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.     

Farmers' preferences for adopting on-farm concentration of raw milk: Results from a discrete choice experiment in Germany

Milk concentrates are used in the manufacturing of dairy products such as yogurt and cheese or are processed into milk powder. Processes for the nonthermal separation of water and valuable milk ingredients are becoming increasingly widespread at farm level. The technical barriers to using farm-manufactured milk concentrate in dairies are minimal, hence the suspicion that the practice of on-farm raw milk concentration is still fairly uncommon for economic reasons. This study, therefore, set out to investigate farmers' potential willingness to adopt a raw milk concentration plant. The empirical analysis was based on discrete choice experiments with 75 German dairy farmers to identify preferences and the possible adoption of on-farm raw milk concentration. The results showed that, in particular, farmers who deemed the current milk price to be insufficient viewed on-farm concentration using membrane technology as an option for diversifying their milk sales. We found no indication that adoption would be impeded by a lack of trustworthy information on milk processing technologies or capital.     

Estimates of daily oxygen consumption,carbon dioxide and methane emissions,and heat production for beef and dairy cattle using spot gas sampling

A simulation study was conducted to examine accuracy of estimating daily O₂ consumption, CO₂ and CH₄ emissions, and heat production (HP) using a spot sampling technique and to determine optimal spot sampling frequency (FQ). Data were obtained from 3 experiments where daily O₂ consumption, emissions of CO₂ and CH₄, and HP were measured using indirect calorimetry (respiration chamber or headbox system). Experiment 1 used 8 beef heifers (ad libitum feeding; gaseous exchanges measured every 30 min over 3 d in respiration chambers); Experiment 2 used 56 lactating Holstein-Friesian cows (restricted feeding; gaseous exchanges measured every 12 min over 3 d in respiration chambers); Experiment 3 used 12 lactating Jersey cows (ad libitum feeding; gaseous exchanges measured every hour for 1 d using headbox style chambers). Within experiment, averages of all measurements (FQALL) and averages of measurements selected at time points with 12, 8, 6, or 4 spot sampling FQ (i.e., sampling every 2, 3, 4, and 6 h in a 24-h cycle, respectively; FQ12, FQ8, FQ6, and FQ4, respectively) were compared. Within study a mixed model was used to compare gaseous exchanges and HP among FQALL, FQ12, FQ8, FQ6, and FQ4, and an interaction of dietary treatment by FQ was examined. A regression model was used to evaluate accuracy of spot sampling within study [i.e., FQALL (observed) vs. FQ12, FQ8, FQ6, or FQ4 (estimated)]. No interaction of diet by FQ was observed for any variables except for CH₄ production in experiment 1. No FQ effect was observed for gaseous exchanges and HP except in experiment 2 where CO₂ production was less (5,411 vs. 5,563 L/d) for FQ4 compared with FQALL, FQ12, and FQ8. A regression analysis between FQALL and each FQ within study showed that slopes and intercepts became farther from 1 and 0, respectively, for almost all variables as FQ decreased. Most variables for FQ12 and FQ8 had root mean square prediction error (RMSPE) less than 10% of the mean and concordance correlation coefficient (CCC) greater than 0.80, and RMSPE increased and CCC decreased as FQ decreased. When a regression analysis was conducted with combined data from the 3 experiments (mixed model with study as a random effect), results agreed with those from the analysis for the individual studies. Prediction errors increased and CCC decreased as FQ decreased. Generally, all the estimates from FQ12, FQ8, FQ6, and FQ4 had RMSPE less than 10% of the means and CCC greater than 0.90 except for FQ6 and FQ4 for O₂ consumption and CH₄ production. In conclusion, the spot sampling simulation with 3 indirect calorimetry experiments indicated that FQ of at least 8 samples (every 3 h in a 24-h cycle) was required to estimate daily O₂ consumption, CO₂ and CH₄ production, and HP and to detect changes in those in response to dietary treatments. This sampling FQ may be considered when using techniques that measure spot gas exchanges such as the GreenFeed and face mask systems.     

空间曲线的特征识别与高质量非均匀采样

为避免传统均匀采样方法因忽视曲线重要特征而生成不理想的采样结果,获得给定数量且由特征点和辅助点组成的采样点序列,提出基于特征识别的高质量空间曲线非均匀采样方法.首先使用抛物线插值法得到曲线上所有曲率极大值点和挠率极大值点的近似位置,经筛选后产生特征点,以更好地抓住空间曲线的轮廓特征.然后定义基于弧长、曲率和挠率加权组合的特征函数,并以此自适应地选取曲线上的辅助点.与3种主流采样方法比较的实验结果表明,该方法能够获得更高质量的采样结果且具有更好的实用性,从而进一步改善空间曲线的B样条拟合效果.     

Process knowledge-based random forest regression for model predictive control on a nonlinear production process with multiple working conditions

In process industry, predictive control approaches have been widely used for nonlinear production processes. Practically, the predictor in a predictive controller is extremely important since it provides future states for the optimization problem of controllers. The conventional predictive controller with precise mathematical predictors approximating the state space of physical systems is difficult and time-consuming for nonlinear production processes, and it performs poorly over a wide range of working conditions and with significant disturbances. To address the challenges, the trend of applying artificial intelligence emerges. However, the industrial process-specific knowledge is ignored in most cases. In this study, a predictive controller with a control process knowledge-based random forest (RF) model is proposed. Specifically, working data are clustered at first to handle diverse working conditions. Then, a process knowledge-based forest predictor, namely MIW-RF model with a redesigned cascading RF structure, is proposed to incorporate control process knowledge into modeling. Thus, future states of controlled variables could be more accurately acquired for the optimizer. A simplified version of the predictive model is also developed with quick model training and updating. The proposed predictive methods are finally introduced into the controller design. According to the empirical results, the proposed methods deliver a better control performance against benchmarks, including more accurate anticipated controlled-variable responses, better set-point tracking and disturbance rejection capability.     

Superswelling Microneedle Arrays for Dermal Interstitial Fluid (Prote)Omics

The noninvasive sampling of dermal interstitial fluid (ISF) for the monitoring of clinical biomarkers is a greatly appealing area of research. The identification of molecular biomarkers in biological fluids has been accelerated with -omics analyses but remains limited in ISF because of its time-consuming and complex extraction process. Here, the generation of microneedle (MN) patches made of superabsorbent acrylate-based hydrogels for the rapid sampling of dermal ISF is described to explore its proteome. In depth, iterative optimization allows the identification of novel acrylate-based compositions with the required chemical, mechanical, and biocompatibility properties allowing proteomic analysis of the extracted ISF for the first time after sampling with swelling MNs. The generated MN arrays show no cytotoxic effect, successfully cross the stratum corneum, and can collect up to 6 µL of dermal ISF in 10 min in vivo. Proteomics lead to the detection of 176 clinically relevant biomarkers in the collected samples validating the use of ISF as a relevant bodily fluid for disease monitoring and diagnostic. Importantly, it is discovered that extraction fingerprint is strongly dependent on the MNs chemistry, and thus specific biomarkers could be selectively extracted by tuning the composition of the patch, making the system versatile and specific.     

A novel adaptive sampling based methodology for feasible region identification of compute intensive models using artificial neural network

Identification of feasible region of operations in multivariate processes is a problem of interest in several fields. This is particularly challenging when the process model is black-box in nature and/or is computationally expensive, as analytical solutions are not available and the number of possible model evaluations is limited. An efficient methodology is required to identify samples where the model is evaluated for developing a computationally efficient surrogate model. In this work, an artificial neural network based surrogate model is proposed which is integrated with a statistical-based approach (Jack-knifing) to estimate the variance of the surrogate model prediction. This allows implementation of an adaptive sampling approach where new samples are identified close to the feasible region boundary or in regions of high prediction uncertainty. The proposed approach performs better than a previously published kriging based method for different dimensionality case studies.     

Food-grade carrageenans and their implications in health and disease

Food additives, often used to guarantee the texture, shelf-life, taste, and appearance of processed foods, have gained widespread attention due to their increased link to the growing incidence of chronic diseases. As one of the most common additives, carrageenans have been used in human diets for hundreds of years. While classified as generally recognized as safe (GRAS) for human consumption, numerous studies since the 1980s have suggested that carrageenans, particularly those with random coil conformations, may have adverse effects on gastrointestinal health, including aggravating intestinal inflammation. While these studies have provided some evidence of adverse effects, the topic is still controversial. Some have suggested that the negative consequence of the consumption of carrageenans may be structure dependent. Furthermore, pre-existing conditions may predispose individuals to varied outcomes of carrageenan intake. In this review, structure–function relationships of various carrageenans in the context of food safety are discussed. We reviewed the molecular mechanisms by which carrageenans exert their biological effects. We summarized the findings associated with carrageenan intake in animal models and clinical trials. Moreover, we examined the interactions between carrageenans and the gut microbiome in the pathogenesis of gastrointestinal disorders. This review argues for personalized guidance on carrageenan intake based on individuals’ health status. Future research efforts that aim to close the knowledge gap on the effect of low-dose and chronic carrageenan intake as well as interactions among food additives should be conducive to the improved safety profile of carrageenans in processed food products.     

电商平台产品共同购买网络的影响因素研究

共同购买网络的推荐系统应用越加广泛，仅基于网络内生结构变量研究其共同购买链接的经济意义已有局限，故加入网络口碑这一外生变量，进行更全面的分析。采用了社会网络方法中指数随机图模型进行建模，主要围绕产品销售量、产品入度、差评率和评论数4个方面因素，探究其对共同购买网络中共同购买链接形成的影响。结果显示，销售量、产品入度和评论数对共同购买链接形成的影响呈正比关系，而差评率则会显著地降低产品共同购买的几率。该指数随机图构建出的共同购买网络为在线电商平台管理网络口碑和推荐系统优化设计提供有益参考。     

A three-dimensional surface measurement system implemented with Gaussian process based adaptive sampling

Self-adaptive surface measurements that can reduce data redundancy and improve time efficiency are in high demand in many fields of science and technology. For this purpose, a system implemented with Gaussian process (GP) adaptive sampling is developed. The non-parametric GP model is applied to reconstruct the topography and guide the subsequent sampling position, which is determined from the inference uncertainty estimation. A criterion is proposed to terminate the GP adaptive measurement automatically without any prior model or data of the topography. Experiments on typical surfaces validate the intelligence, adaptability, and high accuracy of the GP method along with the stabilization of the automatic iteration termination. Compared with traditional raster sampling, data redundancy is reduced and the time efficiency is improved without sacrificing the surface reconstruction accuracy. The proposed method can be implemented in other systems with similar measurement principles, thus benefitting surface characterizations.