact polysorbate oxidation rate, including types of elemental impurities, peroxide content, pH, light exposure, grades of polysorbate, etc. Even though there are many publications in this field, the impact of primary container closure system on PS80 oxidation has not been systematically studied or reported. The purpose of the current study is to close this gap. METHODS: Placebo PS80 formulations were prepared and filled into different container-closure systems (CCS), including different types of glass vials and polymer vials. Oleic acid content was monitored on stability as a surrogate value for PS80 content, which will decline upon oxidation. ICP-MS analysis and metal spiking studies were carried out to correlate the PS80 oxidation rate with metals leached from primary containers. RESULTS: PS80 degrades via oxidation at the fastest rate in glass vials with high coefficient of expansion (COE), followed by glass vials with low coefficient of expansion, while polymer vials minimized the oxidation of PS80 in most formulation conditions explored in this paper. ICP-MS analysis demonstrated that 1) 51 COE glass has more metal leachables than 33 COE glass in this study; and 2) More metal leachables correlates with faster PS80 oxidation. Metal spiking studies confirmed the hypothesis that aluminum and iron have a synergistic catalysis effect on PS80 oxidation. CONCLUSIONS: Primary containers of drug products play a significant role in the rate of PS80 oxidation. This study revealed a new major contributor to PS80 oxidation and potential mitigation strategy for biological drug products.

Aedes aegypti oviposition-sites choice under semi-field conditions.

Vector control is still the recommended approach to avoid arbovirus outbreaks. Herein, we investigate oviposition preferences of Aedes aegypti (Diptera: Culicidae) females under a semi-field structure Rio de Janeiro, Brazil. For that, in Experiment 1, we used two settings: 'Single items', which included as containers drain, beer bottle, bucket, car tyre, water tank, and a potted Peace Lily (Spathiphyllum wallisii) in a saucer with water, or 'Multiple containers', as an urban simulation, in which one drain, two additional beer bottles, and an extra plant pot saucer were added. Experiment 2 (sensory cues) used five variations of potted plant, each one varying in the range of sensory cues known to attract gravid females to oviposition containers. Our results indicate that gravid Ae. aegypti prefer to oviposit close to the ground and in open water containers with organic compounds from plant watering. Domestic large artificial containers containing tap water received significantly fewer eggs, except for the car tyre, which exhibited as many eggs as the potted plant. We also show that visual (potted plant shape) and olfactory clues (odour of the plant or from water containing organic matter) were equally attractive separately as were these stimuli together.

Accidents, diseases and health complaints among seafarers on German-flagged container ships.

BACKGROUND: For seafarers on the high seas health hazards are various and due to the setting also specific. The spectrum of job-related health impairments and accidents is mainly influenced by the maritime characteristics. The aim of this study is to assess the kind of accidents and the frequency of diseases and health complaints among seafarers on German container ships by evaluating medical log books. METHODS: A systematic analysis of 14,628 medical entries from 95 medical log books of 58 container ships under German flag from 1995 to 2015 was performed. This monocentric retrospective and descriptive study used information on accidents, diseases and health complaints among different occupational groups and medical treatment procedures for the analysis and evaluation. RESULTS: The analysis showed that more than one third of all consultations with the Health Officer on board are related to internal (33.7%) and surgical (31.3%) symptoms. Almost twenty percent of consultations were due to respiratory infections (19.6%) and accidents (17.9%). Accidents represented the most frequent reason for unfitness for sea service (31.2%). Based on occupational categories, most injuries occurred among deck crew (22.5%), followed by ratings working in the engine room (18.9%). In 106 cases, telemedical contact with a physician ashore was necessary. In total, 15 seafarers had to be evacuated from the ship for further medical treatment onshore. Medicine/drug application was the most common therapeutic measure on board, accounting for 77% of all consultations. CONCLUSIONS: The high proportion of health complaints and accidents among seafarers shows that there is a need to optimize medical care at sea and accident prevention, e.g. by standardized treatment algorithms or improving the medical training of Health Officers. The development and introduction of a digital patient file to record medical treatments on the vessels could also improve medical documentation on board.

Humans can sense small numbers of objects in a box by touch alone.

Everyday experiences suggest that a container, such as a box of chocolate sprinkles, can convey pertinent information about the nature of its content. Despite the familiarity of the experience, we do not know whether people can perceive the number of objects in the container from touch alone and how accurately they can do so. In three experiments, participants handled containers holding between one and five objects and verbally estimated their number. Containers were small cardboard jewelry boxes, and objects were round beads of varying diameter and weight. Any useful visual and auditory cues were precluded. Experiment 1 demonstrated very accurate performance, provided the objects were of sufficient weight. Experiment 2 demonstrated that withholding information about the possible number of objects inside the container does not affect accuracy at a group level but does produce occasional overestimations at an individual level. Experiment 3 demonstrated that removing the weight cue leads to systematic underestimations but does not eliminate people's ability to distinguish between different numbers of objects in the container. This study contributes to a growing picture that container haptics is surprisingly capable.

Revealing the intersectoral material flow of plastic containers and packaging in Japan.

The Japanese government developed a strategy for plastics and laid out ambitious targets including the reduction of 25% for single-use plastic waste and the reuse/recycling of 60% for plastic containers and packaging by 2030. However, the current usage situation of single-use plastics including containers and packaging, which should be a basis of the strategy, is unclear. Here, we identify the nationwide material flow of plastics in Japan based on input-output tables. Of the domestic plastic demand of 8.4 Mt in 2015, 1.6 and 2.5 Mt were estimated to be for containers and packaging comprising household and industry inflows, respectively, through the purchase/procurement of products, services, and raw materials. Considering the current amount of recycling collected from households (1.0 Mt) and industries (0.3 to 0.4 Mt), the reuse/recycling target has already been achieved if the goal is limited to household container and packaging waste, as is the focus of Japan's recycling law. Conversely, the results indicate that it will be extremely difficult to reach the target collectively with industries. Therefore, it is essential that efforts be made throughout the entire supply chain. Food containers and packaging that flowed into the food-processing and food service sectors accounted for 15% of the inflow of containers and packaging into industries. Thus, the key to achieving the reuse/recycling target will comprise the collection of plastic food packaging from not only households but also the food industry. Furthermore, the collection of flexible plastic films used between industry sectors will put the target within reach.

Liquid Content Detection In Transparent Containers: A Benchmark.

Various substances that possess liquid states include drinking water, various types of fuel, pharmaceuticals, and chemicals, which are indispensable in our daily lives. There are numerous real-world applications for liquid content detection in transparent containers, for example, service robots, pouring robots, security checks, industrial observation systems, etc. However, the majority of the existing methods either concentrate on transparent container detection or liquid height estimation; the former provides very limited information for more advanced computer vision tasks, whereas the latter is too demanding to generalize to open-world applications. In this paper, we propose a dataset for detecting liquid content in transparent containers (LCDTC), which presents an innovative task involving transparent container detection and liquid content estimation. The primary objective of this task is to obtain more information beyond the location of the container by additionally providing certain liquid content information which is easy to achieve with computer vision methods in various open-world applications. This task has potential applications in service robots, waste classification, security checks, and so on. The presented LCDTC dataset comprises 5916 images that have been extensively annotated through axis-aligned bounding boxes. We develop two baseline detectors, termed LCD-YOLOF and LCD-YOLOX, for the proposed dataset, based on two identity-preserved human posture detectors, i.e., IPH-YOLOF and IPH-YOLOX. By releasing LCDTC, we intend to stimulate more future works into the detection of liquid content in transparent containers and bring more focus to this challenging task.

The Strength of Rail Vehicles Transported by a Ferry Considering the Influence of Sea Waves on Its Hull.

The article presents the results of a determination of the load attributed to rail vehicles transported by a ferry, considering the influence of sea waves on its hull. A mathematic model describing the displacements of a train ferry, which transported rail vehicles on its decks during rolling oscillations, was created. Calculated accelerations were used to identify the load of components from a dynamics point of view and they were subsequently applied as an input to the analysis of the strength of the open wagon main-bearing structure in a standard scheme of interaction with a train ferry deck. The calculated maximal equivalent stresses in the structure of the fastening units exceeded the valid permissible values. To confirm the theoretical results, experimental studies focused on the strength analysis of the open wagon placed on the railway ferry deck, which was performed in real operational conditions. Electrical voltage sensors were used to determine stress distribution in the areas where the body was attached to the deck. In this case, sensors of the strain gauges, i.e., tensiometers, were used. The base of 25 mm is a dimensional parameter and the resistance, 124 Ohms, is the tensiometer parameter. Verification has been performed and, based on the obtained experimental results, it has been established that the hypothesis' adequacy is not rejected. The authors developed some measures for adaption of the lashing devices for rail cars on train ferries, which can ensure their safe transportation by sea. The strength calculation demonstrated that, in the new scheme of securing the transported railway vehicles on the railway train ferry, the stresses in its structure do not exceed the permissible values. The article also includes information about the results of the strength calculation of a container placed on a roll trailer transported by a train ferry. This research will contribute to the development of measures regarding the safety of railway vehicle transportation by sea ferry and better efficiency of train ferry transportation.

ConGPS: A Smart Container Positioning System Using Inertial Sensor and Electronic Map with Infrequent GPS.

Real-time global positioning is important for container-based logistics. However, a challenge in real-time global positioning arises from the frequency of both global positioning system (GPS) calls and GPS-denied environments during transportation. This paper proposes a novel system named ConGPS that integrates both inertial sensor and electronic map data. ConGPS estimates the speed and heading direction of a moving container based on the inertial sensor data, the container trajectory, and the speed limit information provided by an electronic map. The directional information from magnetometers, coupled with map-matching algorithms, is employed to compute container trajectories and current positions. ConGPS significantly reduces the frequency of GPS calls required to maintain an accurate current position. To evaluate the accuracy of the system, 280 min of driving data, covering a distance of 360 km, are collected. The results demonstrate that ConGPS can maintain positioning accuracy within a GPS-call interval of 15 min, even if using low-cost inertial sensors in GPS-denied environments.

Performance Evaluation of Container Orchestration Tools in Edge Computing Environments.

Edge computing is a viable approach to improve service delivery and performance parameters by extending the cloud with resources placed closer to a given service environment. Numerous research papers in the literature have already identified the key benefits of this architectural approach. However, most results are based on simulations performed in closed network environments. This paper aims to analyze the existing implementations of processing environments containing edge resources, taking into account the targeted quality of service (QoS) parameters and the utilized orchestration platforms. Based on this analysis, the most popular edge orchestration platforms are evaluated in terms of their workflow that allows the inclusion of remote devices in the processing environment and their ability to adapt the logic of the scheduling algorithms to improve the targeted QoS attributes. The experimental results compare the performance of the platforms and show the current state of their readiness for edge computing in real network and execution environments. These findings suggest that Kubernetes and its distributions have the potential to provide effective scheduling across the resources on the network's edge. However, some challenges still have to be addressed to completely adapt these tools for such a dynamic and distributed execution environment as edge computing implies.

Cloud-Native Workload Orchestration at the Edge: A Deployment Review and Future Directions.

Cloud-native computing principles such as virtualization and orchestration are key to transferring to the promising paradigm of edge computing. Challenges of containerization, operative models and scarce availability of established tools make a thorough review indispensable. Therefore, the authors have described the practical methods and tools found in the literature as well as in current community-led development projects, and have thoroughly exposed the future directions of the field. Container virtualization and its orchestration through Kubernetes have dominated the cloud computing domain, while major efforts have been recently recorded focused on the adaptation of these technologies to the edge. Such initiatives have addressed either the reduction of container engines and the development of specific tailored operating systems or the development of smaller K8s distributions and edge-focused adaptations (such as KubeEdge). Finally, new workload virtualization approaches, such as WebAssembly modules together with the joint orchestration of these heterogeneous workloads, seem to be the topics to pay attention to in the short to medium term.

Elastic Provisioning of Network and Computing Resources at the Edge for IoT Services.

The fast growth of Internet-connected embedded devices demands new system capabilities at the network edge, such as provisioning local data services on both limited network and computational resources. The current contribution addresses the previous problem by enhancing the usage of scarce edge resources. It designs, deploys, and tests a new solution that incorporates the positive functional advantages offered by software-defined networking (SDN), network function virtualization (NFV), and fog computing (FC). Our proposal autonomously activates or deactivates embedded virtualized resources, in response to clients' requests for edge services. Complementing existing literature, the obtained results from extensive tests on our programmable proposal show the superior performance of the proposed elastic edge resource provisioning algorithm, which also assumes an SDN controller with proactive OpenFlow behavior. According to our results, the maximum flow rate for the proactive controller is 15% higher; the maximum delay is 83% smaller; and the loss is 20% smaller compared to when the non-proactive controller is in operation. This improvement in flow quality is complemented by a reduction in control channel workload. The controller also records the time duration of each edge service session, which can enable the accounting of used resources per session.