CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.

Over a decade has passed since the development of the Hi-C method for genome-wide analysis of 3D genome organization. Hi-C utilizes next-generation sequencing (NGS) technology to generate large-scale chromatin interaction data, which has accumulated across a diverse range of species and cell types, particularly in eukaryotes. There is thus a growing need to streamline the process of Hi-C data analysis to utilize these data sets effectively. Hi-C generates data that are much larger compared to other NGS techniques such as chromatin immunoprecipitation sequencing (ChIP-seq) or RNA-seq, making the data reanalysis process computationally expensive. In an effort to bridge this resource gap, the 4D Nucleome (4DN) Data Portal has reanalyzed approximately 600 Hi-C data sets, allowing users to access and utilize the analyzed data. In this chapter, we provide detailed instructions for the implementation of the common workflow language (CWL)-based Hi-C analysis pipeline adopted by the 4DN Data Portal ecosystem. This reproducible and portable pipeline generates standard Hi-C contact matrices in formats such as .hic or .mcool from FASTQ files. It enables users to output their own Hi-C data in the same format as those registered in the 4DN Data portal, facilitating comparative analysis using data registered in the portal. Our custom-made scripts are available on GitHub at https://github.com/kuzobuta/4dn_cwl_pipeline .

3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data.

RNA sequencing is the gold-standard method to quantify transcriptomic changes between two conditions. The overwhelming majority of data analysis methods available are focused on polyadenylated RNA transcribed from single-copy genes and overlook transcripts from repeated sequences such as transposable elements (TEs). These self-autonomous genetic elements are increasingly studied, and specialized tools designed to handle multimapping sequencing reads are available. Transfer RNAs are transcribed by RNA polymerase III and are essential for protein translation. There is a need for integrated software that is able to analyze multiple types of RNA. Here, we present 3t-seq, a Snakemake pipeline for integrated differential expression analysis of transcripts from single-copy genes, TEs, and tRNA. 3t-seq produces an accessible report and easy-to-use results for downstream analysis starting from raw sequencing data and performing quality control, genome mapping, gene expression quantification, and statistical testing. It implements three methods to quantify TEs expression and one for tRNA genes. It provides an easy-to-configure method to manage software dependencies that lets the user focus on results. 3t-seq is released under MIT license and is available at https://github.com/boulardlab/3t-seq.

A required medical student collaborative case presentation with a pathologist in the surgery clerkship.

In medical education, pathology has traditionally been concentrated in only the preclinical years, often without sufficient emphasis on its practical application in clinical practice. Correspondingly, medical students' interest in pathology as a career has been low. To address this issue and foster a deeper understanding of pathology's clinical relevance and encourage appropriate utilization, we introduced a required exposure to pathology in the surgery clerkship featuring clinicopathological case review in a small group setting. Unlike other approaches, we wanted to create a program that concentrates on pathology cases directly linked to patients whom students cared for during their clerkship rotation, emphasizing the relevance of pathology diagnosis. Feedback has been overwhelmingly positive from participating students, who report an increased awareness of pathology's importance in patient management and of the significance of interdisciplinary collaboration between pathologists and clinicians. A notable feature of this program is its relatively low time and personnel requirements, which facilitate inclusion in the busy clerkship and acceptance in the Department of Pathology. Challenges, such as timely case selection and administrative co-ordination, are being addressed to optimize the program's implementation. In the future, we are considering expanding this model to other clerkships. By rekindling interest in pathology through practical engagement and highlighting its real-world relevance, this approach offers a promising strategy to counteract recruitment challenges in this crucial medical field.

Machine learning-assisted rapid determination for traditional Chinese Medicine Constitution.

The aim of this study was to develop a machine learning-assisted rapid determination methodology for traditional Chinese Medicine Constitution. Based on the Constitution in Chinese Medicine Questionnaire (CCMQ), the most applied diagnostic instrument for assessing individuals' constitutions, we employed automated supervised machine learning algorithms (i.e., Tree-based Pipeline Optimization Tool; TPOT) on all the possible item combinations for each subscale and an unsupervised machine learning algorithm (i.e., variable clustering; varclus) on the whole scale to select items that can best predict body constitution (BC) classifications or BC scores. By utilizing subsets of items selected based on TPOT and corresponding machine learning algorithms, the accuracies of BC classifications prediction ranged from 0.819 to 0.936, with the root mean square errors of BC scores prediction stabilizing between 6.241 and 9.877. Overall, the results suggested that the automated machine learning algorithms performed better than the varclus algorithm for item selection. Additionally, based on an automated machine learning item selection procedure, we provided the top three ranked item combinations with each possible subscale length, along with their corresponding algorithms for predicting BC classification and severity. This approach could accommodate the needs of different practitioners in traditional Chinese medicine for rapid constitution determination.

TopicTracker - An advanced software pipeline for text mining on PubMed data: Bridging the gap between off-the-shelf tools and code based approaches.

Background: The ever-increasing volume of academic literature necessitates efficient and sophisticated tools for researchers to analyze, interpret, and uncover trends. Traditional search methods, while valuable, often fail to capture the nuance and interconnectedness of vast research domains. Results: TopicTracker, a novel software tool, addresses this gap by providing a comprehensive solution from querying PubMed databases to creating intricate semantic network maps. Through its functionalities, users can systematically search for desired literature, analyze trends, and visually represent co-occurrences in a given field. Our case studies, including support for the WHO on ethical considerations in infodemic management and mapping the evolution of ethics pre- and post-pandemic, underscore the tool's applicability and precision. Conclusions: TopicTracker represents a significant advancement in academic research tools for text mining. While it has its limitations, primarily tied to its alignment with PubMed, its benefits far outweigh the constraints. As the landscape of research continues to expand, tools like TopicTracker may be instrumental in guiding scholars in their pursuit of knowledge, ensuring they navigate the large amount of literature with clarity and precision.

Inspiring Careers in Mental Health: Piloting a Pipeline Program for Underserved High School Students.

OBJECTIVE: Given mental health workforce shortages, academic psychiatry departments have a compelling interest in developing pipeline programs. This article examines a pilot program for high school students within an academic psychiatry department, assessing whether it successfully informs students about mental health career options and increases their interest in them. METHODS: The authors recruited all program participants in 2022 and 2023 during data collection. The program served as an intervention, teaching participants about mental health career options, clinical practice, and client experiences via presentations from psychiatrists and other mental health professionals. Participants completed a pretest at the start of the two-week program and a posttest at the end. On both the pretest and posttest, participants rated their agreement with 22 statements relating to mental health career knowledge, attitudes, and interest. The authors analyzed the data using dependent means t tests. RESULTS: The program increased participants' knowledge of the roles and paths to pursuing different mental health careers. It also increased participants' belief that they could pursue a mental health career. The program improved some but not all measured attitudes toward mental health and mental health careers. In 2023, the program increased participants' likelihood of pursuing a mental health career. CONCLUSIONS: A pipeline program for underserved high school students delivered by an academic psychiatry department is feasible, and it was effective in changing attitudes and increasing the likelihood of pursuing a mental health career.

Study on vibration characteristics of the dike crossing pipeline based on EWT and CWT.

The dike crossing pipeline is an important part of urban water transmission and supply projects. Identifying effective vibration analysis methods to determine the primary vibration sources and coupling vibration characteristics of pipelines is crucial for targeted vibration reduction and reinforcement of vulnerable pipeline sections. Therefore, this paper proposes a coupled vibration characteristics analysis method for the dike crossing pipeline based on EWT and CWT, taking the 6# dike crossing pipeline of Yang'er water plant in Foshan city, Guangdong province as the research object, firstly, the main vibration sources of the dike crossing pipeline are analyzed with the help of the prototype observation data using the mutual correlation power spectral, and the characteristics of the main vibration sources of the pipe are extracted using the empirical wavelet transform (EWT); then, focusing on the main vibration source, wavelet transform is used to analyze the source characteristics of the dike crossing pipeline; finally, the pipeline coupled vibration characteristics are analyzed using the cross wavelet transform (CWT). The research results show that: 1) The vibration of the 6# dike crossing pipeline of Yang'er water plant is mainly caused by the multiple rotational frequency such as 29.5 Hz, 36.5 Hz and the leaf frequency 59.0 Hz; 2) The EWT method can effectively remove the interference signal and extract the characteristic frequencies 29.5 Hz, 36.5 Hz and 59.0 Hz; 3) Analyzing the coupled vibration characteristics of the dike crossing pipeline based on the CWT, the peak energy of the coupled vibration of the 6# pipeline is generally concentrated at the frequency of 29.5 Hz, and the source of the coupled vibration is the multiple rotational frequency of the 6# pipeline unit. The results of this study can offer new insights into the identification of vibration characteristics of the dike crossing pipeline, and can provide technical support for the analysis of vibration characteristics and reduction needs of similar projects.

Can linear transportation infrastructure verges constitute a habitat and/or a corridor for vascular plants in temperate ecosystems? A systematic review.

BACKGROUND: Linear transportation infrastructures (roads, railways, oil and gas pipelines, powerlines and waterways) are recognized as important contributors to the fragmentation of species habitats. On the other hand, verges of linear transportation infrastructures (road and railway embankments, strips of grass under power lines or above buried pipelines, or waterway banks) form vast networks of continuous habitats. While the loss of natural habitats still poses a significant threat to biodiversity, verges can provide habitats or corridors in anthropogenic areas, although this potential for conservation remains controversial. The current paper is the first synthesis of evidence addressing this topic for vascular plants (except strictly aquatic species) in temperate ecosystems. We asked the following question: can linear transportation infrastructure verges constitute habitats and/or corridors for vascular plants in temperate ecosystems? METHODS: We conducted a systematic literature survey using two online bibliographic databases, three search engines, specialist websites, and by sending a call for literature to subject experts. We also integrated studies from a previous systematic review with an overlapping scope. We successively screened the articles for relevance on titles, abstracts and full texts using criteria detailed in an a priori protocol. We then used six specific questions to categorize the selected studies and critically assess them. These questions encompassed the potential of verges as habitats and corridors for vascular plants, and the effects of landscape and management on these potentialities. We created a database of the studies with low and medium risk of bias. We synthesized results for specific questions in narrative syntheses. Finally, studies about the habitat role of verges that met the criteria for a meta-analysis were used for quantitative syntheses. REVIEW FINDINGS: Our systematic literature survey yielded 101,524 search results. After critical appraisal, we included in our systematic review 294 articles that reported 316 studies. Most studies were conducted along road verges or waterway banks, with only a handful of studies involving powerlines, railways or pipelines. We were not able to draw conclusions on the role of verges as corridors for vascular plants as too few relevant studies were obtained. Regarding the habitat function of verges however, meta-analyses were conducted based on 205 cases from 47 primary studies that compared abundance and/or species richness in verges vs habitats away from transportation infrastructure for exotic, native or all species together. For non-highway road verges, both the abundance and richness of exotic species were higher on non-highway road verges, but we found no significant differences among species in general, or for native species specifically, which implies that alien species would often add but not subtract species. A wide variety of management practices were also represented in the evidence base. Overall, systematic impacts on species richness or abundance rarely emerged, but human interventions were seldom neutral and usually altered, at least temporarily, the balance between the native and exotic flora or among various functional groups. CONCLUSIONS: We identified a major knowledge gap regarding the potential of linear transportation infrastructure verges as corridors for vascular plants. Thus, we call for more research on this particular topic, especially as the evidence synthesis underlined the potential of verges as habitat for exotic and invasive flora.

Value of difference in diameters between Pipeline embolization device and parent artery in assessing aneurysm outcome.

OBJECTIVE: In vitro trials have demonstrated that oversized stents are associated with reduced metal coverage and increased porosity. However, the relationship between stent selection and aneurysm outcome is inconclusive, and determination of this was the authors' purpose in conducting this study. METHODS: This was a single-center retrospective study. Patients who underwent Pipeline embolization device treatment at the authors' center between January 1, 2018, and June 15, 2023, were enrolled. The authors constructed multiple logistic regression models and restricted cubic spline plots to examine the effect of the difference in diameters between the stent and parent artery (Dd) on aneurysm outcome. The authors also performed stratified analyses. Then, Dd was included in the logistic regression analysis as a categorical variable. The cutoff value for Dd was determined according to the principle of the maximum Youden's index. RESULTS: In total, 302 patients were included in this study. The median Dd was 0.52 mm. With a median follow-up time of 7 months, the aneurysm occlusion rate was 80.1%. The restricted cubic spline plots showed a decreasing aneurysm occlusion rate as Dd increased. After stratification by age and adjunctive embolization, the restricted cubic splines aligned with the results of the main analysis. Compared with the group with a smaller Dd (Dd < 0.3625 mm), the group with a larger Dd showed an OR of 0.439 (p = 0.026). Additionally, patients with diabetes mellitus (OR 0.306, p = 0.018), age ≥ 65 years (OR 0.968, p = 0.03), aneurysm incorporation with a branch (OR 0.253, p < 0.001), and aneurysm neck ≥ 4 mm (OR 0.872, p = 0.003) were independent predictors of aneurysm persistence, whereas Pipeline embolization device plus coiling (OR 4.949, p < 0.001) and smoking history (OR 5.86, p = 0.025) were predictors of aneurysm occlusion. CONCLUSIONS: The authors' retrospective analysis demonstrated that the aneurysm occlusion rate declined when Dd increased within a certain range. The authors suggested that Dd with an interval of -0.25 to 0.5 mm may be proper in clinical practice.

Telescoping Flow Diverters for the Treatment of Brain Aneurysms: Indications and Outcome.

OBJECTIVE: Few studies have reported the impact of telescoping flow diverters (FDs) in intracranial aneurysm treatment. Our study compared aneurysms treated using telescoping FDs to those treated with a single FD and identified predictors of telescoping. METHODS: This was a single-center retrospective review of a prospectively maintained database of aneurysms treated with FDs between 2011 and 2023. All patients who were treated with FDs for intracranial aneurysms were included in the study. RESULTS: The study comprised 750 patients with 750 aneurysms treated using 871 FDs. The study cohort was divided into 85 patients requiring telescoping FDs and 655 who did not. Rates of hemorrhage (7.1% vs. 1.8%, P < 0.001), symptomatic stroke (5.9% vs. 2.6, P < 0.001), and asymptomatic stroke (1.2% vs. 0.8%, P < 0.001) were significantly higher in the telescoping cohorts. At final follow-up, the rate of nonocclusion (9.8% vs. 5.1%, P = 0.029) and the rate of complete occlusion (88.5% vs. 81.1%, P = 0.029) were significantly higher in the telescoping cohort. On multivariate analysis, fusiform morphology (odds ratio [OR]: 2.4, 95% confidence interval [CI] 1.0-5.0, P = 0.03), increasing aneurysm height (OR: 1.0, 95% CI 1.0-1.1, P= 0.034), and the use of the Pipeline Embolization Device FD (OR: 2.4, 95% CI 1.3-4.4, P = 0.005) were independent predictors of telescoping. CONCLUSIONS: Aneurysms with fusiform morphology, increasing aneurysm height and those that underwent flow diversion using Pipeline Embolization Device had higher odds for telescoping. Significantly higher rates of angiographic occlusion with the use of telescoping FD add to the literature on its efficacy in treating aneurysms of varying morphology.

Clarifying urban flood response characteristics and improving interpretable flood prediction with sparse data considering the coupling effect of rainfall and drainage pipeline siltation.

With climate warming and accelerated urbanisation, severe urban flooding has become a common problem worldwide. Frequent extreme rainfall events and the siltation of drainage pipes further increase the burden on urban drainage networks. However, existing studies have not fully considered the effects of rainfall and pipeline siltation on the response characteristics of flooding when constructing numerical models of urban flooding simulations. To solve this problem, a surface-subsurface coupling model was constructed by combining the Saint-Venant equation, Manning equation, a one-dimensional pipeline model (SWMM), and a two-dimensional surface overflow model (LISFLOOD-FP). Then, the SWMM model considering pipeline siltation and the two-dimensional surface overflow model (LISFLOOD-FP) were coupled with the flow exchange governing equation, and the urban flooding response characteristics considering the coupling effect of "rainfall and drainage pipeline siltation" were analysed. To enhance the solvability of waterlogging prediction, an intelligent prediction model of urban flooding based on Bayes-CNN-BLSTM was established by combining a convolutional neural network (CNN), bidirectional long short-term memory neural network (BLSTM), Bayesian optimisation (Bayes), and an interpretable loss function error correction method. The actual rainfall events and flooding processes recorded by the monitoring equipment at Huizhou University were used to calibrate and verify the model. The results show that in the Rainfall 1 and Rainfall 2 scenarios, the overload rates of the pipelines in the current siltation scenario were 60.06 % and 68.37 %, respectively, and the proportions of overflow nodes were 24.87 % and 25.89 %, respectively. When the drainage network was initially put into operation, the overload rates of the pipeline were 36.67 % and 41.16 %, and the overflow nodes accounted for 3.05 % and 4.06 %, respectively. The inundated area and volume of urban flooding increased when the combined siltation coefficient (CSC) was 0.2; therefore, two desilting schemes were determined. Under Rainfall 1, Rainfall 2, and the four rainfall recurrence periods, the Bayes-CNN-BLSTM model had clear advantages in terms of accuracy, reliability, and robustness.

Effect of flavin adenine dinucleotide (FAD) on Desulfovibrio desulfuricans corrosion of pipeline welded joint.

The impact of Flavin adenine dinucleotide (FAD) on sulfate-reducing bacteria (SRB) corrosion of a pipeline welded joint (WJ) was investigated under anaerobic condition in this paper. The results showed that the thickness of the corrosion product on heat affected zone (HAZ) was lower than that on base metal (BM) and welded zone (WZ), and the FAD addition enhanced the development of the protruding microbial tubercles on the WJ. The local corrosion degrees of the BM and WZ coupons were significantly higher than that of the HAZ coupon. Besides, the FAD addition simultaneously promoted local corrosion of all three zones of the WJ in the SRB inoculated environment, and the promotion role was much more pronounced on the WZ coupons. The selective promotion effect of FAD on SRB corrosion in the WJ was attributed to the special structure of the WZ, the selected SRB attachment and the FAD/FADH2 redox feedback cycle.

Research on hydrogen distribution characteristics in town hydrogen-doped methane pipeline.

The study of hydrogen concentration distribution law of hydrogen-doped methane pipeline is directly related to the safety and stability of hydrogen-doped methane pipeline network. Based on the theory of fluid dynamics, this paper established a model of hydrogen-doped methane pipeline and simulated the operation and shutdown status of hydrogen-doped methane pipeline by adopting the computational fluid dynamics method and selecting the mixture multiphase model and standard k - ε turbulence model. This paper investigates the hydrogen concentration distribution law in hydrogen-doped methane pipelines as well as the influence law of different hydrogen-doping ratios, operating flow velocities, operating pressures, shutdown time and gas usage on the hydrogen concentration distribution in gas pipeline. The results show that: under the operation condition, there is a weak uneven distribution of hydrogen in the pipeline, the hydrogen-doping ratio, flow velocity, pressure on the hydrogen volume fraction of the change in the 0.9% or less, the effect can be ignored; in the shutdown status, there is a clear stratification phenomenon, the hydrogen-doping ratio increased from 10 to 25%, the change in the volume fraction of hydrogen in the 11.2% or less, a positive correlation; with the extension of the shutdown time to 900s, the pipeline firstly appeared obvious stratification phenomenon in the branch pipe, the thickness of the gas with hydrogen volume fraction above 40% on the upper wall surface of the branch pipe increased to 0.7 mm, and after the shutdown time was extended to 10 h, obvious stratification phenomenon appeared in the main pipeline, and the volume fraction of hydrogen near the top of the main pipe of about 16.5 mm was above 30%, which was positively correlated; In the shutdown status, the shutdown time has the greatest effect on the stratification phenomenon in the pipe, followed by the hydrogen-doping ratio, and the gas usage has the least effect.

MetMiner: A user-friendly pipeline for large-scale plant metabolomics data analysis.

The utilization of metabolomics approaches to explore the metabolic mechanisms underlying plant fitness and adaptation to dynamic environments is growing, highlighting the need for an efficient and user-friendly toolkit tailored for analyzing the extensive datasets generated by metabolomics studies. Current protocols for metabolome data analysis often struggle with handling large-scale datasets or require programming skills. To address this, we present MetMiner (https://github.com/ShawnWx2019/MetMiner), a user-friendly, full-functionality pipeline specifically designed for plant metabolomics data analysis. Built on R shiny, MetMiner can be deployed on servers to utilize additional computational resources for processing large-scale datasets. MetMiner ensures transparency, traceability, and reproducibility throughout the analytical process. Its intuitive interface provides robust data interaction and graphical capabilities, enabling users without prior programming skills to engage deeply in data analysis. Additionally, we constructed and integrated a plant-specific mass spectrometry database into the MetMiner pipeline to optimize metabolite annotation. We have also developed MDAtoolkits, which include a complete set of tools for statistical analysis, metabolite classification, and enrichment analysis, to facilitate the mining of biological meaning from the datasets. Moreover, we propose an iterative weighted gene co-expression network analysis strategy for efficient biomarker metabolite screening in large-scale metabolomics data mining. In two case studies, we validated MetMiner's efficiency in data mining and robustness in metabolite annotation. Together, the MetMiner pipeline represents a promising solution for plant metabolomics analysis, providing a valuable tool for the scientific community to use with ease.

Research on the Erosion Law and Protective Measures of L360N Steel for Surface Pipelines Used in Shale Gas Extraction.

The erosion of surface pipelines induced by proppant flowback during shale gas production is significant. The surface pipelines in a shale gas field in the Sichuan Basin experienced perforation failures after only five months of service. To investigate the erosion features of L360N, coatings, and ceramics and optimize the selection of two protective materials, a gas-solid two-phase flow jet erosion experimental device was used to explore the erosion resistance of L360N, coatings, and ceramics under different impact velocities (15 m/s, 20 m/s, and 30 m/s). An energy dispersive spectroscope, a scanning electron microscope, and a laser confocal microscope were employed to analyze erosion morphologies. With the increase in flow velocity, the erosion depth and erosion rate of L360N, coating, and ceramic increased and peaked under an impact velocity of 30 m/s. The maximum erosion rate and maximum erosion depth of L360N were, respectively, 0.0350 mg/g and 37.5365 µm. Its primary material removal mechanism was the plowing of solid particles, and microcracks were distributed on the material surface under high flow velocities. The maximum erosion rate and maximum erosion depth of the coating were, respectively, 0.0217 mg/g and 18.9964 µm. The detachment of matrix caused by plowing is the main material removal mechanism. The maximum erosion rate and maximum erosion depth of ceramics were, respectively, 0.0108 mg/g and 12.4856 µm. The erosion mechanisms were micro-cutting and plowing. Under different particle impact velocities, different erosion morphologies were observed, but the primary erosion mechanism was the same. The erosion resistance of the ceramics was higher than that of the coatings. Therefore, ceramic lining materials could be used to protect the easily eroded parts, such as pipeline bends and tees, and reduce the failure rate by more than 93%. The study provided the data and theoretical basis for the theoretical study on oil and gas pipeline erosion and pipeline material selection.

Severe Microbial Corrosion of L245 Transportation Pipeline Triggered by Wild Sulfate Reducing Bacteria in Shale Gas Produced Water.

The development of pitting corrosion on L245 carbon steel in a culture medium solution containing sulfate-reducing bacteria (SRB) was investigated. The results showed that the occurrence of corrosion in L245 carbon steel is closely linked to the evolution of biofilm and product film. As the test duration extended, overall corrosion was inhibited. Simultaneously, bacteria beneath the film layer promoted the generation and development of pitting corrosion, and the aggregation of bacteria (colonies) led to the aggregation of pitting corrosion.

Effects of Surface Crack Shape on Fracture Behavior of Oil Pipelines Based on the MMC Criterion.

This study employs a hybrid numerical-experimental calibration method based on phenomena to determine the fracture parameters of the Modified Mohr-Coulomb (MMC) model. Using a self-developed VUMAT subroutine and the element deletion technique, the fracture process of a wide plate pipeline is thoroughly analyzed. This study investigates the impact of various crack shapes on the fracture response under tensile loading and the influence of surface crack size on the initiation location of a wide plate. These results demonstrate the calibrated MMC fracture model's accurate prediction of the toughness fracture behavior of X80 pipeline steel. Under equal area conditions of the dangerous section, circular cracks exhibit lower bearing capacity compared to elliptical cracks. Elliptical cracks predominantly propagate in the thickness direction, whereas circular cracks show nearly uniform growth in all directions. Furthermore, when the crack depth is less than half of the wall thickness, the damage accumulation value at the midpoint of the crack front is maximized; conversely, when the crack front is closer to the internal measurement point of the wide plate, the damage accumulation value is maximized.

Spatiotemporal variation of microplastics along the long-distance raw water pipeline.

Raw water pipelines are considered a significant pathway for human exposure to microplastics (MPs, <5 mm) in surface water. However, there is currently very limited information on the longitudinal distribution characteristics of microplastics in raw water pipelines. This study assessed the abundance and distribution characteristics of microplastics in surface water from two different water sources in Jiangsu Province during different seasons. The correlation between conventional water quality indicators and microplastics was also explored. Specifically, the longitudinal variation of microplastics in raw water pipelines was investigated. Results showed that microplastics were detected in both basins during different seasons. In Basin 1, the abundance of MPs ranged from 34 ± 1 to 58 ± 2 n/L in March and from 3 ± 1 to 6.7 ± 4 n/L in June. In Basin 2, the abundance ranged from 6.5 ± 1 to 14 ± 1 n/L in March and from 2 ± 1 to 7.7 ± 1 n/L in June. The abundance of microplastics showed a decreasing trend along the pipeline. Polymethyl methacrylate (PMMA) was the main polymer type detected in both basins. Polyethylene terephthalate (PE) and polyurethane (PU) showed higher removal rates in the pipeline due to their higher density. The predominant size ranges of microplastics in the raw water were 10-50 µm and 50-100 µm. Additionally, the average particle size of MPs increased with the transportation distance, likely due to microbial colonization. This study is the first comprehensive investigation of the distribution characteristics of microplastics in raw water pipeline systems. The removal of microplastics in raw water pipelines contributes significantly to the elimination of microplastics at the source. This research helps to fill the knowledge gap regarding the fate of microplastics in raw water pipeline systems.

Review of techniques, challenges, and gaps in the subsurface gas release knowledge base.

Underground pipelines serve as critical infrastructure for gas transmission, strategically buried for safety, environmental, and economic considerations. Despite their importance, operational challenges and external interferences can lead to underground gas leaks with potentially catastrophic consequences for both human safety and the environment. The presence of a protective soil bed introduces complexities in understanding subsurface transport phenomena and quantifying gas releases accurately. Herein, this review presents a systematic analysis of published research in the field of underground gas releases, with an emphasis on interdisciplinary approaches that connect the lithosphere and atmosphere. The analysis highlights the broad spectrum of employed methods, including theoretical models based on fundamental principles, empirical formulations derived from experimental data, and sophisticated computational tools. A clear fundamental understanding and computational analysis, and to a lesser extent experimental, have been established to describe the migration regime. In contrast, more empirical research has addressed the crater formation regime, though focus was given to the far-field modelling following the soil ejection rather than the transient phenomena leading to the formation of the crater. Additionally, this review touches upon practical and conceptual topics, such as detection and localization techniques, and flow regimes in other gaseous flows through soil and powder beds, putting into question the applicability of some presumed granulated concepts to the flowing behavior expected beyond migration. The research landscape predominantly focuses on investigating the influence of release parameters on the release phenomena only from the atmospheric or soil domain perspective. This work provides insights that aim to first transcend both domains and then bridge the three distinct flow regimes-migration, uplift, and crater formation-despite the limited acknowledgment of the necessity of addressing all regimes concurrently through a universal approach. This review serves as a valuable resource for engineers to develop innovative solutions for the management of risks associated with underground gas leaks.

Screening of polyurethane-degrading microbes using a quenching fluorescence probe by microfluidic droplet sorting.

Excessive use of polyurethane (PU) polymers has led contributed to serious environmental pollution. The plastic recycling technology using microorganisms and enzymes as catalysts offers a promising green and low-carbon approach for managing plastic waste. However, current methods for screening PU-degrading strains suffer from drawbacks such as being time-consuming and inefficient. Herein, we present a novel approach for screening PU-degrading microorganisms using a quenching fluorescent probe along with the fluorescence-activated droplet sorting (FADS). The FPAP could specifically recognize the 4,4'-methylenedianiline (MDA) derivates released from PU degradation, with fluorescence quenching as a response. Based on the approach, we successfully screen two PU-degrading strains (Burkholderia sp. W38 and Bacillus sp. C1). After 20 d of cultivation, strain W38 and C1 could degrade 41.58% and 31.45% of polyester-PU film, respectively. Additionally, three metabolites were identified during the degradation of PU monomer (2,4-toluene diamine, 2,4-TDA) and a proposed degradation pathway was established. Consequently, the fluorescence probe integrated with microfluidic droplet systems, demonstrates potential for the development of innovative PU-biocatalysts. Furthermore, the identification of the 2,4-TDA degradation pathway provides valuable insights that can propel advancements in the field of PU biodegradation.