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To standardize metabolomics data analysis and facilitate future computational developments, it is essential to have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a full-featured Python-centric pipeline. We demonstrate the performance of the pipeline, and the details in annotation and quality control using large-scale LC-MS metabolomics and lipidomics data and LC-MS/MS data. Multiple previously published datasets are also reanalyzed to showcase its utility in biological data analysis. This pipeline allows users to streamline data processing, quality control, annotation, and standardization in an efficient and transparent manner. This work fills a major gap in the Python ecosystem for computational metabolomics. [ABSTRACT FROM AUTHOR]

Consumption of human breast milk (HBM) attenuates the incidence of necrotizing enterocolitis (NEC), which remains a leading and intractable cause of mortality in preterm infants. Here, we report that this diminution correlates with alterations in the gut microbiota, particularly enrichment of Propionibacterium species. Transfaunation of microbiota from HBM-fed preterm infants or a newly identified and cultured Propionibacterium strain, P. UF1, to germfree mice conferred protection against pathogen infection and correlated with profound increases in intestinal Th17 cells. The induction of Th17 cells was dependent on bacterial dihydrolipoamide acetyltransferase (DlaT), a major protein expressed on the P. UF1 surface layer (S-layer). Binding of P. UF1 to its cognate receptor, SIGNR1, on dendritic cells resulted in the regulation of intestinal phagocytes. Importantly, transfer of P. UF1 profoundly mitigated induced NEC- like injury in neonatal mice. Together, these results mechanistically elucidate the protective effects of HBM and P. UF1- induced immunoregulation, which safeguard against proinflammatory diseases, including NEC., Introduction Despite major advancements in medicine, the rate of preterm birth has not decreased and remains one of the leading global causes of infant mortality (1). Maternal pathogen-induced inflammation potentially [...]

Pile base resistance is an important part of the ultimate bearing capacity, and the soil within a certain range above and below the pile end contributes to the pile base resistance. In general, pile base resistance is calculated according to the average value of soil strength within a certain range of the pile end in the current calculating method, so it is very important to determine the influence range of pile base resistance. Based on the soil parameters and the results of the cone penetration test of the LiuHua 11-1 site in the South China Sea, the difference of pile base resistance calculated by different methods, the regularity of pile base resistance affected by calculation depth range is revealed. Additionally, the numerical simulation method is used to analyze the distribution of a plastic zone around the pile end in homogeneous soil and stratified soil, the results show the influence depth range of pile base resistance is 0.12 D above the pile end to 0.83 D below the pile end in clay, and the influence depth range is 0.9 D above the pile end to 1.3 D below the pile end in stratified soil. [ABSTRACT FROM AUTHOR]

The GCN2 kinase is shown to have a protective role in the regulation of intestinal inflammation during amino acid starvation in a mouse model of colitis. Gut inflammation reduction by amino acid starvation This study shows that the amino acid sensing protein kinase GCN2 suppresses gut inflammation during amino acid starvation. GCN2 deficiency correlates with impaired induction of autophagy in intestinal antigen presenting cells and epithelial cells, increased reactive oxygen species production and increased inflammasome activation in a mouse model for colitis. The integrated stress response (ISR) is a homeostatic mechanism by which eukaryotic cells sense and respond to stress-inducing signals, such as amino acid starvation. General controlled non-repressed (GCN2) kinase is a key orchestrator of the ISR, and modulates protein synthesis in response to amino acid starvation. Here we demonstrate in mice that GCN2 controls intestinal inflammation by suppressing inflammasome activation. Enhanced activation of ISR was observed in intestinal antigen presenting cells (APCs) and epithelial cells during amino acid starvation, or intestinal inflammation. Genetic deletion of Gcn2 (also known as Eif2ka4) in CD11c.sup.+ APCs or intestinal epithelial cells resulted in enhanced intestinal inflammation and T helper 17 cell (T.sub.H17) responses, owing to enhanced inflammasome activation and interleukin (IL)-1[beta] production. This was caused by reduced autophagy in Gcn2.sup.-/- intestinal APCs and epithelial cells, leading to increased reactive oxygen species (ROS), a potent activator of inflammasomes.sup.1. Thus, conditional ablation of Atg5 or Atg7 in intestinal APCs resulted in enhanced ROS and T.sub.H17 responses. Furthermore, in vivo blockade of ROS and IL-1[beta] resulted in inhibition of T.sub.H17 responses and reduced inflammation in Gcn2.sup.-/- mice. Importantly, acute amino acid starvation suppressed intestinal inflammation via a mechanism dependent on GCN2. These results reveal a mechanism that couples amino acid sensing with control of intestinal inflammation via GCN2., Author(s): Rajesh Ravindran [sup.1] , Jens Loebbermann [sup.1] , Helder I. Nakaya [sup.2] , Nooruddin Khan [sup.3] , Hualing Ma [sup.1] , Leonardo Gama [sup.2] , Deepa K. Machiah [sup.4] [...]

A large-diameter thin-walled steel cylinder as the protective structure of a submarine production system is vulnerable to the spudcan penetration because of its shallow buried depth and large foundation size. Centrifuge model tests are carried out to investigate the behaviour of steel cylinders caused by spudcan penetration. Then, CEL method verified by centrifuge test is used to analyse the influence of spudcan penetration on the stability of steel cylinders under different spudcan-cylinder clearances. The results show that the deformation mode of the adjacent cylinder is affected by comprehensive factors such as spudcan-cylinder clearance, spudcan penetration depth, soil deformation modulus, and soil strength. The displacement and stress of the cylinder decrease exponentially with the increase in the spudcan-cylinder clearance. The affected distance of the spudcan penetration on the cylinder can reach more than two times the spudcan diameter. [ABSTRACT FROM AUTHOR]

China National Offshore Oil Corporation (CNOOC) currently is developing a mat-supported wellhead production platform concept as an alternative solution to conventional jacket platforms in shallow-water oil fields. The platform is towed to the site with the mat foundation elevated. The mat then is lowered and embedded in the seabed as the hull is jacked out of the water. Steel pipe piles subsequently are driven through the tubular legs of the platform. After grouting the connection, the pile foundations provide permanent support for the platform. The mat foundation therefore provides only temporary support to the platform. This paper presents a case study focusing on the installation behavior of the mat foundation in a soft soil site as part of the platform concept development and suitability evaluation. The study determined (1) the expected penetration depth under the platform's self-weight considering its irregular geometry and soft over stiff clay stratigraphy; (2) the target center of gravity to achieve even penetration and the potential for tilt development in the case of offset from the target position; (3) the effectiveness of using ballast tanks to correct the tilt; and (4) settlement after the installation due to dissipation of pore pressure and creep. Advanced large-deformation finite-element simulations featuring a strain softening soil model and analytical analyses were performed. A dedicated lab testing program geared was designed and executed to provide the necessary soil parameters for the analyses. This paper presents the techniques and considerations that were applied in this study and insights gained into the installation and subsequent postinstallation behavior of large-area mat foundations. [ABSTRACT FROM AUTHOR]

Archived metabolomics data represent a broad resource for the scientific community. However, the absence of tools for the meta‐analysis of heterogeneous data types makes it challenging to perform direct comparisons in a single and cohesive workflow. Here, we present a framework for the meta‐analysis of metabolic pathways and interpretation with proteomic and transcriptomic data. This framework facilitates the comparison of heterogeneous types of metabolomics data from online repositories (eg, XCMS Online, Metabolomics Workbench, GNPS, and MetaboLights) representing tens of thousands of studies, as well as locally acquired data. As a proof of concept, we apply the workflow for the meta‐analysis of (a) independent colon cancer studies, further interpreted with proteomics and transcriptomics data, (b) multimodal data from Alzheimer's disease and mild cognitive impairment studies, demonstrating its high‐throughput capability for the systems level interpretation of metabolic pathways. Moreover, the platform has been modified for improved knowledge dissemination through a collaboration with Metabolomics Workbench and LIPID MAPS. We envision that this meta‐analysis tool combined with our in‐source fragmentation/annotation (ISA) technology will help overcome the primary bottleneck in analyzing diverse datasets and facilitate the full exploitation of archival metabolomics data for addressing a broad array of questions in metabolism research and systems biology. [ABSTRACT FROM AUTHOR]