The effects of washing a collagen sample prior to TEM examination

Transmission electron microscopy (TEM) is an important analysis technique to visualize (bio)macromolecules and their assemblies, including collagen fibers. Many protocols for TEM sample preparation of collagen involve one or more washing steps to remove excess salts from the dispersion that could hamper analysis when dried on a TEM grid. Such protocols are not standardized and washing times as well as washing solvents vary from procedure to procedure, with each research group typically having their own protocol. Here, we investigate the influence of washing with water, ethanol, but also methanol and 2-propanol, for both mineralized and unmineralized collagen samples via a protocol based on centrifugation. Washing with water maintains the hydrated collagen structure and the characteristic banding pattern can be clearly observed. Conversely, washing with ethanol results in dehydration of the fibrils, often leading to aggregation of the fibers and a less obvious banding pattern, already within 1 min of ethanol exposure. As we show, this process is fully reversible. Similar observations were made for methanol and propanol. Based on these results, a standardized washing protocol for collagenous samples is proposed.     

Experimental study and model predictions on helium release in an enclosure with single or multiple vents

This paper presents experiments performed at Canadian Nuclear Laboratories (CNL) to examine the dispersion behaviour of helium in a polycarbonate enclosure that was representative of a residential parking garage. The purpose was to gain a better understanding of the effect of buoyancy- or wind-driven natural ventilation on hydrogen dispersion behaviour. Although hydrogen dispersion studies have been reported extensively in the literature, gaps still exist in predictive methods for hazard analysis. Helium, a simulant for hydrogen, was injected near the centre of the floor with a flow rate ranging from 5 to 75 standard litres per minute through an upward-facing nozzle, resulting in an injection Richardson number ranging between 10^?1 and 10². The location of the nozzle varied from the bottom of the enclosure to near the ceiling to examine the impact of the nozzle elevation on the development of a stratified layer in the upper region of the enclosure. When the injection nozzle was placed at a sufficiently low elevation, the vertical helium profile always consisted of a homogenous layer at the top overlaying a stratified layer at the bottom. To simulate outdoor environmental conditions, a fan was placed in front of each vent to examine the effect of opposing or assisting wind on the dispersion. The helium transients in the uniform layer predicted with analytical models were in good agreement with the measured transients for most tests. Model improvements are required for adequately predicting transients with primarily stratified profiles or strong opposing wind.     

Tabular data: Deep learning is not all you need

A key element in solving real-life data science problems is selecting the types of models to use. Tree ensemble models (such as XGBoost) are usually recommended for classification and regression problems with tabular data. However, several deep learning models for tabular data have recently been proposed, claiming to outperform XGBoost for some use cases. This paper explores whether these deep models should be a recommended option for tabular data by rigorously comparing the new deep models to XGBoost on various datasets. In addition to systematically comparing their performance, we consider the tuning and computation they require. Our study shows that XGBoost outperforms these deep models across the datasets, including the datasets used in the papers that proposed the deep models. We also demonstrate that XGBoost requires much less tuning. On the positive side, we show that an ensemble of deep models and XGBoost performs better on these datasets than XGBoost alone.     

基于多通道的ICU脑血管疾病死亡风险预测模型

死亡风险预测指根据病人临床体征监测数据来预测未来一段时间的死亡风险。对于ICU病患，通过死亡风险预测可以有针对性地对病人做出临床诊断，以及合理安排有限的医疗资源。基于临床使用的MEWS和Glasgow昏迷评分量表，针对ICU病人临床监测的17项生理参数，提出一种基于多通道的ICU脑血管疾病死亡风险预测模型。引入多通道概念应用于BiLSTM模型，用于突出每个生理参数对死亡风险预测的作用。采用Attention机制用于提高模型预测精度。实验数据来自MIMIC [Ⅲ]数据库，从中提取3?080位脑血管疾病患者的16?260条记录用于此次研究，除了六组超参数实验之外，将所提模型与LSTM、Multichannel-BiLSTM、逻辑回归（logistic regression）和支持向量机（support vector machine, SVM）四种模型进行了对比分析，准确率Accuracy、灵敏度Sensitive、特异性Specificity、AUC-ROC和AUC-PRC作为评价指标，实验结果表明，所提模型性能优于其他模型，AUC值达到94.3%。     

Data fusion and transfer learning empowered granular trust evaluation for Internet of Things

In the Internet of Things (IoT), a huge amount of valuable data is generated by various IoT applications. As the IoT technologies become more complex, the attack methods are more diversified and can cause serious damages. Thus, establishing a secure IoT network based on user trust evaluation to defend against security threats and ensure the reliability of data source of collected data have become urgent issues, in this paper, a Data Fusion and transfer learning empowered granular Trust Evaluation mechanism (DFTE) is proposed to address the above challenges. Specifically, to meet the granularity demands of trust evaluation, time–space empowered fine/coarse grained trust evaluation models are built utilizing deep transfer learning algorithms based on data fusion. Moreover, to prevent privacy leakage and task sabotage, a dynamic reward and punishment mechanism is developed to encourage honest users by dynamically adjusting the scale of reward or punishment and accurately evaluating users’ trusts. The extensive experiments show that: (i) the proposed DFTE achieves high accuracy of trust evaluation under different granular demands through efficient data fusion; (ii) DFTE performs excellently in participation rate and data reliability.     

Learn decision trees with deep visual primitives

In this paper, we strive to propose a self-interpretable framework, termed PrimitiveTree, that incorporates deep visual primitives condensed from deep features with a conventional decision tree, bridging the gap between deep features extracted from deep neural networks (DNNs) and trees’ transparent decision-making processes. Specifically, we utilize a codebook, which embeds the continuous deep features into a finite discrete space (deep visual primitives) to distill the most common semantic information. The decision tree adopts the spatial location information and the mapped primitives to present the decision-making process of the deep features in a tree hierarchy. Moreover, the trained interpretable PrimitiveTree can inversely explain the constituents of the deep features, highlighting the most critical and semantic-rich image patches attributing to the final predictions of the given DNN. Extensive experiments and visualization results validate the effectiveness and interpretability of our method.     

A data-driven digital-twin prognostics method for proton exchange membrane fuel cell remaining useful life prediction

Prognostics and health management of proton exchange membrane fuel cell (PEMFC) systems have driven increasing research attention in recent years as the durability of PEMFC stack remains as a technical barrier for its large-scale commercialization. To monitor the health state during PEMFC operation, digital twin (DT), as a smart manufacturing technique, is applied in this paper to establish an ensemble remaining useful life prediction system. A data-driven DT is constructed to integrate the physical knowledge of the system and a deep transfer learning model based on stacked denoising autoencoder is used to update the DT with online measurement. A case study with experimental PEMFC degradation data is presented where the proposed data-driven DT prognostics method has applied and reached a high prediction accuracy. Furthermore, the predicted results are proved to be less affected even with limited measurement data.     

高深溜井井筒堵塞的爆破处理实践

溜井是采用平硐-溜井方式开拓矿山的运输咽喉,溜井正常与否对矿山生产影响极大。本文通过黑沟铁矿高深溜井井筒堵塞处理实例,对其堵塞爆破处理方法及经验做了系统分析。重点介绍的爆破冲击波破拱疏通高深溜井井筒高位堵塞的爆破方法,富有新意,可供国内外同类型矿山参考借鉴。     

Structural Aspects and Prediction of Calmodulin-Binding Proteins

Calmodulin (CaM) is an important intracellular protein that binds Ca²⁺ and functions as a critical second messenger involved in numerous biological activities through extensive interactions with proteins and peptides. CaM’s ability to adapt to binding targets with different structures is related to the flexible central helix separating the N- and C-terminal lobes, which allows for conformational changes between extended and collapsed forms of the protein. CaM-binding targets are most often identified using prediction algorithms that utilize sequence and structural data to predict regions of peptides and proteins that can interact with CaM. In this review, we provide an overview of different CaM-binding proteins, the motifs through which they interact with CaM, and shared properties that make them good binding partners for CaM. Additionally, we discuss the historical and current methods for predicting CaM binding, and the similarities and differences between these methods and their relative success at prediction. As new CaM-binding proteins are identified and classified, we will gain a broader understanding of the biological processes regulated through changes in Ca²⁺ concentration through interactions with CaM.     

In Silico Analysis of the Molecular-Level Impact of SMPD1 Variants on Niemann-Pick Disease Severity

Sphingomyelin phosphodiesterase (SMPD1) is a key enzyme in the sphingolipid metabolism. Genetic SMPD1 variants have been related to the Niemann-Pick lysosomal storage disorder, which has different degrees of phenotypic severity ranging from severe symptomatology involving the central nervous system (type A) to milder ones (type B). They have also been linked to neurodegenerative disorders such as Parkinson and Alzheimer. In this paper, we leveraged structural, evolutionary and stability information on SMPD1 to predict and analyze the impact of variants at the molecular level. We developed the SMPD1-ZooM algorithm, which is able to predict with good accuracy whether variants cause Niemann-Pick disease and its phenotypic severity; the predictor is freely available for download. We performed a large-scale analysis of all possible SMPD1 variants, which led us to identify protein regions that are either robust or fragile with respect to amino acid variations, and show the importance of aromatic-involving interactions in SMPD1 function and stability. Our study also revealed a good correlation between SMPD1-ZooM scores and in vitro loss of SMPD1 activity. The understanding of the molecular effects of SMPD1 variants is of crucial importance to improve genetic screening of SMPD1-related disorders and to develop personalized treatments that restore SMPD1 functionality.