Gene Expression Patterns最新文献_第7页

Robust secret image sharing scheme resistance to maliciously tampered shadows by AMBTC and quantization 基于AMBTC和量化的鲁棒秘密图像共享方案抗阴影恶意篡改

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2022-09-01 DOI: 10.1016/j.gep.2022.119267

Yuyuan Sun , Ching-Nung Yang , Xuehu Yan , Yuliang Lu , Lei Sun

引用次数: 1

AMB-Wnet: Embedding attention model in multi-bridge Wnet for exploring the mechanics of disease AMB-Wnet:在多桥Wnet中嵌入注意力模型，用于探索疾病的机制

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2022-09-01 DOI: 10.1016/j.gep.2022.119259

Chunxing Wang , Xiaodong Jiang , Zixuan Wang , Xiaorui Guo , Wenbo Wan , Jian Wang

{"title":"AMB-Wnet: Embedding attention model in multi-bridge Wnet for exploring the mechanics of disease","authors":"Chunxing Wang , Xiaodong Jiang , Zixuan Wang , Xiaorui Guo , Wenbo Wan , Jian Wang","doi":"10.1016/j.gep.2022.119259","DOIUrl":"10.1016/j.gep.2022.119259","url":null,"abstract":"<div><p><span>In recent years, progressive application of convolutional neural networks in image processing has successfully filtered into medical diagnosis. As a prerequisite for images detection and classification, object segmentation in medical images has attracted a great deal of attention. This study is based on the fact that most of the analysis of pathological diagnoses requires nuclei detection as the starting phase for obtaining an insight into the underlying </span>biological process and further diagnosis. In this paper, we introduce an embedded attention model in multi-bridge Wnet (AMB-Wnet) to achieve suppression of irrelevant background areas and obtain good features for learning image semantics and modality to automatically segment nuclei, inspired by the 2018 Data Science Bowl. The proposed architecture, consisting of the redesigned down sample group, up-sample group, and middle block (a new multiple-scale convolutional layers block), is designed to extract different level features. In addition, a connection group is proposed instead of skip-connection to transfer semantic information among different levels. In addition, the attention model is well embedded in the connection group, and the performance of the model is improved without increasing the amount of calculation. To validate the model's performance, we evaluated it using the BBBC038V1 data sets for nuclei segmentation. Our proposed model achieves 85.83% F1-score, 97.81% accuracy, 86.12% recall, and 83.52% intersection over union. The proposed AMB-Wnet exhibits superior results compared to the original U-Net, MultiResUNet, and recent Attention U-Net architecture.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39992815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimization assisted framework for thyroid detection and classification: A new ensemble technique 优化辅助甲状腺检测和分类框架:一种新的集成技术

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2022-09-01 DOI: 10.1016/j.gep.2022.119268

Rajole Bhausaheb Namdeo , Gond Vitthal Janardan

{"title":"Optimization assisted framework for thyroid detection and classification: A new ensemble technique","authors":"Rajole Bhausaheb Namdeo , Gond Vitthal Janardan","doi":"10.1016/j.gep.2022.119268","DOIUrl":"10.1016/j.gep.2022.119268","url":null,"abstract":"<div><p>Ultrasound (US) is an inexpensive and non-invasive technique for capturing the image of the thyroid gland and nearby tissue. The classification and detection of thyroid disorders is still in its infant stage. This study aims to present a new thyroid diagnosis approach, which consists of three phases like “(i) feature extraction, (ii) feature dimensionality reduction, and (iii) classification”. Initially, the thyroid images as well as its related data are given as input. From the input image, the features such as“ Grey Level Co-occurrence Matrix(GLCM), Grey level Run Length Matrix(GLRM), proposed Local Binary Pattern(LBP), and Local Tetra Patterns (LTrP)” are extracted. Meanwhile, from the input data, the higher-order statistical features like skewness, kurtosis<span><span>, entropy, as well as moment get retrieved. Consequently, the Linear Discriminant Analysis (LDA) based dimensionality reduction is processed to resolve the problem of “curse of dimensionality”. Finally, the classification is carried out via two phases: Image features are classified using an ensemble classifier that includes Support Vector Machine (SVM)& Neural Network(NN) models. The data features are subjected to Recurrent Neural Network(RNN) based classification, which is optimized by an Adaptive Elephant Herding Algorithm (AEHO) via tuning the optimal weight. At last, the performance of the adopted scheme is compared to the extant models in terms of various measures. Especially, the mean value of the suggested RNN + AEHO model is 4.35%, 3.54%, 6.07%, 3.8%, 1.69%, 2.85%, 2.07%, 2.54%, 0.13%, 0.035%, and 8.53% better than the existing CNN, </span>NB<span>, RF, KNN, Levenberg, RNN + EHO, RNN + FF, RNN + WOA, WF-CS, FU-SLnO and HFBO methods respectively.</span></span></p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40594612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

V - Channel magnification enabled by hybrid optimization algorithm: Enhancement of video super resolution 混合优化算法使V通道放大:增强视频超分辨率

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2022-09-01 DOI: 10.1016/j.gep.2022.119264

Rohita H. Jagdale , Sanjeevani K. Shah

{"title":"V - Channel magnification enabled by hybrid optimization algorithm: Enhancement of video super resolution","authors":"Rohita H. Jagdale , Sanjeevani K. Shah","doi":"10.1016/j.gep.2022.119264","DOIUrl":"10.1016/j.gep.2022.119264","url":null,"abstract":"<div><p>Although being a really active area of research, television super-resolution remains a difficult problem. Additionally, it is noted that the blur motion and computational crisis hinder the enhancement. As a result, the goal of this research is to present a brand-new smart SR framework for the camera shot. To create High Resolution (HR) videos, first frames in RGB format are converted to HSV and then the V-channel is enhanced. In order to create enriched video frames, a high - dimension grid with enhanced pixel intensity is then created. This paper introduces a particular progression to enable this: Motion estimation, Cubic Spline Interpolation, and Deblurring or Sharpening are the three methods. By carefully adjusting the parameters, the cubic spline interpolation is improved during operation. A brand-new hybrid technique dubbed Lion with Particle Swarm Velocity Update (LPSO-VU), which combines the principles of the Lion Algorithm (LA) and Particle Swarm Optimization (PSO) algorithms, is presented for this optimal tuning purpose. Finally, using the BRISQUE, SDME, and ESSIM metrics, the adequacy of the method is contrasted to other traditional models, and its superiority is demonstrated. Accordingly, the analysis shows that the suggested LPSO-VU model for video frame 1 is 16.6%, 25.56%, 26.2%, 26.2%, and 27.2% superior to the previous systems like PSO, GWO, WOA, ROA, MF-ROA, and LA, respectively, in terms of BRISQUE.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40615936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Differential expression of the Tmem132 family genes in the developing mouse nervous system. Tmem132家族基因在发育中的小鼠神经系统中的差异表达。

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2022-06-08 DOI: 10.2139/ssrn.4100200

Yuan Wang, Graham Herzig, Cassandra Molano, Aimin Liu

引用次数: 4

Embryonic expression patterns of Wnt genes in the RTA-clade spider Cupiennius salei rta枝蜘蛛Wnt基因的胚胎表达模式

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2022-06-01 DOI: 10.1016/j.gep.2022.119247

Ralf Janssen , Bo Joakim Eriksson

{"title":"Embryonic expression patterns of Wnt genes in the RTA-clade spider Cupiennius salei","authors":"Ralf Janssen , Bo Joakim Eriksson","doi":"10.1016/j.gep.2022.119247","DOIUrl":"10.1016/j.gep.2022.119247","url":null,"abstract":"<div><p>Spiders represent widely used model organisms for chelicerate and even arthropod development and evolution. Wnt genes are important and evolutionary conserved factors that control and regulate numerous developmental processes. Recent studies comprehensively investigated the complement and expression of spider Wnt genes revealing conserved as well as diverged aspects of their expression and thus (likely) function among different groups of spiders representing Mygalomorphae (tarantulas), and both main groups of Araneae (true spiders) (Haplogynae/Synspermiata and Entelegynae). The allegedly most modern/derived group of entelegyne spiders is represented by the RTA-clade of which no comprehensive data on Wnt expression were available prior to this study. Here, we investigated the embryonic expression of all Wnt genes of the RTA-clade spider <em>Cupiennius salei</em>. We found that most of the Wnt expression patterns are conserved between <em>Cupiennius</em> and other spiders, especially more basally branching species. Surprisingly, most differences in Wnt gene expression are seen in the common model spider <em>Parasteatoda tepidariorum</em> (a non-RTA clade entelegyne species). These results show that data and conclusions drawn from research on one member of a group of animals (or any other organism) cannot necessarily be extrapolated to the group as a whole, and instead highlight the need for comprehensive taxon sampling.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567133X22000175/pdfft?md5=52ae1e5367b3f207f7d69559f8d29499&pid=1-s2.0-S1567133X22000175-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88382672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Expression and distribution of Nob1 in the developing rat cochleae Nob1在发育中的大鼠耳蜗的表达和分布

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2022-06-01 DOI: 10.1016/j.gep.2022.119235

Xiaogang An , Ye Wang , Bang Han , Liu Hong , Dingjun Zha , Yu Han

{"title":"Expression and distribution of Nob1 in the developing rat cochleae","authors":"Xiaogang An , Ye Wang , Bang Han , Liu Hong , Dingjun Zha , Yu Han","doi":"10.1016/j.gep.2022.119235","DOIUrl":"10.1016/j.gep.2022.119235","url":null,"abstract":"<div><h3>Background</h3><p>Mammalian inner ear cells are produced during embryonic development<span>. NIN1/RPN12 binding protein 1 homolog (Nob1), a ribosome assembly factor, is believed to be involved in transcriptional regulation and may play an important role in mediating certain physiological and pathological functions.</span></p></div><div><h3>Methods</h3><p>We investigated the expression levels and distribution patterns of Nob1 in rat cochlea at different developmental stages using reverse transcription-polymerase chain reaction (RT-PCR), Western blot analysis, and immunofluorescence microscopy (P0, P3, P7, P14, and P30, n = 11 per age group).</p></div><div><h3>Results</h3><p>The expression of Nob1 was gradually upregulated from Postnatal day (P) 0 to P14 and stabilized at P30. Our results analyzing Nob1 expression at P0 and P3 in the rat cochleae revealed expression in the greater epithelial ridge cells, lesser epithelial ridge cells, and spiral ganglion neurons (SGNs), whereas low levels of Nob1 expression were observed in the stria vascularis cells. During the development of the cochlea, the organ of Corti undergoes dramatic architectural remodeling. Nob1 expression was stably detected in supporting cells and hair cells from P7 to P30, and its expression gradually increased in the SGNs.</p></div><div><h3>Conclusions</h3><p>Thus, the present study revealed that upregulation of Nob1 might explain the maturation of the cytoarchitecture<span> in the cochlea during the postnatal period, and a complete understanding of its function in the mammalian inner ear may help to develop strategies to resolve auditory hair cell loss.</span></p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85223221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A new transgenic reporter line reveals expression of protocadherin 9 at a cellular level within the zebrafish central nervous system 一种新的转基因报告系揭示了斑马鱼中枢神经系统中原钙粘蛋白9在细胞水平上的表达

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2022-06-01 DOI: 10.1016/j.gep.2022.119246

Judith Habicher , Remy Manuel , Andrea Pedroni , Charles Ferebee , Konstantinos Ampatzis , Henrik Boije

{"title":"A new transgenic reporter line reveals expression of protocadherin 9 at a cellular level within the zebrafish central nervous system","authors":"Judith Habicher , Remy Manuel , Andrea Pedroni , Charles Ferebee , Konstantinos Ampatzis , Henrik Boije","doi":"10.1016/j.gep.2022.119246","DOIUrl":"10.1016/j.gep.2022.119246","url":null,"abstract":"<div><p>The wiring of neuronal networks is far from understood. One outstanding question is how neurons of different types link up to form subnetworks within the greater context. Cadherins have been suggested to create an inclusion code where interconnected neurons express the same subtypes. Here, we have used a CRISPR/Cas9 knock-in approach to generate a transgenic zebrafish reporter line for protocadherin 9 (<em>pcdh9</em>), which is predominantly expressed within the central nervous system. Expression of eGFP was detected in subsets of neurons in the cerebellum, retina and spinal cord, in both larvae and juveniles. A closer characterization of the spinal locomotor network revealed that a portion of distinct classes of both excitatory and inhibitory interneurons, as well as motor neurons, expressed <em>pcdh9</em>. This transgenic line could thus be used to test the cadherin network hypothesis, through electrophysiological characterization of eGFP positive cells, to show if these are synaptically connected and form a discrete network within the spinal cord.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567133X22000163/pdfft?md5=c4c251f4174dc8361615278519c3ea5a&pid=1-s2.0-S1567133X22000163-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82023473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Identification and functional analysis of foxl2 and nodal in sea cucumber, Apostichopus japonicus Apostichopus japonicus海参foxl2和nodal的鉴定及功能分析

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2022-06-01 DOI: 10.1016/j.gep.2022.119245

Juan-Juan Sun , Zhi-Hui Sun , Jin-Liang Wei, Jun Ding, Jian Song, Ya-Qing Chang

{"title":"Identification and functional analysis of foxl2 and nodal in sea cucumber, Apostichopus japonicus","authors":"Juan-Juan Sun , Zhi-Hui Sun , Jin-Liang Wei, Jun Ding, Jian Song, Ya-Qing Chang","doi":"10.1016/j.gep.2022.119245","DOIUrl":"10.1016/j.gep.2022.119245","url":null,"abstract":"<div><p>Sea cucumber (<span><em>Apostichopus japonicus</em></span><span>) is an important mariculture species in China. To date, the mechanisms of sex determination and differentiation in sea cucumber remain unclear. Identifying sex-specific molecular markers<span> is an effective method for revealing the genetic basis of sex determination and sex differentiation. In this study, </span></span><em>foxl2</em> and <em>nodal</em> homologous genes were identified in <em>A. japonicus</em>. <em>Foxl2</em> exhibited dynamic and sexually dimorphic expression patterns in the gonads, with prominent expression in the ovaries and minimal expression in the testis according to real-time quantitative PCR (RT-qPCR) study. As <em>nodal</em> was specifically expressed in the ovary, it could serve as an ovary-specific marker in sea cucumber. Additionally, knockdown of <em>foxl2</em> or <em>nodal</em> using RNA interference (RNAi) led to the down-regulation of <span><em>piwi</em></span>, <em>germ cell-less</em>, and <em>dmrt1</em>, suggesting that <em>foxl2</em> and <em>nodal</em> may play important roles in gonad maintenance of sea cucumber. Overall, this study adds to our understanding of the roles of <em>foxl2</em> and <em>nodal</em><span> in the gonadal development of </span><em>A. japonicus</em>, which provides further insight into the mechanisms of sea cucumber sex determination and differentiation.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77734907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Cornifelin expression during Xenopus laevis metamorphosis and in response to spinal cord injury 非洲爪蟾变形过程中cornifin的表达及对脊髓损伤的反应

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2022-03-01 DOI: 10.1016/j.gep.2022.119234

Sol Torruella-Gonzalez , Paula G. Slater , Dasfne Lee-Liu , Juan Larraín

{"title":"Cornifelin expression during Xenopus laevis metamorphosis and in response to spinal cord injury","authors":"Sol Torruella-Gonzalez , Paula G. Slater , Dasfne Lee-Liu , Juan Larraín","doi":"10.1016/j.gep.2022.119234","DOIUrl":"10.1016/j.gep.2022.119234","url":null,"abstract":"<div><h3>Background</h3><p><span>In a high-throughput RNA sequencing analysis, comparing the transcriptional response between </span><span><em>Xenopus laevis</em></span><span> regenerative and non-regenerative stages to spinal cord injury, cornifelin was found among the most highly differentially expressed genes. Cornifelin is mainly expressed in stratified squamous epithelia, but its expression in the spinal cord and other central nervous structures has only been described during early development.</span></p></div><div><h3>Results</h3><p><span>Here, we report cornifelin expression in the spinal cord, retina, and cornea throughout metamorphosis and in the spinal cord after injury. Cornifelin was detected in the grey matter and meninges of the spinal cord from NF-50 to NF-66, with decreased expression in the grey matter during metamorphosis. In the retina, cornifelin was expressed in the </span>ganglion cell<span><span> layer, the inner and outer nuclear layer, and the outer segment from NF-50 to NF-66. After spinal cord injury, we only observed cornifelin upregulation in NF-66 but no significant changes in NF-50. However, we found cornifelin positive cells in NF-50 meninges closing the spinal cord stumps 1 day after injury and delineating the borders of the spinal cord following the continuity of tissue regeneration in the following days after injury. Instead, in NF-66, cornifelin positive cells were distributed to the ventral side of the spinal cord at 6 days after injury, and at the injury gap </span>at 10 days after injury.</span></p></div><div><h3>Conclusions</h3><p>Cornifelin is expressed in the <em>Xenopus laevis</em> spinal cord and eye during metamorphosis and plays a role in the meningeal response to spinal cord injury.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39789291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0