Transgenerational Effects of Di(2-Ethylhexyl) Phthalate on Anogenital Distance,Sperm Functions and DNA Methylation in Rat Offspring

Di(2-ethylhexyl) phthalate (DEHP) is widely used as a plasticizer in the manufacture of polyvinylchloride plastics and has been associated with concerns regarding male reproductive toxicity. In this study, we hypothesized that maternal exposure to DEHP induces transgenerational inheritance of adult-onset adverse reproductive outcomes through the male germline in the F1, F2, and F3 generations of male offspring. Pregnant rats were treated with 5 or 500 mg of DEHP/kg/day through gavage from gestation day 0 to birth. The offspring body weight, anogenital distance (AGD), anogenital index (AGI), sperm count, motility, and DNA fragmentation index (DFI) were measured for all generations. Methyl-CpG binding domain sequencing was performed to analyze sperm DNA methylation status in the F3. DEHP exposure at 500 mg/kg affected AGD, AGI, sperm count, mean DFI, and %DFI in the F1; AGD, sperm count, and mean DFI in the F2; and AGD, AGI, mean DFI, and %DFI in the F3. DEHP exposure at 5 mg/kg affected AGD, AGI, sperm count, and %DFI in the F1; sperm count in the F2; and AGD and AGI in F3. Compared with the control group, 15 and 45 differentially hypermethylated genes were identified in the groups administered 5 mg/kg and 500 mg/kg DEHP, respectively. Moreover, 130 and 6 differentially hypomethylated genes were observed in the groups administered 5 mg/kg and 500 mg/kg DEHP. Overall, these results demonstrated that prenatal exposure to DEHP caused transgenerational epigenetic effects, which may explain the observed phenotypic changes in the male reproductive system.     

Feature selection methods for root-cause analysis among top-level product attributes

Manufacturing companies not only strive to deliver flawless products but also monitor product failures in the field to identify potential quality issues. When product failures occur, quality engineers must identify the root cause to improve any affected product and process. This root-cause analysis can be supported by feature selection methods that identify relevant product attributes, such as manufacturing dates with an increased number of product failures. In this paper, we present different methods for feature selection and evaluate their ability to identify relevant product attributes in a root-cause analysis. First, we compile a list of feature selection methods. Then, we summarize the properties of product attributes in warranty case data and discuss these properties regarding the challenges they pose for machine learning algorithms. Next, we simulate datasets of warranty cases, which emulate these product properties. Finally, we compare the feature selection methods based on these simulated datasets. In the end, the univariate filter information gain is determined to be a suitable method for a wide range of applications. The comparison based on simulated data provides a more general result than other publications, which only focus on a single use case. Due to the generic nature of the simulated datasets, the results can be applied to various root-cause analysis processes in different quality management applications and provide a guideline for readers who wish to explore machine learning methods for their analysis of quality data.     

DNA Methylation Signatures of Bone Metabolism in Osteoporosis and Osteoarthritis Aging-Related Diseases: An Updated Review

DNA methylation is one of the most studied epigenetic mechanisms that play a pivotal role in regulating gene expression. The epigenetic component is strongly involved in aging-bone diseases, such as osteoporosis and osteoarthritis. Both are complex multi-factorial late-onset disorders that represent a globally widespread health problem, highlighting a crucial point of investigations in many scientific studies. In recent years, new findings on the role of DNA methylation in the pathogenesis of aging-bone diseases have emerged. The aim of this systematic review is to update knowledge in the field of DNA methylation associated with osteoporosis and osteoarthritis, focusing on the specific tissues involved in both pathological conditions.     

Adaptation to Endoplasmic Reticulum Stress Enhances Resistance of Oral Cancer Cells to Cisplatin by Up-Regulating Polymerase η and Increasing DNA Repair Efficiency

Endoplasmic reticulum (ER) stress response is an adaptive program to cope with cellular stress that disturbs the function and homeostasis of ER, which commonly occurs during cancer progression to late stage. Late-stage cancers, mostly requiring chemotherapy, often develop treatment resistance. Chemoresistance has been linked to ER stress response; however, most of the evidence has come from studies that correlate the expression of stress markers with poor prognosis or demonstrate proapoptosis by the knockdown of stress-responsive genes. Since ER stress in cancers usually persists and is essentially not induced by genetic manipulations, we used low doses of ER stress inducers at levels that allowed cell adaptation to occur in order to investigate the effect of stress response on chemoresistance. We found that prolonged tolerable ER stress promotes mesenchymal–epithelial transition, slows cell-cycle progression, and delays the S-phase exit. Consequently, cisplatin-induced apoptosis was significantly decreased in stress-adapted cells, implying their acquisition of cisplatin resistance. Molecularly, we found that proliferating cell nuclear antigen (PCNA) ubiquitination and the expression of polymerase η, the main polymerase responsible for translesion synthesis across cisplatin-DNA damage, were up-regulated in ER stress-adaptive cells, and their enhanced cisplatin resistance was abrogated by the knockout of polymerase η. We also found that a fraction of p53 in stress-adapted cells was translocated to the nucleus, and that these cells exhibited a significant decline in the level of cisplatin-DNA damage. Consistently, we showed that the nuclear p53 coincided with strong positivity of glucose-related protein 78 (GRP78) on immunostaining of clinical biopsies, and the cisplatin-based chemotherapy was less effective for patients with high levels of ER stress. Taken together, this study uncovers that adaptation to ER stress enhances DNA repair and damage tolerance, with which stressed cells gain resistance to chemotherapeutics.     

Knowledge-Based Virtual Modeling and Simulation of Manufacturing Processes for Industry 4.0

Abstract

Industry 4.0 aims at providing a digital representation of a production landscape, but the challenges in building, maintaining, optimizing, and evolving digital models in inter-organizational production chains have not been identified yet in a systematic manner. In this paper, various Industry 4.0 research and technical challenges are addressed, and their present scenario is discussed. Moreover, in this article, the novel concept of developing experience-based virtual models of engineering entities, process, and the factory is presented. These models of production units, processes, and procedures are accomplished by virtual engineering object (VEO), virtual engineering process (VEP), and virtual engineering factory (VEF), using the knowledge representation technique of Decisional DNA. This blend of the virtual and physical domains permits monitoring of systems and analysis of data to foresee problems before they occur, develop new opportunities, prevent downtime, and even plan for the future by using simulations. Furthermore, the proposed virtual model concept not only has the capability of Query Processing and Data Integration for Industrial Data but also real-time visualization of data stream processing.     

A new reverse reduce-error ensemble pruning algorithm

Although greedy algorithms possess high efficiency, they often receive suboptimal solutions of the ensemble pruning problem, since their exploration areas are limited in large extent. And another marked defect of almost all the currently existing ensemble pruning algorithms, including greedy ones, consists in: they simply abandon all of the classifiers which fail in the competition of ensemble selection, causing a considerable waste of useful resources and information. Inspired by these observations, an interesting greedy Reverse Reduce-Error (RRE) pruning algorithm incorporated with the operation of subtraction is proposed in this work. The RRE algorithm makes the best of the defeated candidate networks in a way that, the Worst Single Model (WSM) is chosen, and then, its votes are subtracted from the votes made by those selected components within the pruned ensemble. The reason is because, for most cases, the WSM might make mistakes in its estimation for the test samples. And, different from the classical RE, the near-optimal solution is produced based on the pruned error of all the available sequential subensembles. Besides, the backfitting step of RE algorithm is replaced with the selection step of a WSM in RRE. Moreover, the problem of ties might be solved more naturally with RRE. Finally, soft voting approach is employed in the testing to RRE algorithm. The performances of RE and RRE algorithms, and two baseline methods, i.e., the method which selects the Best Single Model (BSM) in the initial ensemble, and the method which retains all member networks of the initial ensemble (ALL), are evaluated on seven benchmark classification tasks under different initial ensemble setups. The results of the empirical investigation show the superiority of RRE over the other three ensemble pruning algorithms.     

Chemical-Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors

Bile acids have been reported as important cofactors promoting human and murine norovirus (NoV) infections in cell culture. The underlying mechanisms are not resolved. Through the use of chemical shift perturbation (CSP) NMR experiments, we identified a low-affinity bile acid binding site of a human GII.4 NoV strain. Long-timescale MD simulations reveal the formation of a ligand-accessible binding pocket of flexible shape, allowing the formation of stable viral coat protein–bile acid complexes in agreement with experimental CSP data. CSP NMR experiments also show that this mode of bile acid binding has a minor influence on the binding of histo-blood group antigens and vice versa. STD NMR experiments probing the binding of bile acids to virus-like particles of seven different strains suggest that low-affinity bile acid binding is a common feature of human NoV and should therefore be important for understanding the role of bile acids as cofactors in NoV infection.     

Expression of Main Toll-Like Receptors in Patients with Different Types of Colorectal Polyps and Their Relationship with Gut Microbiota

Abnormal activation of Toll-like receptor (TLRs) signaling can result in colon cancer development. The aim of this study was to investigate the expression of important TLRs in different histological types of colorectal polyps and evaluate their relationship with intestinal microbiota. The expression levels of TLR2, 3, 4, and 5 were analyzed in intestinal biopsy specimens of 21 hyperplastic polyp (HP), 16 sessile serrated adenoma (SSA), 29 tubular adenoma (TA), 21 villous/tubulovillous (VP/TVP) cases, and 31 normal controls. In addition, selected gut bacteria including Streptococcus bovis, Enterococcus faecalis, Enterotoxigenic Bacteroides fragilis (ETBF), Fusobacterium nucleatum, Porphyromonas spp., Lactobacillus spp., Roseburia spp., and Bifidobacterium spp. were quantified in fecal samples using absolute qRT PCR, and, finally, the association between TLRs and these gut microbiota- was evaluated by Spearman’s correlation coefficient. Higher expression of TLR2 and TLR4 in VP/TVP and TA, and lower expression levels of TLR3 and TLR5 in all type of polyps were observed. The differences in TLR expression patterns was not only dependent on the histology, location, size, and dysplasia grade of polyps but also related to the intestinal microbiota patterns. TLR2 and TLR4 expression was directly associated with the F. nucleatum, E. faecalis, S. bovis, Porphyromonas, and inversely to Bifidobacterium, Lactobacillus, and Roseburia quantity. Furthermore, TLR3 and TLR5 expression was directly associated with Bifidobacterium, Roseburia, and Lactobacillus quantity. Our results suggest a possible critical role of TLRs during colorectal polyp progression. An abnormal regulation of TLRs in relation to gut microbial quantity may contribute to carcinogenesis.     

基于张量分解融合RGB-D图像的物体识别

为了充分利用RGB-D图像的深度图像信息，提出了基于张量分解的物体识别方法。首先将RGB-D图像构造成一个四阶张量，然后将该四阶张量分解为一个核心张量和四个因子矩阵，再利用相应的因子矩阵将原张量进行投影，获得融合后的RGB-D数据，最后输入到卷积神经网络中进行识别。RGB-D数据集中三组相似物体的识别结果表明，利用张量分解融合RGB-D图像的物体识别准确率高于未采用张量分解的物体识别准确率，并且单一错分实例的准确率最高可提升99%。