Explore the vast range of titles available.

Genome-scale metabolic networks (GSMs) are fundamental systems biology representations of a cell’s entire set of stoichiometrically balanced reactions. However, such static GSMs do not incorporate the functional organization of metabolic genes and their dynamic regulation (e.g., operons and regulons). Specifically, there are numerous topologically coupled local reactions through which fluxes are coordinated; the global growth state often dynamically regulates many gene expression of metabolic reactions via global transcription factor regulators. Here, we develop a GSM reconstruction method, Decrem, by integrating locally coupled reactions and global transcriptional regulation of metabolism by cell state. Decrem produces predictions of flux and growth rates, which are highly correlated with those experimentally measured in both wild-type and mutants of three model microorganisms Escherichia coli , Saccharomyces cerevisiae , and Bacillus subtilis under various conditions. More importantly, Decrem can also explain the observed growth rates by capturing the experimentally measured flux changes between wild-types and mutants. Overall, by identifying and incorporating locally organized and regulated functional modules into GSMs, Decrem achieves accurate predictions of phenotypes and has broad applications in bioengineering, synthetic biology, and microbial pathology. Genome-scale metabolic networks (GSMs) are a representation of a cell’s stoichiometrically balanced reactions. Here the authors report Decrem, a GSM reconstruction method, by integrating locally coupled reactions and global transcriptional regulation of metabolism by cell state.

Partial discharge (PD) is not only an important symptom for monitoring the imperfections in the insulation system of a gas-insulated switchgear (GIS), but also the factor that accelerates the degradation. At present, monitoring ultra-high-frequency (UHF) signals induced by PDs is regarded as one of the most effective approaches for assessing the insulation severity and classifying the PDs. Therefore, in this paper, a deep learning-based PD classification algorithm is proposed and realized with a multi-column convolutional neural network (CNN) that incorporates UHF spectra of multiple resolutions. First, three subnetworks, as characterized by their specified designed temporal filters, frequency filters, and texture filters, are organized and then intergraded by a fully-connected neural network. Then, a long short-term memory (LSTM) network is utilized for fusing the embedded multi-sensor information. Furthermore, to alleviate the risk of overfitting, a transfer learning approach inspired by manifold learning is also present for model training. To demonstrate, 13 modes of defects considering both the defect types and their relative positions were well designed for a simulated GIS tank. A detailed analysis of the performance reveals the clear superiority of the proposed method, compared to18 typical baselines. Several advanced visualization techniques are also implemented to explore the possible qualitative interpretations of the learned features. Finally, a unified framework based on matrix projection is discussed to provide a possible explanation for the effectiveness of the architecture.

The recently developed single-cell CRISPR screening techniques, independently termed Perturb-Seq, CRISP-seq, or CROP-seq, combine pooled CRISPR screening with single-cell RNA-seq to investigate functional CRISPR screening in a single-cell granularity. Here, we present MUSIC, an integrated pipeline for model-based understanding of single-cell CRISPR screening data. Comprehensive tests applied to all the publicly available data revealed that MUSIC accurately quantifies and prioritizes the individual gene perturbation effect on cell phenotypes with tolerance for the substantial noise that exists in such data analysis. MUSIC facilitates the single-cell CRISPR screening from three perspectives, i.e., prioritizing the gene perturbation effect as an overall perturbation effect, in a functional topic-specific way, and quantifying the relationships between different perturbations. In summary, MUSIC provides an effective and applicable solution to elucidate perturbation function and biologic circuits by a model-based quantitative analysis of single-cell-based CRISPR screening data. Single-cell CRISPR screening combines pooled CRISPR screening with scRNA-seq analysis to expand the resolution power of genetic screening. Here, the authors develop MUSIC, a computational pipeline for analyzing single-cell CRISPR screening data.

Here, we present a multi-modal deep generative model, the single-cell Multi-View Profiler (scMVP), which is designed for handling sequencing data that simultaneously measure gene expression and chromatin accessibility in the same cell, including SNARE-seq, sci-CAR, Paired-seq, SHARE-seq, and Multiome from 10X Genomics. scMVP generates common latent representations for dimensionality reduction, cell clustering, and developmental trajectory inference and generates separate imputations for differential analysis and cis-regulatory element identification. scMVP can help mitigate data sparsity issues with imputation and accurately identify cell groups for different joint profiling techniques with common latent embedding, and we demonstrate its advantages on several realistic datasets.

The clinical treatment planning of coronary heart disease requires hemodynamic parameters to provide proper guidance. Computational fluid dynamics (CFD) is gradually used in the simulation of cardiovascular hemodynamics. However, for the patient-specific model, the complex operation and high computational cost of CFD hinder its clinical application. To deal with these problems, we develop cardiovascular hemodynamic point datasets and a dual sampling channel deep learning network, which can analyze and reproduce the relationship between the cardiovascular geometry and internal hemodynamics. The statistical analysis shows that the hemodynamic prediction results of deep learning are in agreement with the conventional CFD method, but the calculation time is reduced 600-fold. In terms of over 2 million nodes, prediction accuracy of around 90%, computational efficiency to predict cardiovascular hemodynamics within 1 second, and universality for evaluating complex arterial system, our deep learning method can meet the needs of most situations.Anzai et al. propose a deep learning approach to estimate the 3D hemodynamics of complex aorta-coronary artery geometry in the context of coronary artery bypass surgery. Their method reduces the calculation time 600-fold, while allowing high resolution and similar accuracy as traditional computational fluid dynamics (CFD) method.

To solve the problems of low teaching programming efficiency and poor flexibility in robot welding of complex box girder structures, a method of seam trajectory recognition based on laser scanning displacement sensing was proposed for automated guidance of a welding torch in the skip welding of a spatially intermittent welding seam. Firstly, a laser scanning displacement sensing system for measuring angles adaptively is developed to detect corner features of complex structures. Secondly, a weld trajectory recognition algorithm based on Euclidean distance discrimination is proposed. The algorithm extracts the shape features by constructing the characteristic triangle of the weld trajectory, and then processes the set of shape features by discrete Fourier analysis to solve the feature vector used to describe the shape. Finally, based on the Euclidean distance between the feature vector of the test sample and the class matching library, the class to which the sample belongs is identified to distinguish the weld trajectory. The experimental results show that the classification accuracy rate of four typical spatial discontinuous welds in complex box girder structure is 100%. The overall processing time for weld trajectory detection and classification does not exceed 65 ms. Based on this method, the field test was completed in the folding special container production line. The results show that the system proposed in this paper can accurately identify discontinuous welds during high-speed metal active gas arc welding (MAG) welding with a welding speed of 1.2 m/min, and guide the welding torch to automatically complete the skip welding, which greatly improves the welding manufacturing efficiency and quality stability in the processing of complex box girder components. This method does not require a time-consuming pre-welding teaching programming and visual inspection system calibration, and provides a new technical approach for highly efficient and flexible welding manufacturing of discontinuous welding seams of complex structures, which is expected to be applied to the welding manufacturing of core components in heavy and large industries such as port cranes, large logistics transportation equipment, and rail transit.

Energy-consuming rights trading policies (ECRTPs) represent a significant institutional innovation for China aimed at achieving the dual control targets of total energy consumption and energy consumption intensity. However, the effectiveness of these policies in curbing air pollution remains uncertain. This study treats ECRTPs as a quasi-natural experiment to empirically analyze their impact on air pollution, utilizing panel data encompassing 277 prefecture-level cities in China covering the period from 2011 to 2021. Analytical methods applied include a Difference-in-Differences model, a mediation effects model, and a triple differences model to explore the effects of ECRTPs on air pollution. The findings reveal that ECRTP can significantly suppress air pollution, and this conclusion remains valid even after conducting robustness tests. Mechanism analysis indicates that ECRTPs suppress air pollution by boosting energy efficiency, advancing industrial structure upgrading, and facilitating technological innovation. Further heterogeneous studies show that ECRTPs have a more pronounced inhibitory effect on air pollution in cities that are economically and socially developed, exhibit greater energy-saving potential, are characterized as resource-based cities, and serve as key regions for the prevention and control of air pollution. The research conclusion provides empirical evidence and policy implications for evaluating the environmental effects of ECRTPs and further improving China’s energy-consuming rights trading system, as well as offering references and guidance for other developing countries to put forward ECRTPs.

Background Perioperative nursing care for patients with neuromuscular disorders, especially spinal muscular atrophy (SMA), remains a challenge. There is an obvious lack of guidelines. Methods We retrospectively reviewed the medical charts of patients with type II or III SMA who underwent spinal surgery from 2018 to 2022. Nursing assessments included muscle strength, pulmonary function, the Barthel Index, the Braden Scale, Nutrition Risk Screening 2002, and the Hamilton Anxiety Scale. Preoperative and postoperative anxiety levels were compared using a paired-samples t-test. Results All 24 included patients had severe scoliosis, kyphosis, or kyphoscoliosis, with a mean Cobb angle of 102 degrees. Upon admission, all patients (24/24) presented with muscle weakness, were classified as having total or severe dependency, and were at risk of developing pressure sores; 58.3% (14/24) of the patients had severe pulmonary function impairment, and 50.0% (12/24) were at nutritional risk, with the score unable to be assessed in 8.3% (2/24) of the patients. All patients underwent posterior spinal fusion surgery with bone grafting. Only one patient experienced a major postoperative complication, pneumonia, which was effectively managed. Anxiety level decreased significantly ( P  < 0.01) at discharge compared to that on admission. Complementing regular nursing care, an SMA-specific perioperative nursing care protocol was implemented: (1) Respiratory care protocol: A. Confirmation of SMA type; B. Comprehensive evaluation of symptoms, signs, and pulmonary function test results; C. Development and implementation of a personalized plan including: Plan 1. Training on respiratory function including diaphragmatic breathing exercise, coughing exercise, inhaling exercise, and exhaling exercise; Plan 2. Use of cough assist device, and/or Plan 3. Use of non-invasive ventilator. (2) Postoperative three-step all-involved training protocol of postural adaptation from nurse-led to caregiver-led and inducing patient self-advocacy: A. Preparation for the training; B. Postural adaptation training; C. Postural switch from lying to sitting. Conclusions We implemented an SMA-specific perioperative nursing care protocol, including a respiratory care protocol and a postoperative three-step all-involved training protocol of postural adaptation, complementing standard nursing care. Our approach yielded positive patient outcomes, while we acknowledge the limitation that our protocol is pending comparative evaluations due to the rarity of the disease. The protocol was initially designed for patients with SMA but may also be suitable for other patients with profound muscle weakness.

Background Compared with disease biomarkers in blood and urine, biomarkers in saliva have distinct advantages in clinical tests, as they can be conveniently examined through noninvasive sample collection. Therefore, identifying human saliva-secretory proteins and further detecting protein biomarkers in saliva have significant value in clinical medicine. There are only a few methods for predicting saliva-secretory proteins based on conventional machine learning algorithms, and all are highly dependent on annotated protein features. Unlike conventional machine learning algorithms, deep learning algorithms can automatically learn feature representations from input data and thus hold promise for predicting saliva-secretory proteins. Results We present a novel end-to-end deep learning model based on multilane capsule network (CapsNet) with differently sized convolution kernels to identify saliva-secretory proteins only from sequence information. The proposed model CapsNet-SSP outperforms existing methods based on conventional machine learning algorithms. Furthermore, the model performs better than other state-of-the-art deep learning architectures mostly used to analyze biological sequences. In addition, we further validate the effectiveness of CapsNet-SSP by comparison with human saliva-secretory proteins from existing studies and known salivary protein biomarkers of cancer. Conclusions The main contributions of this study are as follows: (1) an end-to-end model based on CapsNet is proposed to identify saliva-secretory proteins from the sequence information; (2) the proposed model achieves better performance and outperforms existing models; and (3) the saliva-secretory proteins predicted by our model are statistically significant compared with existing cancer biomarkers in saliva. In addition, a web server of CapsNet-SSP is developed for saliva-secretory protein identification, and it can be accessed at the following URL: http://www.csbg-jlu.info/CapsNet-SSP/ . We believe that our model and web server will be useful for biomedical researchers who are interested in finding salivary protein biomarkers, especially when they have identified candidate proteins for analyzing diseased tissues near or distal to salivary glands using transcriptome or proteomics.