Common Module Research Articles

TMIC-13. INTEGRATING SNRNASEQ AND SPATIAL TRANSCRIPTOME (ST) SHOWS DIVERSE TRANSCRIPTOMIC LANDSCAPE FOR TUMOR MICROENVIRONMENT (TME) IN INTRACRANIAL GERMINOMAS

Abstract The incidence of intracranial germ cell tumors is 5-8 times higher in East Asia and histologically, germinoma is well known to show intense lymphocytic infiltrates. In spite of germinoma’s well known immune infiltration, there have only been a few studies on its tumor micro-environment (TME). There has been no study using the recent and comprehensive techniques of single nucleus sequencing or spatial transcriptomics to study its TME. In this study, we studied snRNAseq (Chromium 10X) of FFPE tissues of 24 intracranial germinomas, and spatial transcriptomes (STs) (Visium Spatial) from fresh tissues from ten matched cases. For the TME, in contrast to common belief, macrophages and fibroblasts were equally represented as T- and NK-cells as immune cells. Clinical stage correlated with a lesser proportion of fibroblasts and T- and NK-cells. There was no correlation with proportion of tumor cells with either focal vs bifocal disease or clinical stage. Common gene modules (non-negative matrix factorization) were epithelial-mesenchymal transition (complete and partial), cell cycle and immune cells. Cell interaction analysis showed strong interaction between germ cells and macrophages involving CXCL, MIF and MK pathways. By ligand-receptor analysis, MIF combined with CD74 might promote tumor development. For ten cases, we studied STs with fresh tissues and integrated the results with snRNSeq, deconvoluting the spots for ST using snRNAseq cell types as reference (SPOTight) and achieved integrated single cell expression atlases of the STs (Seurat package). STs revealed a similar CNV plot pattern as those derived from snRNAseqs. Multimodal Intersection Analysis integrated significant genes based on snRNAseq and different regions’ significant genes based on STs. There was correlation between the expression of the four gene modules for tumor and immune cells for cell neighborhood. In conclusion, we showed in details the heterogenous expression landscape of TME of germinomas.

Rapidly Evolved Genes in Three Reaumuria Transcriptomes and Potential Roles of Pentatricopeptide Repeat Superfamily Proteins in Endangerment of R. trigyna.

Reaumuria genus (Tamaricaceae) is widely distributed across the desert and semi-desert regions of Northern China, playing a crucial role in the restoration and protection of desert ecosystems. Previous studies mainly focused on the physiological responses to environmental stresses; however, due to the limited availability of genomic information, the underlying mechanism of morphological and ecological differences among the Reaumuria species remains poorly understood. In this study, we presented the first catalog of expressed transcripts for R. kaschgarica, a sympatric species of xerophyte R. soongorica. We further performed the pair-wise transcriptome comparison to determine the conserved and divergent genes among R. soongorica, R. kaschgarica, and the relict recretohalophyte R. trigyna. Annotation of the 600 relatively conserved genes revealed that some common genetic modules are employed by the Reaumuria species to confront with salt and drought stresses in arid environment. Among the 250 genes showing strong signs of positive selection, eight pentatricopeptide repeat (PPR) superfamily protein genes were specifically identified, including seven PPR genes in the R. soongorica vs. R. trigyna comparison and one PPR gene in the R. kaschgarica vs. R. trigyna comparison, while the cyclin D3 gene was found in the R. soongorica vs. R. trigyna comparison. These findings suggest that genetic variations in PPR genes may affect the fertility system or compromise the extent of organelle RNA editing in R. trigyna. The present study provides valuable genomic information for R. kaschgarica and preliminarily reveals the conserved genetic bases for the abiotic stress adaptation and interspecific divergent selection in the Reaumuria species. The rapidly evolved PPR and cyclin D3 genes provide new insights on the endangerment of R. trigyna and the leaf length difference among the Reaumuria species.

Implementation of an autonomous mobile platform for agricultural tasks in corridor-like environments

AbstractThe role of autonomous vehicles (AVs) in assisting people is recognised and, therefore, is in constant development in numerous fields. Specifically, the ability of an autonomous vehicle (AV) to alleviate global stressors, such as the increased potential for food shortages and the decline in available workers for labor-intensive tasks. An area where the development of AVs are particularly prevalent is in agriculture. However, the few AVs being used in agriculture are often custom-built for specific purposes and require long development time as a result. This article aims to build and evaluate a versatile architecture for a mobile platform that is implemented using off-the-shelf components so that it can be transferred to any agricultural vehicle, thus reducing the development time. The research has involved investigating and incorporating various sensors, and also developing a common software module to perform the localisation, navigation and mapping particularly suited for corridor crop agricultural environments. This architecture has been integrated and implemented on a Yamaha golf cart, integrating it with sensors and electronics to allow a Robotic Operating System (ROS) framework to gather information and control the vehicle. As the architecture is modular in nature, it can be transferred to different customised platforms. To determine the efficacy of the mobile platform, it has undergone evaluation in simulation and in the field. The evaluation demonstrates that both mapping and navigation have satisfactory results, and the mobile platform remains within 5 mm of the specified distance when aiming to follow the row in a vineyard. The results from these experiments demonstrate the ability of the mobile platform to successfully transform a Yamaha golf cart into an autonomous agricultural vehicle.

Co-salient object detection with iterative purification and predictive optimization

BackgroundCo-salient object detection (Co-SOD) aims to identify and segment commonly salient objects in a set of related images. However, most current Co-SOD methods encounter issues with the inclusion of irrelevant information in the co-representation. These issues hamper their ability to locate co-salient objects and significantly restrict the accuracy of detection. MethodsTo address this issue, this study introduces a novel Co-SOD method with iterative purification and predictive optimization (IPPO) comprising a common salient purification module (CSPM), predictive optimizing module (POM), and diminishing mixed enhancement block (DMEB). ResultsThese components are designed to explore noise-free joint representations, assist the model in enhancing the quality of the final prediction results, and significantly improve the performance of the Co-SOD algorithm. Furthermore, through a comprehensive evaluation of IPPO and state-of-the-art algorithms focusing on the roles of CSPM, POM, and DMEB, our experiments confirmed that these components are pivotal in enhancing the performance of the model, substantiating the significant advancements of our method over existing benchmarks. Experiments on several challenging benchmark co-saliency datasets demonstrate that the proposed IPPO achieves state-of-the-art performance.

Reusable Generic Clinical Decision Support System Module for Immunization Recommendations in Resource-Constraint Settings.

Clinical decision support systems (CDSS) are routinely employed in clinical settings to improve quality of care, ensure patient safety, and deliver consistent medical care. However, rule-based CDSS, currently available, do not feature reusable rules. In this study, we present CDSS with reusable rules. Our solution includes a common CDSS module, electronic medical record (EMR) specific adapters, CDSS rules written in the clinical quality language (CQL) (derived from CDC immunization recommendations), and patient records in fast healthcare interoperability resources (FHIR) format. The proposed CDSS is entirely browser-based and reachable within the user's EMR interface at the client-side. This helps to avoid the transmission of patient data and privacy breaches. Additionally, we propose to provide means of managing and maintaining CDSS rules to allow the end users to modify them independently. Successful implementation and deployment were achieved in OpenMRS and OpenEMR during initial testing.

Gene expression–based molecular scoring of pancreas transplant rejection for a quantitative assessment of rejection severity and resistance to treatment

Pancreas transplantation improves glycemic control and mortality in patients with diabetes but requires aggressive immunosuppression to control the alloimmune and autoimmune response. Recent developments in “omics” methods have provided gene transcript-based biomarkers for organ transplant rejection. The tissue Common Response Module (tCRM) score is developed to identify the severity of rejection in kidney, heart, liver, and lung transplants. Still, it has not yet been validated in pancreas transplants (PT). We evaluated the tCRM score’s relevance in PT and additional markers of acute cellular rejection (ACR) for PT. An analysis of 51 pancreas biopsies with ACR identified 37 genes and 56 genes significantly upregulated in the case of grade 3 and grade 2 ACR, respectively (P < .05). Significant differences were seen with higher grades of rejection among several transcripts. Of the 22 genes differentially expressed in grade 3 ACR, 18 were also differentially expressed in grade 2 ACR. The rejection signal was attributable to activated leukocytes’ infiltration. Significantly higher tCRM scores were found in grade 3 ACR (P = .007) and grade 2 ACR (P = .004), compared to normal samples. The tCRM score was able to distinguish treatment-resistant cases from those successfully treated for rejection.

Mechanical Stability of PV Modules

A significant increase in reported glass breakages from the field was recognized during the past three years, where a disproportionately high number of modules were affected by glass breakage. Different substructures and module designs are affected, framed and unframed modules, tracked and fixed systems. What all inquiries have in common, however, is that modules with a double-glazed design with ≤ 2.5 mm glass thicknesses are affected and the problems were observed after just a few months in field operation. Various factors such as heavy weather events, faulty installation or errors in the structural design could be excluded as root causes and our experience points on additional, more fundamental problems that are associated in particular with the continuing trend towards larger modules &gt; 3 m2 and thinner module glass ≤ 2mm. Furthermore, it seems that the residual compressive surface stress of the glass as one major parameter that determines the stability of glass panes has not been considered in this context in the PV module industry yet. In this work, we focus on the glass thickness in combination with the compressive surface stress. Besides qualitative methods, one possibility to investigate the surface stress quantitatively is a scattered light polariscope (SCALP), previously used in the glass industry. In particular, the aim is to validate the SCALP measurement method for the use on PV modules. Furthermore, a potential correlation between the surface compressive stress and the mechanical stability of various common module designs with 2 mm and 1.6 mm glass is investigated.

Next-generation mapping of the salicylic acid signaling hub and transcriptional cascade

For over 60 years, salicylic acid (SA) has been known as a plant immune signal required for basal and systemic acquired resistance. SA activates these immune responses by reprogramming ∼20% of the transcriptome through NPR1. However, components in the NPR1 signaling hub, which appears as nuclear condensates, and the NPR1 signaling cascade have remained elusive due to difficulties in studying this transcriptional cofactor, whose chromatin association is indirect and likely transient. To overcome this challenge, we applied TurboID to divulge the NPR1 proxiome, which detected almost all known NPR1 interactors as well as new components of transcription-related complexes. Testing of new components showed that chromatin remodeling and histone demethylation contribute to SA-induced resistance. Globally, the NPR1 proxiome has a striking similarity to the proxiome of GBPL3 that is involved in SA synthesis, except for associated transcription factors (TFs), suggesting that common regulatory modules are recruited to reprogram specific transcriptomes by transcriptional cofactors, like NPR1, through binding to unique TFs. Stepwise green fluorescent protein-tagged factor cleavage under target and release using nuclease (greenCUT&RUN) analyses showed that, upon SA induction, NPR1 initiates the transcriptional cascade primarily through association with TGACG-binding TFs to induce expression of secondary TFs, predominantly WRKYs. Further, WRKY54 and WRKY70 were identified to play a major role in inducing immune-output genes without interacting with NPR1 at the chromatin. Moreover, loss of condensate formation function of NPR1 decreases its chromatin association and transcriptional activity, indicating the importance of condensates in organizing the NPR1 signaling hub and initiating the transcriptional cascade. Collectively, this study demonstrates how combinatorial applications of TurboID and stepwise greenCUT&RUN transcend traditional genetic methods to globally map signaling hubs and transcriptional cascades for in-depth explorations.

Multimodal semantic enhanced representation network for micro-video event detection

Currently, micro-videos have gained widespread acceptance as a prominent form of user-generated content across various social media platforms. Accurate event analysis of micro-videos can greatly enhance the many diverse social media platforms applications. Although some studies have shown promising results from a multimodal perspective, there is still a challenge in extracting informative cues from inaccurate modalities, particularly for text modality that is prone to inaccuracies and noise. In this paper, we propose a multimodal semantically enhanced representation network (MSERN) for micro-video event detection. To better address inaccurate and noisy text sentences, we first extract visual concepts in the form of adjective-noun pairs (ANPs), through a fine-grained common representation module, to complement the textual descriptions. To maximize the acquisition of modality-specific cues from both visual and textual modalities, we then implement a coarse-grained private representation module to ensure that private representations encompass unique facets of the modalities beyond the common perspective. Finally, because two modules will collaborate, the fine-grained common and coarse-grained private representations are integrated to ensure a reinforced micro-video representation. We evaluate our proposed method on a micro-video event detection dataset and the experimental results show a superior performance compared to the state-of-the-art methods.

Insight into Mantle Cell Lymphoma Pathobiology, Diagnosis, and Treatment Using Network-Based and Drug-Repurposing Approaches.

Mantle cell lymphoma (MCL) is a rare, incurable, and aggressive B-cell non-Hodgkin lymphoma (NHL). Early MCL diagnosis and treatment is critical and puzzling due to inter/intra-tumoral heterogeneity and limited understanding of the underlying molecular mechanisms. We developed and applied a multifaceted analysis of selected publicly available transcriptomic data of well-defined MCL stages, integrating network-based methods for pathway enrichment analysis, co-expression module alignment, drug repurposing, and prediction of effective drug combinations. We demonstrate the "butterfly effect" emerging from a small set of initially differentially expressed genes, rapidly expanding into numerous deregulated cellular processes, signaling pathways, and core machineries as MCL becomes aggressive. We explore pathogenicity-related signaling circuits by detecting common co-expression modules in MCL stages, pointing out, among others, the role of VEGFA and SPARC proteins in MCL progression and recommend further study of precise drug combinations. Our findings highlight the benefit that can be leveraged by such an approach for better understanding pathobiology and identifying high-priority novel diagnostic and prognostic biomarkers, drug targets, and efficacious combination therapies against MCL that should be further validated for their clinical impact.

Development of a non-standard system for simplifying boolean functions

The object of this study is models of low-power digital logic circuits. The problem being solved is the effectiveness of the technique for simplifying Boolean functions to obtain optimal structures of logic circuits. A new theorem of a non-standard system of simplification of Boolean functions has been formulated, according to which in order to obtain a minimal function it will suffice to perform all non-redundant operations of simple and/or super-gluing of variables, which ultimately provides a minimal function in the main basis without using an implicant table. Thus, the problem of simplifying Boolean functions to the simplest normal equivalent is solved in one step. The interpretation of the result is that the properties of 2-(n, b)-design combinatorial systems make it possible to reproduce the definition of logical operations of super-gluing variables, to represent logical operations in a different way, and vice versa. This, in turn, ensures the establishment of the locations of equivalent transformations on the binary structure of the truth table and the implication of a systematic procedure for simplifying Boolean functions by an analytical method. Special feature of the results is that unambiguous identification of the locations of equivalent transformations is possible even when different intervals of the Boolean space containing the 2-(n, b)-design systems have common modules. It has been experimentally confirmed that the non-standard system improves the efficiency of simplifying Boolean functions, including partially defined ones, by 200–300 % compared to analogs. In terms of application, a non-standard system for simplifying Boolean functions will ensure the transfer of innovations to material production: from conducting fundamental research, expanding the capabilities of digital component design technology to organizing serial or mass production of novelties

BioLadder: A bioinformatic platform primarily focused on proteomic data analysis.

BioLadder (https://www.bioladder.cn/) is an online data analysis platform designed for proteomics research, which includes threeclasses of experimental data analysis modules and fourclasses of common data analysis modules. It allows for a variety of proteomics analyses to be conducted easily and efficiently. Additionally, most modules can also be utilized for the analysis of other omics data. To facilitate user experience, we have carefully designed fourdifferent kinds of functions for customers to quickly and accurately utilize the relevant analysis modules.

The main directions of enhancement of digital antenna arrays

The development of modern radio electronic systems causes an increase in the requirements for the parameters of antenna devices (AU) and causes the transition from previously used mirror antennas and passive phased array antennas (FAA) to active FAA (AFAA), the considerable advantage of which is a significant reduction in energy losses of transmitted and received signals by reducing the distance of the low-noise amplifier input and output of power amplifier to the antenna element. Further development of the AU is the transition from AFAA with analog beamforming to digital antenna arrays (DAR) with digital beamforming, the advantages of which are due to the possibility of forming multibeam receiving and transmitting radiation patterns with independent control of the direction and shape of the beams, as well as the possibility of flexible change of operating modes. The use of a DAR with two-dimensional electronic scanning provides a significant increase in the efficiency of radio-electronic systems. Thus, their use in radar provides a gain in the efficiency of using the time, energy, frequency and spatial resources of radar with CAR up to 13 times compared with radar with passive FAA and AFAA with one-dimensional scanning. The disadvantages of the DAR are the high cost and increased energy consumption due to the installation of active elements in each transceiver channel, as well as the long time required to create new products, associated with a large amount of software and a complex structure for building a CAR. To overcome these disadvantages, manufacturers of antenna arrays and developers of the radio-electronic element base are creating new technical solutions. The main directions of development of technologies for the production of DAR functional devices that reduce the cost and reduce the time needed to create new products are shown: the development of common modules that allow you to create scalable DAR, increasing the integration of microwave monolithic integrated circuits with the placement of the maximum number of transceiver channels on one chip, increasing the integration of ASIC, including ADCs, DACs and digital signal processing devices, increasing the clock frequencies of digital functional nodes, as well as the development of circuit solutions for building nodes with low energy consumption.

Quality of life and its related-influencing factors in patients with cervical cancer based on the scale QLICP-CE(V2.0)

BackgroundQuality of life research can guide clinical workers to adopt more targeted treatment and intervention measures, so as to achieve the purpose of improving patients’ quality of life. The objective of this study was to evaluate health-related quality of life in Chinese patients with cervical cancer and to explore its influencing factors.MethodsA total of 186 patients with cervical cancer were investigated by using the QLICP-CE (V2.0) scale (Quality of Life Instruments for Cancer Patients-Cervical Cancer) developed by our group in China. The data were analyzed by t-test, one-way ANOVA, univariate analysis, and multivariate linear regression.ResultsThe total score of quality of life scale for cervical cancer patients was (62.58 ± 12.69), Univariate analysis of objective clinical indexes showed that creatinine concentration was a negative influence factor in the psychological domain, potassium ion concentration was a negative influence factor in the common symptoms and side effect domain, erythrocyte content was a positive influence factor physical domain and common general domain. Multiple linear regression results suggested that clinical staging was the influencing factor of common symptom and side effect domain, common general module and total score of scale. Marital status has different degrees of influence on the psychological, social, and common general domains. The level of education also influenced scores in the social domain.ConclusionThe total score of quality of life in patients with cervical cancer who received active treatment was acceptable. Marital status, clinical staging, and educational level are the factors that affect the quality of life of patients with cervical cancer. At the same time, potassium ion concentration, red blood cell count and creatinine concentration also have important effects on quality of life in patients with cervical cancer. Therefore, it is very important to give personalized treatment and nursing to patients based on various factors.

Reference architecture design for developing data management systems in smart farming

The traditional data management systems prove inadequate to handle the volume, velocity, and variety of the data within farm business processes. Smart farming technologies offer advanced data management systems as a practical solution to these challenges. However, data is complex and originates from many sources; hence many aspects of data must be considered during the data management design of smart farming systems. This study proposes a reference architecture for data management in smart farming, developed through domain analysis and architecture modeling approaches. The domain analysis provides insights into the common and variant features and modules of the smart farming system, resulting in a blueprint representing family features across various smart farming domains. The effectiveness of the proposed reference architecture has been evaluated through two case studies, demonstrating its efficacy in designing data management systems for smart farming. The study found that the percentage of reused modules in the case studies, compared to the provided reference architecture, was 82.6%. The outcomes of this research will pave the way for further exploration in smart farming, particularly addressing data management issues within smart farming systems.

VND Genes Redundantly Regulate Cell Wall Thickening during Parasitic Nematode Infection.

Plant parasitic root-knot nematodes are major agricultural pests worldwide, as they infect plant roots and cause substantial damages to crop plants. Root-knot nematodes induce specialized feeding cells known as giant cells (GCs) in the root vasculature, which serve as nutrient reservoirs for the infecting nematodes. Here, we show that the cell walls of GCs thicken to form pitted patterns that superficially resemble metaxylem cells. Interestingly, VASCULAR-RELATED NAC-DOMAIN1 (VND1) was found to be upregulated, while the xylem-type programmed cell death marker XYLEM CYSTEINE PEPTIDASE 1 was downregulated upon nematode infection. The vnd2 and vnd3 mutants showed reduced secondary cell wall pore size, while the vnd1 vnd2 vnd3 triple mutant produced significantly fewer nematode egg masses when compared with the wild type. These results suggest that the GC development pathway likely shares common signaling modules with the metaxylem differentiation pathway and VND1, VND2, and VND3 redundantly regulate plant-nematode interaction through secondary cell wall formation.

Evolution-guided engineering of trans-acyltransferase polyketide synthases.

Bacterial multimodular polyketide synthases (PKSs) are giant enzymes that generate a wide range of therapeutically important but synthetically challenging natural products. Diversification of polyketide structures can be achieved by engineering these enzymes. However, notwithstanding successes made with textbook cis-acyltransferase (cis-AT) PKSs, tailoring such large assembly lines remains challenging. Unlike textbook PKSs, trans-AT PKSs feature an extraordinary diversity of PKS modules and commonly evolve to form hybrid PKSs. In this study, we analyzed amino acid coevolution to identify a common module site that yields functional PKSs. We used this site to insert and delete diverse PKS parts and create 22 engineered trans-AT PKSs from various pathways and in two bacterial producers. The high success rates of our engineering approach highlight the broader applicability to generate complex designer polyketides.

Research on road Damage Detection Based on Improved YOLOv8

Aiming at the low accuracy of deep learning in road damage detection, a road damage detection method based on improved YOLOv8 is proposed. Firstly, SENetv2 attention module was added to the backbone network of YOLOv8 to improve the model's feature learning ability. Secondly, in the neck network, GSConv is used to replace the common convolutional module to reduce the complexity of the model and improve the accuracy. Finally, the loss function is changed to Wise-iou to reduce the impact of detection due to a small number of low-quality instances. The experimental results show that compared with the traditional YOLOv8, the mAP50 of this model is increased by 2.1 percentage points, and the detection effect is good, which can meet the requirements of accurate detection.

Automated CAD-to-BIM generation of restroom sanitary plumbing system

Abstract Mechanical, electrical, and plumbing (MEP) system experts often have difficulties in converting their designs, in computer-aided design (CAD), into building information models (BIMs) owing to excessive repetitive work, lack of BIM skilled workers, frequent BIM recreations, etc. Therefore, this study aimed to formalize the CAD-to-BIM process of MEP systems, focusing on sanitary plumbing system, including soil, drain system, hot water supply, and cold water supply system. Each system’s process is composed of a combination of the following five common modules: pipeline processing module, pipe connection module, initial level setting module, addition riser nipple module, and clash resolution module. Consequently, a prototype developed based on the formalized process produced a sanitary plumbing BIM model that is identical to the CAD drawings and has no clashes. This study contributes to the MEP BIM theory by identifying considerations for CAD-to-BIM conversion of sanitary plumbing system and formalizing the process reflecting them.

RNA-seq-based comparative transcriptome analysis reveals the role of CsPrx73 in waterlogging-triggered adventitious root formation in cucumber.

Abiotic stressors like waterlogging are detrimental to cucumber development and growth. However, comprehension of the highly complex molecular mechanism underlying waterlogging can provide an opportunity to enhance cucumber tolerance under waterlogging stress. We examined the hypocotyl and stage-specific transcriptomes of the waterlogging-tolerant YZ026A and the waterlogging-sensitive YZ106A, which had different adventitious rooting ability under waterlogging. YZ026A performed better under waterlogging stress by altering its antioxidative machinery and demonstrated a greater superoxide ion (O 2-) scavenging ability. KEGG pathway enrichment analysis showed that a high number of differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis. By pairwise comparison and weighted gene co-expression network analysis analysis, 2616 DEGs were obtained which were categorized into 11 gene co-expression modules. Amongst the 11 modules, black was identified as the common module and yielded a novel key regulatory gene, CsPrx73. Transgenic cucumber plants overexpressing CsPrx73 enhance adventitious root (AR) formation under waterlogging conditions and increase reactive oxygen species (ROS) scavenging. Silencing of CsPrx73 expression by virus-induced gene silencing adversely affects AR formation under the waterlogging condition. Our results also indicated that CsERF7-3, a waterlogging-responsive ERF transcription factor, can directly bind to the ATCTA-box motif in the CsPrx73 promoter to initiate its expression. Overexpression of CsERF7-3 enhanced CsPrx73 expression and AR formation. On the contrary, CsERF7-3-silenced plants decreased CsPrx73 expression and rooting ability. In conclusion , our study demonstrates a novel CsERF7-3-CsPrx73 module that allows cucumbers to adapt more efficiently to waterlogging stress by promoting AR production and ROS scavenging.