Super-Resolution Reconstruction of Images Based on Microarray Camera

In the field of images and imaging, super-resolution (SR) reconstruction of images is a technique that converts one or more low-resolution (LR) images into a highresolution (HR) image. The classical two types of SR methods are mainly based on applying a single image or multiple images captured by a single camera. Microarray camera has the characteristics of small size, multi views, and the possibility of applying to portable devices. It has become a research hotspot in image processing. In this paper, we propose a SR reconstruction of images based on a microarray camera for sharpening and registration processing of array images. The array images are interpolated to obtain a HR image initially followed by a convolution neural network (CNN) procedure for enhancement. The convolution layers of our convolution neural network are 3×3 or 1×1 layers, of which the 1×1 layers are used to improve the network performance particularly. A bottleneck structure is applied to reduce the parameter numbers of the nonlinear mapping and to improve the nonlinear capability of the whole network. Finally, we use a 3×3 deconvolution layer to significantly reduce the number of parameters compared to the deconvolution layer of FSRCNN-s. The experiments show that the proposed method can not only ameliorate effectively the texture quality of the target image based on the array images information, but also further enhance the quality of the initial high resolution image by the improved CNN.     

Influence of ammonia and lysine supplementation on yeast growth and fermentation with respect to gluten-free type brewing using unmalted sorghum grain

Because gluten-free type brewing with unmalted sorghum does not provide adequate nitrogen for complete fermentation, wort supplementation with ammonia (as diammonium phosphate, DAP) or lysine on yeast performance was investigated. By Phenotype Microarray, under aerobic conditions, greater yeast growth was indicated with DAP than lysine both as a single source and combined with sorghum wort amino acids. With sorghum fermentation, both DAP and lysine improved maltose and maltotriose uptake. However, DAP supplementation also maintained yeast numbers (24.0–21.3 × 10⁶ cells mL⁻¹), whereas there was a decline with lysine supplementation. Lysine supplementation also resulted in adverse effects on yeast cell morphology. Neither DAP nor lysine supplementation resulted in evident genetic change to the yeast, but the change in substrate from barley malt wort to unmalted sorghum wort slightly altered the yeast genetically. Therefore, ammonia as DAP has potential as a nitrogen supplement for improving yeast fermentation performance in sorghum gluten-free brewing.     

A New Optimized Wrapper Gene Selection Method for Breast Cancer Prediction

Machine-learning algorithms have been widely used in breast cancer diagnosis to help pathologists and physicians in the decision-making process. However, the high dimensionality of genetic data makes the classification process a challenging task. In this paper, we propose a new optimized wrapper gene selection method that is based on a nature-inspired algorithm (simulated annealing (SA)), which will help select the most informative genes for breast cancer prediction. These optimal genes will then be used to train the classifier to improve its accuracy and efficiency. Three supervised machine-learning algorithms, namely, the support vector machine, the decision tree, and the random forest were used to create the classifier models that will help to predict breast cancer. Two different experiments were conducted using three datasets: Gene expression (GE), deoxyribonucleic acid (DNA) methylation, and a combination of the two. Six measures were used to evaluate the performance of the proposed algorithm, which include the following: Accuracy, precision, recall, specificity, area under the curve (AUC), and execution time. The effectiveness of the proposed classifiers was evaluated through comprehensive experiments. The results demonstrated that our approach outperformed the conventional classifiers as expected in terms of accuracy and execution time. High accuracy values of 99.77%, 99.45%, and 99.45% have been achieved by SA-SVM for GE, DNA methylation, and the combined datasets, respectively. The execution time of the proposed approach was significantly reduced, in comparison to that of the traditional classifiers and the best execution time has been reached by SA-SVM, which was 0.02, 0.03, and 0.02 on GE, DNA methylation, and the combined datasets respectively. In regard to precision and specificity, SA-RF obtained the best result of 100 on GE dataset. While SA-SVM attained the best recall result of 100 on GE dataset.     

miR-140-5P 参与调控颈椎软骨终板退变

目的：探讨表达谱芯片初步分析 microRNA差异表达是否参与调控颈椎软骨终板退变。方法选择25例颈椎软骨终板退变、需要行手术治疗的患者为病例组,15例无椎间盘软骨终板退变患者为对照组。选取病例组2例和对照组2例标本进行microRNA芯片差异表达分析。然后采用miRCURYTM LNA 18．0表达谱芯片进行原位杂交,由 Axon GenePix 4000B microarray扫描仪采集芯片荧光值。芯片结果经病例组15例和对照组15例标本进行 Real-time PCR和Western blot验证。结果病例组发现22个上调和19个下调 microRNA。Real-time PCR验证：病例组miR-140-5P表达量低于对照组的3倍、miR-140-5P的靶基因 Adamts-5和 Dnpep的表达量分别高于对照组的3倍和3．5倍（均P＜0．05）。miR-140-5P 与 Adamts-5和 Dnpep 的 miRNA表达呈负相关（r＝-0．84、-0．76,均P＜0．05）。Western blot结果示：病例组软骨终板 Adamts-5和 Dnpep的蛋白表达分别为0．66±0．46和0．57±0．32,均高于对照组软骨终板的0．22±0．06和0．26±0．08（均P＜0．05）。结论本研究首次报道了 miR-140-5P参与调控颈椎软骨终板退变。进一步研究miR-140-5P不仅有利于揭示软骨终板退变的分子生物学机制,而且其日后也可能成为治疗椎间盘退变的有效靶工具。     

Chemically Synthesized 58‐mer LysM Domain Binds Lipochitin Oligosaccharide

Recognition of carbohydrates by proteins is a ubiquitous biochemical process. In legume–rhizobium symbiosis, lipochitin oligosaccharides, also referred to as nodulation (nod) factors, function as primary rhizobial signal molecules to trigger root nodule development. Perception of these signal molecules is receptor mediated, and nod factor receptor 5 (NFR5) from the model legume Lotus japonicus is predicted to contain three LysM domain binding sites. Here we studied the interactions between nod factor and each of the three NFR5 LysM domains, which were chemically synthesized. LysM domain variants (up to 58 amino acids) designed to optimize solubility were chemically assembled by solid‐phase peptide synthesis (SPPS) with microwave heating. Their interaction with nod factors and chitin oligosaccharides was studied by isothermal titration calorimetry and circular dichroism (CD) spectroscopy. LysM2 showed a change in folding upon nod factor binding, thus providing direct evidence that the LysM domain of NFR5 recognizes lipochitin oligosaccharides. These results clearly show that the L. japonicus LysM2 domain binds to the nod factor from Mesorhizobium loti, thereby causing a conformational change in the LysM2 domain. The preferential affinity for nod factors over chitin oligosaccharides was demonstrated by a newly developed glycan microarray. Besides the biological implications, our approach shows that carbohydrate binding to a small protein domain can be detected by CD spectroscopy.     

Barosensitivity in Saccharomyces cerevisiae is Closely Associated with a Deletion of the COX1 Gene

High hydrostatic pressure causes physical stress to microorganisms; therefore, this technology may be applied to food pasteurization without introducing the unfavorable effects of thermal denaturation. However, its application is limited to high‐value foods because the treatment requires a robust steel vessel and expensive pressurization equipment. To reduce these costs, we studied the pasteurization of Saccharomyces cerevisiae using relatively moderate high‐pressure levels. A mutant strain isolated by ultraviolet mutagenesis showed significant loss of viability under high‐pressure conditions. Gene expression analysis of the mutant strain revealed that it incurred a deletion of the COX1 gene. Our results suggest that the pressure‐sensitivity can readily be introduced into industrial/food microorganisms by complementing a COX1 deleted mitochondria.     

Highly sensitive toxin microarray assay for aflatoxin B1 detection in cereals

We report a rapid, highly sensitive microarray method for quantitative aflatoxin B₁ (AFB₁) detection in cereal samples. Following optimisation using an indirect competitive immunoassay, optimised amounts of AFB₁-bovine serum albumin (AFB₁-BSA)-conjugate were contact-printed onto 16 isolated sub-arrays on multi-pad nitrocellulose coated slides subsequently used in competitive binding assays.The toxin microarray working range for AFB₁ was established in the range of 15 pg g⁻¹ to 3.04 ng g⁻¹, with a detection limit of 1 pg g⁻¹. To determine assay sensitivity in contaminated food models, wheat flour and barley grains samples were spiked with AFB₁ standard dilutions. Following extraction, the working ranges of 0.11–4.15 and 0.18–4.31 ng g⁻¹ were determined, with detection limits of 30 and 90 pg g⁻¹, respectively. The sensitivity of the developed assay is below the European commission limit set for AFB₁ detection and the assay procedure was completed in 3 h time. Good recoveries (98% ± 11%) obtained demonstrate the suitability of the proposed method for rapid and sensitive quantification of AFB₁ in contaminated cereal samples.     

High Cytoplasmic Expression of Krüppel-like Factor 4 Is an Independent Prognostic Factor of Better Survival in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related mortality in the world. Hepatocarcinogenesis is complex, with an extraordinary molecular heterogeneity. Krüppel-like factor 4 (KLF4) plays an important role in cell proliferation and differentiation, and it can function as a tumor suppressor or an oncoprotein, depending on tissue type. The role of KLF4 in HCC remains controversial. The aim of this study was to explore the clinical significance of KLF4 expression in HCC. The study included 205 patients with surgical resection. We performed immunostaining for KLF4 and Ki-67 to investigate the correlations of the clinicopathological parameters of HCC and to examine the proliferative index. KLF4 staining was observed in the cytoplasm of non-tumorous hepatocytes and tumor cells. We subdivided the immunohistological staining results for KLF4 into low expression (Staining 0 and 1+) and high expression (Staining 2+ and 3+) subgroups. The expression of KLF4 was significantly correlated with tumor differentiation (p = 0.001). The Ki-67 proliferative index was significantly lower in well-differentiated HCCs (0.781% ± 1.02% vs. 2.16% ± 3.14%, p = 0.012), but not significantly different between low-KLF4 expression and high-KLF4 expression (1.87% ± 2.93% vs. 2.51% ± 3.28%, p = 0.32). Kaplan–Meier analysis showed that a high expression of KLF4 was significantly correlated with a longer disease-specific survival (p = 0.019). Univariate and multivariate analyses showed that high KLF4 expression was an independent predictor of a better disease-specific survival (p = 0.017; hazard ratio = 0.398; 95% confidence interval: 0.19–0.85). High cytoplasmic expression of KLF4 was associated with better disease-specific survival and was an independently favorable prognostic factor in hepatocellular carcinoma. These promising results suggest that KLF4 may play an anti-oncogenic role in hepatocarcinogenesis.     

杜仲预防UVB致人成纤维细胞光老化的作用及基因水平的机制探讨

以UVB辐射体外培养的人成纤维细胞,探讨了杜仲乙醇提取物乙酸乙酯萃取部分(简称杜仲提取物)预防人成纤维细胞光老化的作用,并利用基因芯片对其可能的作用机制进行了探索。实验结果表明,杜仲提取物可以减少UVB对人成纤维细胞活性的影响,具有较好的预防光老化的作用,且基因芯片结果提示这种防护作用可能与提高细胞的抗氧化、DNA修复、抗凋亡有关,同时可能还具有一定促进细胞增殖和预防黑素细胞瘤的作用。     

Identification and Functional Analysis of MicroRNAs in Mice following Focal Cerebral Ischemia Injury

Numerous studies have demonstrated that genes, RNAs, and proteins are involved in the occurrence and development of stroke. In addition, previous studies concluded that microRNAs (miRNAs or miRs) are closely related to the pathological process of ischemic and hypoxic disease. Therefore, the aims of this study were to quantify the altered expression levels of miRNAs in the infarct region 6 h after middle cerebral artery occlusion (MCAO)-induced focal cerebral ischemia in mice using a large-scale miRNAs microarray. Firstly, MCAO-induced cerebral ischemic injuries were investigated by observing the changes of neurological deficits, infarct volume and edema ratio. One hundred and eighteen differentially expressed miRNAs were identified in the infarct region of mice following the MCAOs compared with sham group (p < 0.05 was considered as significant). Among these 118 significantly expressed microRNAs, we found that 12 miRNAs were up-regulated with fold changes lager than two, and 18 miRNAs were down-regulated with fold changes less than 0.5 in the infarct region of mice following the 6 h MCAOs, compared with the sham group. Then, these 30 miRNAs with expression in fold change larger than two or less than 0.5 was predicted, and the functions of the target genes of 30 miRNAs were analyzed using a bioinformatics method. Finally, the miRNA-gene network was established and the functional miRNA-mRNA pairs were identified, which provided insight into the roles of the specific miRNAs that regulated specified genes in the ischemic injuries. The miRNAs identified in this study may represent effective therapeutic targets for stroke, and further study of the role of these targets may increase our understanding of the mechanisms underlying ischemic injuries.